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Karadağ D, Ergon MC. Investigation of different methods in rapid microbial identification directly from positive blood culture bottles by MALDI-TOF MS. Microbiol Spectr 2024; 12:e0063824. [PMID: 38940589 PMCID: PMC11302275 DOI: 10.1128/spectrum.00638-24] [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: 04/09/2024] [Accepted: 05/21/2024] [Indexed: 06/29/2024] Open
Abstract
Many methods are being tried for rapid and accurate identification of sepsis-causing microorganisms. We analyzed the performance of three different preparation methods [MBT Sepsityper IVD Kit (Bruker Daltonics GmbH, Germany), sodium dodecyl sulfate (SDS) lysis, and differential centrifugation with protein extraction (Centrifugation +PE)] and compared in standard and Sepsityper modules of the Bruker Biotyper MALDI-TOF MS for direct identification of bacteria from 240 positive blood culture bottles of BACTEC FX (Becton Dickinson, USA). By using the standard module, correct identification at species level (score ≥2) was done in 46.7% of the samples with SDS lysis, 44.2% with centrifugation +PE, and 25.4% with the Sepsityper kit. These ratios at the genus level (score range 1.70-1.99) were 34.6%, 31.3%, and 32.5%, respectively. With SDS lysis (195), more bacteria were identified correctly than centrifugation +PE (181) and the Sepsityper kit (139). A statistically significant difference was found between SDS and the Sepsityper kit and Centrifugation +PE and the Sepsityper kit (P < 0.001, both). By using the Sepsityper module, correct identification at species level (score ≥1.8) was determined in 74.2% of the samples with SDS lysis and centrifugation +PE each and 55% with the Sepsityper kit. These ratios at the genus level (score range 1.60-1.79) were 16.3%, 10%, and 19.2%, respectively. SDS lysis (217) had significantly higher identification rates than centrifugation +PE (202) and the Sepsityper kit (178) (P = 0.028 and P < 0.001). A statistically significant difference was also observed between centrifugation +PE and the Sepsityper kit (P < 0.001). Best performance was obtained with SDS lysis among the methods. Although better performance was achieved by using Sepsityper software module, risk of misidentification should not be ignored. IMPORTANCE Sepsis is a life-threatening condition, and rapid and accurate identification of the causative microorganisms from blood cultures is crucial for timely and effective treatment. Although there are many studies on direct identification from blood cultures with MALDI-TOF MS, further standardization is still needed. In our study, we analyzed the performance of three different preparation methods and compared by using two analysis modules of the Bruker Biotyper MALDI-TOF MS for direct identification of bacteria from numerous positive blood culture bottles. The literature reports a limited number of studies that compare different preparation methods for direct blood culture identification, processing a large number of blood samples concurrently and evaluating the same samples as in our study. Moreover, although SDS is used very frequently in medical laboratories, there are few studies on direct identification from blood culture bottles. In our study, the highest correct identification rate was observed with the SDS method.
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Affiliation(s)
- Dilan Karadağ
- Department of Medical Microbiology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
- IMD Labor Oderland, Frankfurt (Oder), Germany
| | - Mahmut Cem Ergon
- Department of Medical Microbiology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
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Konjety P, Chakole VG. Beyond the Horizon: A Comprehensive Review of Contemporary Strategies in Sepsis Management Encompassing Predictors, Diagnostic Tools, and Therapeutic Advances. Cureus 2024; 16:e64249. [PMID: 39130839 PMCID: PMC11315441 DOI: 10.7759/cureus.64249] [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: 06/26/2024] [Accepted: 07/10/2024] [Indexed: 08/13/2024] Open
Abstract
This comprehensive review offers a detailed exposition of contemporary strategies in sepsis management, encompassing predictors, diagnostic tools, and therapeutic advances. The analysis elucidates the dynamic nature of sepsis, emphasizing the crucial role of early detection and intervention. The multifaceted strategies advocate for a holistic and personalized approach to sepsis care from traditional clinical methodologies to cutting-edge technologies. The implications for clinical practice underscore clinicians' need to adapt to evolving definitions, integrate advanced diagnostic tools, and embrace precision medicine. Integrating artificial intelligence and telemedicine necessitates a commitment to training and optimization. Judicious antibiotic use and recognition of global health disparities emphasize the importance of a collaborative, global effort in sepsis care. Looking ahead, recommendations for future research underscore priorities such as longitudinal studies on biomarkers, precision medicine trials, implementation science in technology, global health interventions, and innovative antibiotic stewardship strategies. These research priorities aim to contribute to transformative advancements in sepsis management, ultimately enhancing patient outcomes and reducing the global impact of this critical syndrome.
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Affiliation(s)
- Pavithra Konjety
- Anaesthesiology, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Vivek G Chakole
- Research, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
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Massa-Buck B, Mendoza S, Keiser J, Mohamed MA. Use of Rapid Molecular Polymerase Chain Reaction in Early Detection of Bacteremia in Neonates Prior to Blood Culture Positivity: A Pilot Study. Am J Perinatol 2024; 41:569-574. [PMID: 35148542 DOI: 10.1055/s-0042-1742743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
OBJECTIVE There has been national strive to decrease the time needed to identify microorganisms in blood culture samples to reduce antibiotic use. This study evaluated rapid molecular polymerase chain reaction (PCR) use in identifying microorganisms in negative culture bottles from neonates with suspected bacterial blood stream infection at 20 to 24 hours of incubation. STUDY DESIGN All blood specimens from neonates with suspected blood stream infection were included. Specimens were incubated using a standard blood culturing instrument that would flag positive if bacterial growth was detected. If the specimen was flagged positive at <20 hours, it was tested by PCR and plated for identification as per standard protocol. In our design, if specimen was not flagged at 20 hours of incubation, the bottle was sterilely accessed and a sample was obtained for PCR testing. The bottle would be returned for incubation for 120 hours or until flagged positive. RESULTS A total of 192 blood specimens were included. Four specimens flagged positive at <20 hours and were all found to be positive by PCR. All other samples did not flag positive by 20 hours of incubation and were tested by PCR between 20 and 24 hours. One sample tested positive via PCR at 21.6 hours then flagged positive on the culturing instrument at 23.5 hours. All other specimens were negative by PCR and remained culture negative at 120 hours. The positive and negative predictive value of PCR verified by blood culture were both equal to 1.0. CONCLUSION Using rapid molecular PCR on blood culture specimens at 20 to 24 hours of incubation provides 100% true negative results possibly allowing providers to discontinue antibiotics at 24 hours. KEY POINTS · Antibiotic overuse leads to adverse neonatal outcomes.. · Molecular PCR may have true negative results.. · Larger study is needed to discontinue antibiotics earlier..
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Affiliation(s)
- Beri Massa-Buck
- Department of Neonatology, Children's National Hospital, Washington, District of Columbia
- Division of Newborn Services, The George Washington University Hospital, Washington, District of Columbia
| | - Salome Mendoza
- Department of Pathology, The George Washington University Hospital, Washington, District of Columbia
| | - John Keiser
- Department of Pathology, The George Washington University Hospital, Washington, District of Columbia
| | - Mohamed A Mohamed
- Department of Neonatology, Cleveland Clinic Children's Hospital, Cleveland, Ohio
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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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Papareddy P, Selle M, Partouche N, Legros V, Rieu B, Olinder J, Ryden C, Bartakova E, Holub M, Jung K, Pottecher J, Herwald H. Identifying biomarkers deciphering sepsis from trauma-induced sterile inflammation and trauma-induced sepsis. Front Immunol 2024; 14:1310271. [PMID: 38283341 PMCID: PMC10820703 DOI: 10.3389/fimmu.2023.1310271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/22/2023] [Indexed: 01/30/2024] Open
Abstract
Objective The purpose of this study was to identify a panel of biomarkers for distinguishing early stage sepsis patients from non-infected trauma patients. Background Accurate differentiation between trauma-induced sterile inflammation and real infective sepsis poses a complex life-threatening medical challenge because of their common symptoms albeit diverging clinical implications, namely different therapies. The timely and accurate identification of sepsis in trauma patients is therefore vital to ensure prompt and tailored medical interventions (provision of adequate antimicrobial agents and if possible eradication of infective foci) that can ultimately lead to improved therapeutic management and patient outcome. The adequate withholding of antimicrobials in trauma patients without sepsis is also important in aspects of both patient and environmental perspective. Methods In this proof-of-concept study, we employed advanced technologies, including Matrix-Assisted Laser Desorption/Ionization (MALDI) and multiplex antibody arrays (MAA) to identify a panel of biomarkers distinguishing actual sepsis from trauma-induced sterile inflammation. Results By comparing patient groups (controls, infected and non-infected trauma and septic shock patients under mechanical ventilation) at different time points, we uncovered distinct protein patterns associated with early trauma-induced sterile inflammation on the one hand and sepsis on the other hand. SYT13 and IL1F10 emerged as potential early sepsis biomarkers, while reduced levels of A2M were indicative of both trauma-induced inflammation and sepsis conditions. Additionally, higher levels of TREM1 were associated at a later stage in trauma patients. Furthermore, enrichment analyses revealed differences in the inflammatory response between trauma-induced inflammation and sepsis, with proteins related to complement and coagulation cascades being elevated whereas proteins relevant to focal adhesion were diminished in sepsis. Conclusions Our findings, therefore, suggest that a combination of biomarkers is needed for the development of novel diagnostic approaches deciphering trauma-induced sterile inflammation from actual infective sepsis.
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Affiliation(s)
- Praveen Papareddy
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Michael Selle
- Genomics and Bioinformatics of Infectious Diseases, Institute for Animal Genomics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Nicolas Partouche
- Hôpitaux Universitaires de Strasbourg, Service d’Anesthésie-Réanimation & Médecine Péri-opératoire - Université de Strasbourg, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | - Vincent Legros
- Département d’Anesthésie-Réanimation et Médecine Peri-Operatoire, Centre Hospitalier et Universitaire (CHU) de Reims, Université de Reims Champagne-Ardenne, Reims, France
| | - Benjamin Rieu
- Réanimation Médico-Chirurgicale, Trauma Center, Pôle Médecine Péri-Opératoire, Centre Hospitalier et Universitaire (CHU) de Clermont-Ferrand, Clermont Ferrand, France
| | - Jon Olinder
- Division of Infection Medicine, Helsingborg Hospital and Department of Clinical Sciences Helsingborg, Lund University, Helsingborg, Sweden
| | - Cecilia Ryden
- Division of Infection Medicine, Helsingborg Hospital and Department of Clinical Sciences Helsingborg, Lund University, Helsingborg, Sweden
| | - Eva Bartakova
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, Prague, Czechia
| | - Michal Holub
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, Prague, Czechia
| | - Klaus Jung
- Genomics and Bioinformatics of Infectious Diseases, Institute for Animal Genomics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Julien Pottecher
- Hôpitaux Universitaires de Strasbourg, Service d’Anesthésie-Réanimation & Médecine Péri-opératoire - Université de Strasbourg, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | - Heiko Herwald
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
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Stein A, Soukup D, Rath PM, Felderhoff-Müser U. Diagnostic Accuracy of Multiplex Polymerase Chain Reaction in Early Onset Neonatal Sepsis. CHILDREN (BASEL, SWITZERLAND) 2023; 10:1809. [PMID: 38002900 PMCID: PMC10670518 DOI: 10.3390/children10111809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023]
Abstract
Early onset neonatal sepsis is a significant contributor to neonatal morbidity and mortality. Although blood cultures remain the diagnostic gold standard, they detect pathogens in only a minority of suspected cases. This study compared the accuracy of blood cultures with a rapid multiplex PCR test. Newborns at risk of neonatal sepsis were prospectively screened as recommended per national guidelines. Evaluations included laboratory parameters (CrP, IL6, differential blood count), blood culture, and a molecular multiplex PCR test (ROCHE LightCycler SeptiFast®) identifying 20 common microbial agents. Blood samples were taken simultaneously from umbilical cord or venous sources on the first day of life. Of 229 infants included, 69% were born preterm. Blood culture and multiplex PCR sensitivity were 7.4% and 14.8%, respectively. Specificity, negative and positive predictive values between methods showed no significant variance, although multiplex PCR had more false positives due to contamination. The limited sensitivity of blood cultures for early onset neonatal sepsis is concerning. Despite quicker results, multiplex PCR does not enhance diagnostic accuracy or antibiotic therapy guidance, thus it cannot be recommended for this indication.
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Affiliation(s)
- Anja Stein
- Department of Pediatrics I, Neonatology and Experimental Perinatal Neurosciences, Center for Translational and Behavioral Neuroscience, CTNBS, University Hospital Essen, Faculty of Medicine, University Duisburg-Essen, Hufelandstraße 55, 45147 Essen, Germany; (D.S.); (U.F.-M.)
| | - Daniel Soukup
- Department of Pediatrics I, Neonatology and Experimental Perinatal Neurosciences, Center for Translational and Behavioral Neuroscience, CTNBS, University Hospital Essen, Faculty of Medicine, University Duisburg-Essen, Hufelandstraße 55, 45147 Essen, Germany; (D.S.); (U.F.-M.)
- Service de Réanimation Pédiatrique, Centre Hospitalier Universitaire de Bordeaux, Place Amélie Raba Léon, 33000 Bordeaux, France
| | - Peter-Michael Rath
- Institute for Medical Microbiology, University Hospital Essen, Hufelandstraße 55, 45147 Essen, Germany;
| | - Ursula Felderhoff-Müser
- Department of Pediatrics I, Neonatology and Experimental Perinatal Neurosciences, Center for Translational and Behavioral Neuroscience, CTNBS, University Hospital Essen, Faculty of Medicine, University Duisburg-Essen, Hufelandstraße 55, 45147 Essen, Germany; (D.S.); (U.F.-M.)
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Sial MU, Farooq T, Khalaf LK, Rahman S, Asad M, Ahamad Paray B. Two-step method for rapid isolation of genomic DNA and validation of R81T insecticide resistance mutation in Myzus persicae. Saudi J Biol Sci 2023; 30:103791. [PMID: 37711971 PMCID: PMC10497781 DOI: 10.1016/j.sjbs.2023.103791] [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: 06/12/2023] [Revised: 08/14/2023] [Accepted: 08/27/2023] [Indexed: 09/16/2023] Open
Abstract
Isolation and amplification of nucleic acid (DNA) is considered a vital and potent instrument in molecular biological research. However, its functioning outside of a laboratory setting is difficult because of complex procedures that demand expert personnel and expensive equipment in addition to the fulfillment of several additional requirements. DNA isolation from minute insects is sometimes difficult, making diagnostic and genotyping procedures problematic. Thus, the current work offers a high-throughput, cost-effective, straightforward, and faster approach for isolating DNA from the aphid Myzus persicae. Intriguingly, two-step DNA extraction process yielded a high yield of extremely pure genomic DNA and required only 10 s to complete. PCR investigation aiming at amplifying the non-synonymous R81T region on the loop D site of the nAChR gene of M. persicae was subsequently utilized to successfully validate the recovered DNA. Moreover, the proposed method was compared in terms of yield and purity with conventionally used DNA isolation methods including, phenol:chloroform, salt out, and commercially available kits. In conclusion, this newly developed method would enable researchers to quickly process many biological samples used to analyze genetic diversity, mutant screening, and large spectrum diagnosis both in laboratory and field conditions.
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Affiliation(s)
- Muhammad Umair Sial
- Department of Entomology, University of Agriculture, Faisalabad 38000, Pakistan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, PR China
| | - Tahir Farooq
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
| | - Luaay Kahtan Khalaf
- Department of Plant Protection, College of Agricultural Engineering Science, University of Baghdad, Baghdad, Iraq
| | - Saqib Rahman
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, PR China
| | - Muhammad Asad
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Bilal Ahamad Paray
- Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
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Chatelard PA, Rousseau N, Parmeland L, Metral P, Pariset C, Vivier E. Shortening identification times: comparative observational study of three early blood culture testing protocols. Front Cell Infect Microbiol 2023; 13:1192002. [PMID: 37533929 PMCID: PMC10390722 DOI: 10.3389/fcimb.2023.1192002] [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: 03/22/2023] [Accepted: 06/27/2023] [Indexed: 08/04/2023] Open
Abstract
Background While early appropriate antibiotic therapy is a proven means of limiting the progression of infections, especially bacteremia, empirical antibiotic therapy in sepsis is ineffective up to 30%. The aim of this study was to compare early blood culture testing protocols in terms of their ability to shorten the delay between blood sampling and appropriate antibiotic therapy. Methods In this french observational study, we compared three blood culture testing protocols. Positive blood cultures were tested using either GenMark ePlex panels (multiplex PCR period), a combination of MRSA/SA PCR, β-Lacta and oxidase tests (multitest period), or conventional identification and susceptibility tests only (reference period). Conventional identification and susceptibility tests were performed in parallel for all samples, as the gold standard. Results Among the 270 patients with positive blood cultures included, early and conventional results were in good agreement, especially for the multitest period. The delay between a blood culture positivity and initial results was 3.8 (2.9-6.9) h in the multiplex PCR period, 2.6 (1.3-4.5) h in the multitest period and 3.7 (1.8-8.2) h in the reference period (p<0.01). Antibiotic therapy was initiated or adjusted in 68 patients based on early analysis results. The proportion of patients receiving appropriate antibiotic therapy within 48 h of blood sampling was higher in the multiplex PCR and multitest periods, (respectively 90% and 88%) than in the reference period (71%). Conclusion These results suggest rapid bacterial identification and antibiotic resistance tests are feasible, efficient and can expedite appropriate antibiotic therapy.
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Affiliation(s)
| | - Nathalie Rousseau
- Centre Hospitalier Saint Joseph Saint Luc, Laboratoire de biologie médicale, Lyon, France
| | - Laurence Parmeland
- Centre Hospitalier Saint Joseph Saint Luc, Laboratoire de biologie médicale, Lyon, France
| | - Pierre Metral
- Centre Hospitalier Saint Joseph Saint Luc, Département d’Information Médicale, Lyon, France
| | - Caroline Pariset
- Centre Hospitalier Saint Joseph Saint Luc, Maladies Infectieuses, Lyon, France
| | - Emmanuel Vivier
- Centre Hospitalier Saint Joseph Saint Luc, Médecine Intensive Réanimation, Lyon, France
- Centre Hospitalier Saint Joseph Saint Luc, Unité de Recherche Clinique, Lyon, France
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Mahmoud FM, Khedr RAE, Ebeid E, El-Mahallawy HA, Hassan SS. Impact of Rapid Molecular Diagnostic Technique on Time to Optimal Antimicrobial Therapy and Hospital Outcomes in Pediatric Cancer Patients with Sepsis. Asian Pac J Cancer Prev 2023; 24:2465-2471. [PMID: 37505781 PMCID: PMC10676468 DOI: 10.31557/apjcp.2023.24.7.2465] [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: 03/26/2023] [Accepted: 07/03/2023] [Indexed: 07/29/2023] Open
Abstract
BACKGROUND sepsis is a leading cause of morbidity and mortality in pediatric cancer patients. We sought to assess the impact of using rapid molecular diagnostic techniques on time to pathogen identification, early administration of targeted antimicrobial treatment, and hospital outcomes. PATIENTS AND METHODS This prospective study was conducted at the Egyptian National Cancer Institute (1/2018-1/2019) on pediatric cancer patients with suspected sepsis. The cohort was divided into two groups. In one group, blood samples were sent for rapid molecular detection [multiplex-Polymerase Chain Reaction (PCR)] and blood cultures (PCR-group). While only blood cultures were collected for the second group (BC-group). RESULTS In the entire cohort (n=120), the most common bacteria identified on blood cultures was Escherichia Coli (n=33,27.5%) followed by Klebsiella (n=31,25.8%). Multidrug-resistant bacteria were identified in 63 patients (52.5%). The median turnaround time to initial results was 5 hours in PCR-group (n=60), and 120 hours in BC-group (n=60)(P<0.001). For PCR-group, agreement in pathogen identification between the rapid molecular detection kit (PCR) and blood cultures was noted in 56 patients (93.3%). While the remaining four patients had no bacterial growth on blood cultures. The empirical antibiotic treatment for the PCR-group was modified based on the result of the PCR test. Antibiotic shift, based on blood culture sensitivity results, was done in 29 patients (48%) in PCR-group, compared to 45 patients (75%) in BC-group (P=0.003). Median sepsis episode duration [8-days vs. 10-days,P=0.361), and hospital mortality (42% vs. 50%, P=0.360) were slightly lower in PCR-group. However, this did not reach statistical significance. CONCLUSION There was a substantial agreement in pathogen identification between the rapid molecular detection method (PCR) and blood culture results. PCR had a much shorter turnaround time, which allows for earlier start of optimal antimicrobial treatment, and might potentially improve hospital outcomes, which in turn will reduce associated health care costs.
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Affiliation(s)
- Farida M. Mahmoud
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Egypt.
| | | | - Emad Ebeid
- Department of Pediatric Oncology, National Cancer Institute, Cairo University, Egypt.
| | - Hadir A. El-Mahallawy
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Egypt.
| | - Safaa Shawky Hassan
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Egypt.
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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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Dierikx T, Budding A, Bos M, van Laerhoven H, van der Schoor S, Niemarkt H, Benninga M, van Kaam A, Visser D, de Meij T. Potential of Molecular Culture in Early Onset Neonatal Sepsis Diagnosis: A Proof of Principle Study. Microorganisms 2023; 11:microorganisms11040960. [PMID: 37110382 PMCID: PMC10145526 DOI: 10.3390/microorganisms11040960] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/24/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Delay in the time-to-positivity of a peripheral blood culture (PBC), the gold standard for early onset neonatal sepsis (EOS) diagnosis, has resulted in excessive use of antibiotics. In this study, we evaluate the potential of the rapid Molecular Culture (MC) assay for quick EOS diagnosis. In the first part of this study, known positive and spiked blood samples were used to assess the performance of MC. In the in vivo clinical study, the second part of this study, all infants receiving antibiotics for suspicion of EOS were included. At initial EOS suspicion, a blood sample was collected for PBC and MC. MC was able to detect bacteria present in the spiked samples even when the bacterial load was low. In the clinical study, MC was positive in one infant with clinical EOS (Enterococcus faecalis) that was not detected by PBC. Additionally, MC was positive in two infants without clinical sepsis (Streptococcus mitis and multiple species), referred to as contamination. The other 37 samples were negative both by MC and PBC. MC seems to be able to detect bacteria even when the bacterial load is low. The majority of MC and PBC results were comparable and the risk for contamination and false positive MC results seems to be limited. Since MC can generate results within 4 h following sampling compared with 36-72 h in PBC, MC may have the potential to replace conventional PBC in EOS diagnostics in order to guide clinicians on when to discontinue antibiotic therapy several hours after birth.
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Affiliation(s)
- Thomas Dierikx
- Department of Pediatric Gastroenterology, Amsterdam UMC Location University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ Amsterdam, The Netherlands
- Department of Neonatology, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Reproduction & Development, 1105 AZ Amsterdam, The Netherlands
| | | | | | | | | | - Hendrik Niemarkt
- Department of Neonatology, Máxima Medisch Centrum, 5504 DB Veldhoven, The Netherlands
| | - Marc Benninga
- Department of Pediatric Gastroenterology, Amsterdam UMC Location University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ Amsterdam, The Netherlands
| | - Anton van Kaam
- Department of Neonatology, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Reproduction & Development, 1105 AZ Amsterdam, The Netherlands
| | - Douwe Visser
- Department of Neonatology, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Reproduction & Development, 1105 AZ Amsterdam, The Netherlands
| | - Tim de Meij
- Department of Pediatric Gastroenterology, Amsterdam UMC Location University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ Amsterdam, The Netherlands
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12
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Neyton LPA, Langelier CR, Calfee CS. Metagenomic Sequencing in the ICU for Precision Diagnosis of Critical Infectious Illnesses. Crit Care 2023; 27:90. [PMID: 36941644 PMCID: PMC10027598 DOI: 10.1186/s13054-023-04365-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
This article is one of ten reviews selected from the Annual Update in Intensive Care and Emergency Medicine 2023. Other selected articles can be found online at https://www.biomedcentral.com/collections/annualupdate2023 . Further information about the Annual Update in Intensive Care and Emergency Medicine is available from https://link.springer.com/bookseries/8901 .
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Affiliation(s)
- Lucile P A Neyton
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
| | - Charles R Langelier
- Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Carolyn S Calfee
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
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13
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Caunedo-Jiménez M, Fernández-Colomer B, Fernández-Suárez J, Arias-Llorente RP, Lareu-Vidal S, Mantecón-Fernández L, Solís-Sánchez G, Suárez-Rodríguez M. Clinical Utility of the FilmArray® Blood Culture Identification (BCID) Panel for the Diagnosis of Neonatal Sepsis. Microorganisms 2023; 11:microorganisms11030732. [PMID: 36985305 PMCID: PMC10059247 DOI: 10.3390/microorganisms11030732] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/20/2023] [Accepted: 03/10/2023] [Indexed: 03/16/2023] Open
Abstract
This prospective single-center study was designed to assess the clinical utility of the FilmArray® blood culture identification (BCID) panel for improving the diagnostic accuracy in neonatal sepsis. Results obtained using the FilmArray® BCID panel were correlated with results of blood culture in all consecutive neonates with suspicion of early-onset (EOS) and late-onset sepsis (LOS) attended in our service over a two-year period. A total of 102 blood cultures from 92 neonates were included, 69 (67.5%) in cases of EOS and 33 (32.3%) in LOS. The FilmArray® BCID panel was performed in negative culture bottles at a median of 10 h of blood culture incubation (IQR 8–20), without differences by the type of sepsis. The FilmArray® BCID panel showed a 66.7% sensitivity, 100% specificity, 100% positive predictive value, and 95.7% negative predictive value. There were four false-negative cases, three of which were Streptococcus epidermidis in neonates with LOS, and there was one case of Granulicatella adiacens in one neonate with EOS. We conclude that the use of the FilmArray® BCID panel in negative blood cultures from neonates with clinical suspicion of sepsis is useful in decision-making of starting or early withdrawal of empirical antimicrobials because of the high specificity and negative predictive values of this assay.
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Affiliation(s)
- María Caunedo-Jiménez
- Division of Neonatology, Department of Pediatrics, Central University Hospital of Asturias, Av. Roma s/n, E-33011 Oviedo, Spain
| | - Belén Fernández-Colomer
- Division of Neonatology, Department of Pediatrics, Central University Hospital of Asturias, Av. Roma s/n, E-33011 Oviedo, Spain
- Correspondence:
| | - Jonathan Fernández-Suárez
- Department of Microbiology, Central University Hospital of Asturias and Instituto de Investigación Sanitaria del Principado de Asturias, E-33011 Oviedo, Spain
| | - Rosa Patricia Arias-Llorente
- Division of Neonatology, Department of Pediatrics, Central University Hospital of Asturias, Av. Roma s/n, E-33011 Oviedo, Spain
| | - Sonia Lareu-Vidal
- Division of Neonatology, Department of Pediatrics, Central University Hospital of Asturias, Av. Roma s/n, E-33011 Oviedo, Spain
| | - Laura Mantecón-Fernández
- Division of Neonatology, Department of Pediatrics, Central University Hospital of Asturias, Av. Roma s/n, E-33011 Oviedo, Spain
| | - Gonzalo Solís-Sánchez
- Division of Neonatology, Department of Pediatrics, Central University Hospital of Asturias, Av. Roma s/n, E-33011 Oviedo, Spain
| | - Marta Suárez-Rodríguez
- Division of Neonatology, Department of Pediatrics, Central University Hospital of Asturias, Av. Roma s/n, E-33011 Oviedo, Spain
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14
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Peterson SW, Demczuk W, Martin I, Adam H, Bharat A, Mulvey MR. Identification of bacterial and fungal pathogens directly from clinical blood cultures using whole genome sequencing. Genomics 2023; 115:110580. [PMID: 36792020 DOI: 10.1016/j.ygeno.2023.110580] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 01/17/2023] [Accepted: 02/11/2023] [Indexed: 02/16/2023]
Abstract
Bloodstream infections are a major cause of morbidity and mortality worldwide. Early administration of appropriate antimicrobial therapy can improve patient survival and prevent antimicrobial resistance (AMR). Whole genome sequencing (WGS) can provide information for pathogen identification, AMR prediction and sequence typing earlier than current phenotypic diagnostic methods. WGS was performed on 97 clinical blood specimens and matched culture isolate pairs. Specimen/isolate pairs were MLST sequence-typed and further characterization was performed on Streptococcus species. WGS correctly identified 91.7% of clinical specimens and 93.2% of matched isolates representing 35 different microbial species. MLST types were assigned for 89.9% of matched cultures and 21.7% of blood specimens, with higher success for blood culture specimens extracted within 3 days (52% characterized) than 7 days (9.3%). This study demonstrates the potential use of WGS for identification and characterization of pathogens directly from blood culture specimens to facilitate timely initiation of appropriate antimicrobial therapies.
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Affiliation(s)
- S W Peterson
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - W Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - I Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - H Adam
- Diagnostic Services, Shared Health Manitoba, Health Sciences Centre, Winnipeg, Manitoba, Canada
| | - A Bharat
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
| | - M R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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15
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Ultrafast Determination of Antimicrobial Resistant Staphylococcus aureus Specifically Captured by Functionalized Magnetic Nanoclusters. ACS Sens 2022; 7:3491-3500. [PMID: 36278860 DOI: 10.1021/acssensors.2c01837] [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] [Indexed: 01/31/2023]
Abstract
Sepsis, the systemic response to infection, is a life-threatening situation for patients and leads to high mortality, especially when caused by antimicrobial resistant pathogens. Prompt diagnosis and identification of the pathogenic bacteria, including their antibiotic resistance, are highly desired to yield a timely decision for treatment. Here, we aim to develop a platform for rapid isolation and efficient identification of Staphylococcus aureus, the most frequently occurring pathogen in sepsis. A peptide (VPHNPGLISLQG, SA5-1), specifically binding to S. aureus, was conjugated to the PEGylated magnetic nanoclusters, successfully enabling the specific capture and enrichment of S. aureus from blood serum. Consequently, fast detection of the antimicrobial resistance of the collected S. aureus was achieved within 30 min using a novel luminescent probe. These magnetic nanoclusters manifest a promising diagnostic prospect to combat sepsis.
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16
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Acquier M, Zabala A, de Précigout V, Delmas Y, Dubois V, de la Faille R, Rubin S, Combe C, M'Zali F, Kaminski H. Performance of real-time PCR in suspected haemodialysis catheter-related bloodstream infection: a proof-of-concept study. Clin Kidney J 2022; 16:494-500. [PMID: 36865002 PMCID: PMC9972837 DOI: 10.1093/ckj/sfac242] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Indexed: 11/13/2022] Open
Abstract
Background Catheter-related bloodstream infections (CRBIs) remain a major cause of mortality in haemodialysis (HD) patients with central venous catheters (CVCs), especially because of the non-specific symptomatology and the delay in microbiological diagnosis with possible use of non-optimal empiric antibiotics. Moreover, empiric broad-spectrum antibiotics increase antibiotic resistance development. This study aims to evaluate the diagnostic performance of real-time polymerase chain reaction (rt-PCR) in suspected HD CRBIs compared with blood cultures. Methods A blood sample for rt-PCR was collected simultaneously with each pair of blood cultures for suspected HD CRBI. The rt-PCR was performed on the whole blood, without any enrichment stage and with specific DNA primers: 16S (universal bacterial), Staphylococcus spp., Staphylococcus aureus and mecA. Each successive patient with a suspected HD CRBI in the HD centre of Bordeaux University Hospital was included. Performance tests were used to compare the result obtained in each rt-PCR assay with its corresponding routine blood culture. Results Eighty-four paired samples were collected and compared for 40 suspected HD CRBI events in 37 patients. Among these, 13 (32.5%) were diagnosed as HD CRBI. All rt-PCRs except mecA (insufficient number of positive samples) showed high diagnostic performances within 3.5 h: 16S (sensitivity 100%, specificity 78%), Staphylococcus spp. (sensitivity 100%, specificity 97%), S. aureus (sensitivity 100%, specificity 99%). Based on the rt-PCR results, antibiotics could be more appropriately targeted, thus cutting anti-cocci Gram-positive therapy from 77% to 29%. Conclusions The performance of rt-PCR in suspected HD CRBI events showed fast and high diagnostic accuracy. Its use would improve HD CRBI management with an antibiotic consumption decrease.
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Affiliation(s)
| | - Arnaud Zabala
- UMR 5234 CNRS, Université de Bordeaux, Bordeaux, France
| | - Valérie de Précigout
- Service de Néphrologie-Transplantation-Dialyse-Aphérèses, Hôpital Pellegrin, CHU de Bordeaux,Bordeaux, France
| | - Yahsou Delmas
- Service de Néphrologie-Transplantation-Dialyse-Aphérèses, Hôpital Pellegrin, CHU de Bordeaux,Bordeaux, France
| | - Véronique Dubois
- Laboratoire de Bactériologie, Hôpital Pellegrin, CHU de Bordeaux,Bordeaux, France
| | - Renaud de la Faille
- Service de Néphrologie-Transplantation-Dialyse-Aphérèses, Hôpital Pellegrin, CHU de Bordeaux,Bordeaux, France
| | - Sébastien Rubin
- Service de Néphrologie-Transplantation-Dialyse-Aphérèses, Hôpital Pellegrin, CHU de Bordeaux,Bordeaux, France,Unité Inserm, UMR1034, Biologie des Maladies Cardiovasculaires, Université de Bordeaux, Pessac, France
| | - Christian Combe
- Service de Néphrologie-Transplantation-Dialyse-Aphérèses, Hôpital Pellegrin, CHU de Bordeaux,Bordeaux, France,Unité Inserm 1026 Biotis, Université de Bordeaux, Bordeaux, France
| | - Fatima M'Zali
- UMR 5234 CNRS, Université de Bordeaux, Bordeaux, France
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17
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Zhang E, Ou H, Jia L, Zhang W, Wang Y, Wang X. Comparative analysis of loop-mediated isothermal amplification combined with microfluidic chip technology and q-PCR in the detection of clinical infectious pathogens. J Clin Lab Anal 2022; 36:e24565. [PMID: 35754145 PMCID: PMC9396168 DOI: 10.1002/jcla.24565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/15/2022] [Accepted: 06/07/2022] [Indexed: 11/07/2022] Open
Abstract
Background Rapid diagnosis of infectious pathogens at an early stage is crucial to stabilize the patient's condition, reduce medical costs, and shorten hospital stays. Currently, some point‐of‐care tests have their own shortcomings. Therefore, we built a microfluidic chip based on loop‐mediated isothermal amplification to can quickly and sensitively detect infectious pathogens. Methods We extracted the DNA of S. aureus, MRSA, Shigella and Klebsiella pneumoniae. Then, the DNA samples were diluted by 10‐fold and examined by two methods: LAMP‐microfluidic chip and q‐PCR, the sensitivity of whom was also compared. In addition, the specificity of the two was also examined by detecting the target bacteria and other microorganisms using the same methods. Finally, we extracted and tested the DNA of clinically infected humoral samples to determine the coincidence rate between the two methods and the bacterial culture method. Results For S. aureus, MRSA, Shigella, and Klebsiella pneumoniae, the detection limits of the chip were 2.25 × 103 copies/μl, 5.32 × 103 copies/μl, 2.89 × 103 copies/μl, 6.53 × 102 copies/μl, and the detection limits of q‐PCR were 2.25 × 102 copies/μl, 5.32 × 101 copies/μl, 2.89 × 102 copies/μl, 6.53 × 101 copies/μl, respectively. In terms of detection specificity, neither method cross‐reacted with other strains. For the detection of infectious humoral samples, the total coincidence rate between the q‐PCR and bacterial culture method was 85.7%, 95%, 95%, and 95.5%, and the total coincidence rate between the chip and bacterial culture method was 81%, 95%, 90%, and 86.4%, respectively. Conclusion LAMP‐microfluidic chip provides a simple, sensitive, specific, convenient, and rapid pathogen detection method for clinically infected humoral samples without relying on expensive equipment or technical personnels.
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Affiliation(s)
- Enqi Zhang
- The Postgraduate Training Base of Jinzhou Medical University (The PLA Rocket Force Characteristic Medical Center), Beijing, China
| | - Hongling Ou
- Department of Clinical Laboratory, The PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - Lianling Jia
- Department of Clinical Laboratory, The PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - Wang Zhang
- Department of Clinical Laboratory, The PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - Yemei Wang
- The Postgraduate Training Base of Jinzhou Medical University (The PLA Rocket Force Characteristic Medical Center), Beijing, China
| | - Xinru Wang
- Department of Clinical Laboratory, The PLA Rocket Force Characteristic Medical Center, Beijing, China
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18
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Song Y, Neff M, Gyarmati P. Challenges and advances in the diagnosis of bloodstream infection. Future Microbiol 2022; 17:311-314. [PMID: 35172600 DOI: 10.2217/fmb-2021-0304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Yajing Song
- Cancer Biology and Pharmacology, University of Illinois College of Medicine, Peoria, IL, USA
| | - Michael Neff
- Cancer Biology and Pharmacology, University of Illinois College of Medicine, Peoria, IL, USA
| | - Peter Gyarmati
- Cancer Biology and Pharmacology, University of Illinois College of Medicine, Peoria, IL, USA
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19
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Bandemia as an Early Predictive Marker of Bacteremia: A Retrospective Cohort Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19042275. [PMID: 35206462 PMCID: PMC8872314 DOI: 10.3390/ijerph19042275] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/09/2022] [Accepted: 02/15/2022] [Indexed: 12/13/2022]
Abstract
This single-center retrospective observational study aimed to verify whether a diagnosis of bandemia could be a predictive marker for bacteremia. We assessed 970 consecutive patients (median age 73 years; male 64.8%) who underwent two or more sets of blood cultures between April 2015 and March 2016 in both inpatient and outpatient settings. We assessed the value of bandemia (band count > 10%) and the percentage band count for predicting bacteremia using logistic regression models. Bandemia was detected in 151 cases (15.6%) and bacteremia was detected in 188 cases (19.4%). The incidence of bacteremia was significantly higher in cases with bandemia (52.3% vs. 13.3%; odds ratio (OR) = 7.15; 95% confidence interval (CI) 4.91–10.5). The sensitivity and specificity of bandemia for predicting bacteremia were 0.42 and 0.91, respectively. The bandemia was retained as an independent predictive factor for the multivariable logistic regression model (OR, 6.13; 95% CI, 4.02–9.40). Bandemia is useful for establishing the risk of bacteremia, regardless of the care setting (inpatient or outpatient), with a demonstrable relationship between increased risk and bacteremia. A bandemia-based electronic alert for blood-culture collection may contribute to the improved diagnosis of bacteremia.
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20
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Cupaiolo R, Cherkaoui S, Serrano G, Dauby N, Georgala A, Blumental S, Maillart E, Hites M, Hallin M, Martiny D. Antimicrobial susceptibly testing determined by Alfred 60/AST (Alifax®) in a multi-sites' lab: performance's evaluation and optimisation of workflow. METHODS IN MICROBIOLOGY 2022; 194:106433. [PMID: 35150789 DOI: 10.1016/j.mimet.2022.106433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 02/01/2022] [Accepted: 02/06/2022] [Indexed: 11/28/2022]
Abstract
PURPOSE New techniques are needed to speed-up the identification and antimicrobial susceptibility testing (AST) of bacteria associated with bloodstream infections. Alfred 60/AST (Alifax®, Polverara, Italy) performs AST by light scattering directly from positive blood cultures. METHODS We evaluated Alfred 60/AST performances for 4 months. Each new episode of bacteraemia was included and AST were compared to either our rapid automated AST (Vitek® 2) or disk diffusion method. The discrepancies were investigated using Etest®. The time-to-result (TTR) was evaluated by comparing the blood volume inserted into Alfred 60/AST, i.e. 2 versus 7 blood drops. Taking into account the TTR, the workflow of positive blood cultures and the availability of AST results was studied in order to optimize the implementation of Alfred 60/AST. RESULTS A total of 249 samples and 1108 antibiotics for AST were tested. After exclusion of unavailable results, 1008 antibiotics were analysed. 94.9% (n = 957/1008) of the antibiotics showed categorical agreement. There were 14 very major errors (VME), 24 major errors (ME) and 13 minor errors (mE). The VME were mostly related to clindamycin (64.3%) whereas meropenem and piperacillin-tazobactam constituted the major part (37.5% and 61.5%) of ME and mE respectively. Results were highly reliable for Enterobacterales and enterococci. The mean TTR ranged between 4.3 and 6.3 h and was statistically 20 min faster when applying the 7 blood drops protocol. We showed that Alfred 60/AST could give relievable results within working hours for positive blood culture which are flagged the same day between 12:00 am and 12:00 pm. CONCLUSION Our study confirmed that Alfred 60/AST gives reliable AST results in a short period of time, especially for Enterobacterales and enterococci. AST are thus obtained the same day of a positive blood culture. Clinical impact studies are mandatory to validate a 24/24 working.
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Affiliation(s)
- R Cupaiolo
- Microbiology Department, Laboratoire Hospitalier Universitaire de Bruxelles - Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles, Brussels, Belgium.
| | - S Cherkaoui
- Microbiology Department, Laboratoire Hospitalier Universitaire de Bruxelles - Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles, Brussels, Belgium
| | - G Serrano
- Microbiology Department, Laboratoire Hospitalier Universitaire de Bruxelles - Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles, Brussels, Belgium
| | - N Dauby
- Infectious Diseases Department, Centre Hospitalier Universitaire (CHU) Saint-Pierre - Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - A Georgala
- Infectious Diseases Department, Institut Jules Bordet - Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - S Blumental
- Paediatric Infectious Diseases Department, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - E Maillart
- Infectious Diseases Department, Centre Hospitalier Universitaire (CHU) Brugmann - Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - M Hites
- Infectious Diseases Department, Hôpital Erasme - Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - M Hallin
- Microbiology Department, Laboratoire Hospitalier Universitaire de Bruxelles - Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles, Brussels, Belgium
| | - D Martiny
- Microbiology Department, Laboratoire Hospitalier Universitaire de Bruxelles - Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles, Brussels, Belgium; Medicine and Pharmacy departments, University of Mons (UMONS), Mons, Belgium
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21
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Lazzaro A, De Girolamo G, Filippi V, Innocenti GP, Santinelli L, Ceccarelli G, Trecarichi EM, Torti C, Mastroianni CM, d’Ettorre G, Russo A. The Interplay between Host Defense, Infection, and Clinical Status in Septic Patients: A Narrative Review. Int J Mol Sci 2022; 23:ijms23020803. [PMID: 35054993 PMCID: PMC8776148 DOI: 10.3390/ijms23020803] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/05/2022] [Accepted: 01/09/2022] [Indexed: 01/08/2023] Open
Abstract
Sepsis is a life-threatening condition that arises when the body's response to an infection injures its own tissues and organs. Despite significant morbidity and mortality throughout the world, its pathogenesis and mechanisms are not clearly understood. In this narrative review, we aimed to summarize the recent developments in our understanding of the hallmarks of sepsis pathogenesis (immune and adaptive immune response, the complement system, the endothelial disfunction, and autophagy) and highlight novel laboratory diagnostic approaches. Clinical management is also discussed with pivotal consideration for antimicrobic therapy management in particular settings, such as intensive care unit, altered renal function, obesity, and burn patients.
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Affiliation(s)
- Alessandro Lazzaro
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00161 Rome, Italy; (A.L.); (G.D.G.); (V.F.); (G.P.I.); (L.S.); (G.C.); (C.M.M.); (G.d.)
| | - Gabriella De Girolamo
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00161 Rome, Italy; (A.L.); (G.D.G.); (V.F.); (G.P.I.); (L.S.); (G.C.); (C.M.M.); (G.d.)
| | - Valeria Filippi
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00161 Rome, Italy; (A.L.); (G.D.G.); (V.F.); (G.P.I.); (L.S.); (G.C.); (C.M.M.); (G.d.)
| | - Giuseppe Pietro Innocenti
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00161 Rome, Italy; (A.L.); (G.D.G.); (V.F.); (G.P.I.); (L.S.); (G.C.); (C.M.M.); (G.d.)
| | - Letizia Santinelli
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00161 Rome, Italy; (A.L.); (G.D.G.); (V.F.); (G.P.I.); (L.S.); (G.C.); (C.M.M.); (G.d.)
| | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00161 Rome, Italy; (A.L.); (G.D.G.); (V.F.); (G.P.I.); (L.S.); (G.C.); (C.M.M.); (G.d.)
| | - Enrico Maria Trecarichi
- Infectious and Tropical Disease Unit, Department of Medical and Surgical Sciences, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy; (E.M.T.); (C.T.)
| | - Carlo Torti
- Infectious and Tropical Disease Unit, Department of Medical and Surgical Sciences, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy; (E.M.T.); (C.T.)
| | - Claudio Maria Mastroianni
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00161 Rome, Italy; (A.L.); (G.D.G.); (V.F.); (G.P.I.); (L.S.); (G.C.); (C.M.M.); (G.d.)
| | - Gabriella d’Ettorre
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00161 Rome, Italy; (A.L.); (G.D.G.); (V.F.); (G.P.I.); (L.S.); (G.C.); (C.M.M.); (G.d.)
| | - Alessandro Russo
- Infectious and Tropical Disease Unit, Department of Medical and Surgical Sciences, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy; (E.M.T.); (C.T.)
- Correspondence:
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Trung NT, Lien TT, Sang VV, Hoan NX, Manh ND, Thau NS, Quyen DT, Hien TTT, Hoan PQ, Bang MH, Velavan TP, Song LH. Circulating miR-147b as a diagnostic marker for patients with bacterial sepsis and septic shock. PLoS One 2021; 16:e0261228. [PMID: 34914790 PMCID: PMC8675720 DOI: 10.1371/journal.pone.0261228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 11/24/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Early diagnosis, precise antimicrobial treatment and subsequent patient stratification can improve sepsis outcomes. Circulating biomarkers such as plasma microRNAs (miRNAs) have proven to be surrogates for diagnosis, severity and case management of infections. The expression of four selected miRNAs (miR-146-3p, miR-147b, miR-155 and miR-223) was validated for their prognostic and diagnostic potential in a clinically defined cohort of patients with sepsis and septic shock. METHODS The expression of plasma miRNAs was quantified by quantitative PCR (qPCR) in patients with bacterial sepsis (n = 78), in patients with septic shock (n = 52) and in patients with dengue haemorrhagic fever (DHF; n = 69) and in healthy controls (n = 82). RESULTS The expression of studied miRNA was significantly increased in patients with bacterial sepsis and septic shock. The plasma miR-147b was able to differentiate bacterial sepsis from non-sepsis and septic shock (AUC = 0.77 and 0.8, respectively, p≤ 0.05), while the combination of plasma miR-147b and procalcitonin (PCT) predicted septic shock (AUC = 0.86, p≤ 0.05). CONCLUSIONS The plasma miR-147b may be an useful biomarker independently or in combination with PCT to support clinical diagnosis of sepsis and equally prognosis of patients with septic shock.
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Affiliation(s)
- Ngo Tat Trung
- Centre for Genetics Consultation and Cancer Screening, Hanoi, Vietnam
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam
- Department of Molecular Biology, Hanoi, Vietnam
- * E-mail: (LHS); (NTT)
| | - Tran Thi Lien
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam
| | - Vu Viet Sang
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam
- Institute of Clinical Infectious Diseases, Hanoi, Vietnam
| | - Nghiem Xuan Hoan
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam
- Department of Molecular Biology, Hanoi, Vietnam
| | - Nguyen Dang Manh
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam
- Institute of Clinical Infectious Diseases, Hanoi, Vietnam
| | - Nguyen Sy Thau
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam
- Institute of Clinical Infectious Diseases, Hanoi, Vietnam
| | - Dao Thanh Quyen
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam
- Department of Molecular Biology, Hanoi, Vietnam
| | | | | | - Mai Hong Bang
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam
- Department of Gastroenterology, Hanoi, Vietnam
| | - Thirumalaisamy P. Velavan
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Le Huu Song
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam
- Institute of Clinical Infectious Diseases, Hanoi, Vietnam
- * E-mail: (LHS); (NTT)
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23
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Liu D, Zhou H, Xu T, Yang Q, Mo X, Shi D, Ai J, Zhang J, Tao Y, Wen D, Tong Y, Ren L, Zhang W, Xie S, Chen W, Xing W, Zhao J, Wu Y, Meng X, Ouyang C, Jiang Z, Liang Z, Tan H, Fang Y, Qin N, Guan Y, Gai W, Xu S, Wu W, Zhang W, Zhang C, Wang Y. Multicenter assessment of shotgun metagenomics for pathogen detection. EBioMedicine 2021; 74:103649. [PMID: 34814051 PMCID: PMC8608867 DOI: 10.1016/j.ebiom.2021.103649] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Shotgun metagenomics has been used clinically for diagnosing infectious diseases. However, most technical assessments have been limited to individual sets of reference standards, experimental workflows, and laboratories. METHODS A reference panel and performance metrics were designed and used to examine the performance of shotgun metagenomics at 17 laboratories in a coordinated collaborative study. We comprehensively assessed the reliability, key performance determinants, reproducibility, and quantitative potential. FINDINGS Assay performance varied significantly across sites and microbial classes, with a read depth of 20 millions as a generally cost-efficient assay setting. Results of mapped reads by shotgun metagenomics could indicate relative and intra-site (but not absolute or inter-site) microbial abundance. INTERPRETATION Assay performance was significantly impacted by the microbial type, the host context, and read depth, which emphasizes the importance of these factors when designing reference reagents and benchmarking studies. Across sites, workflows and platforms, false positive reporting and considerable site/library effects were common challenges to the assay's accuracy and quantifiability. Our study also suggested that laboratory-developed shotgun metagenomics tests for pathogen detection should aim to detect microbes at 500 CFU/mL (or copies/mL) in a clinically relevant host context (10^5 human cells/mL) within a 24h turn-around time, and with an efficient read depth of 20M. FUNDING This work was supported by National Science and Technology Major Project of China (2018ZX10102001).
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Affiliation(s)
- Donglai Liu
- National Institutes for Food and Drug Control, Beijing 100050, China
| | - Haiwei Zhou
- National Institutes for Food and Drug Control, Beijing 100050, China
| | - Teng Xu
- Key Laboratory of Animal Gene Editing and Animal Cloning in Yunnan Province and College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
| | - Qiwen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xi Mo
- The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Dawei Shi
- National Institutes for Food and Drug Control, Beijing 100050, China
| | - Jingwen Ai
- Department of Infectious Diseases, Huashan Hospital affiliated to Fudan University, Shanghai 200040, China
| | - Jingjia Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yue Tao
- The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Donghua Wen
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200123, PR China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology. Beijing 100029
| | - Lili Ren
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, PR China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, PR China
| | - Wen Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing 102206, China
| | - Shumei Xie
- Vision Medicals Center for Infectious Diseases, Guangzhou, Guangdong 510000, China
| | - Weijun Chen
- BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen 518083, China
| | - Wanli Xing
- School of Medicine Tsinghua University, Beijing, China; CapitalBio Technology Co., Ltd., Yizhuang Biomedical Park Beijing, China
| | - Jinyin Zhao
- Dalian GenTalker Clinical Laboratory, Dalian 116635, China
| | - Yilan Wu
- Guangzhou Sagene Biotech Co., Ltd., Guangzhou, China
| | - Xianfa Meng
- Guangzhou Kingmed Diagnostics, Guangzhou, Guangdong 510330, China
| | - Chuan Ouyang
- Hangzhou MatriDx Biotechnology Co., Ltd, Hangzhou, China
| | - Zhi Jiang
- Genskey Medical Technology, Co., Ltd., Beijing 102206, China
| | - Zhikun Liang
- Guangzhou Darui Biotechnology, Co., Ltd., Guangzhou 510663, China
| | - Haiqin Tan
- Hangzhou IngeniGen XunMinKang Biotechnology Co., Ltd., Hangzhou 311121, China
| | - Yuan Fang
- Dinfectome Inc, Shanghai 201321, China
| | - Nan Qin
- Realbio Genomics Institute, Shanghai 201114, China
| | | | - Wei Gai
- WillingMed Technology Beijing Co., Ltd., Beijing, China
| | - Sihong Xu
- National Institutes for Food and Drug Control, Beijing 100050, China.
| | - Wenjuan Wu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200123, PR China.
| | - Wenhong Zhang
- Department of Infectious Diseases, Huashan Hospital affiliated to Fudan University, Shanghai 200040, China.
| | - Chuntao Zhang
- National Institutes for Food and Drug Control, Beijing 100050, China.
| | - Youchun Wang
- National Institutes for Food and Drug Control, Beijing 100050, China.
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24
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Impact of Short-Incubation MALDI-TOF MS on Rapid Identification of Pathogens and Antibiotic Therapy. Jundishapur J Microbiol 2021. [DOI: 10.5812/jjm.117279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: It can be a critical point for reducing pathogen identification time and accurate antibiotic treatment for patients with blood circulation infection since it causes high mortality. Objective: The objectives of this study were to evaluate the time differences between conventional identification and MALDI-TOF conventional identification and short-incubation MALDI-TOF identification for positive blood cultures, and to explore the impact of short-incubation matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS) identification on empirical antibiotic therapy. Methods: Positive blood cultures were collected in our hospital from 2017 to 2019, clinical data were collected from the medical records, which were analyzed retrospectively to determine the empirical antibiotic therapy. Results: Compared with the conventional identification method, the short-incubation MALDI-TOF identification time to initial identification of Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, Acinetobacter baumannii, Staphylococcus aureus, Enterococcus faecium, and E. faecalis decreased by 22.28 h, 22 h, 23.59 h, 23.63 h, 22.63 h, 23.92 h, and 21.59 h, respectively (P < 0.05). The time to final reporting was decreased by 48.85 h, 47.99 h, 55.40 h, 51.07 h, 49.60 h, 51.78h, and 51.73h, respectively (P < 0.05). However, the antimicrobial susceptibility test time of E. coli, A. baumannii, and S. aureus increased to 2.02 h, 2.19 h, and 3.86 h, respectively (P < 0.05). The coincidence rate of antimicrobial susceptibility was 98.48% between short-incubation MALDI-TOF identification and conventional identification method of all Gram-negative bacilli, and there were no extremely major errors or major errors. The coincidence rate of antimicrobial susceptibility of Gram-positive cocci was 99.53%, one strain of E. faecium and S. aureus had major errors. Patients received earlier correct empirical antibiotic 19.89 h earlier by short-incubation MALDI-TOF identification than the conventional identification method (P < 0.001). Conclusions: The short-incubation MALDI-TOF identification significantly shortens the pathogen identification time and the final report time, it is a reliable method for rapid identification of positive blood cultures; the results of antimicrobial susceptibility are highly consistent, which significantly lead to earlier appropriate empirical therapy of bacteremia.
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25
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Krämer M, Kissmann AK, Raber HF, Xing H, Favella P, Müller I, Spellerberg B, Weil T, Kubiczek D, Sihler S, Ziener U, Rosenau F. BSA Hydrogel Beads Functionalized with a Specific Aptamer Library for Capturing Pseudomonas aeruginosa in Serum and Blood. Int J Mol Sci 2021; 22:ijms222011118. [PMID: 34681780 PMCID: PMC8537436 DOI: 10.3390/ijms222011118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/05/2021] [Accepted: 10/11/2021] [Indexed: 12/19/2022] Open
Abstract
Systemic blood stream infections are a major threat to human health and are dramatically increasing worldwide. Pseudomonas aeruginosa is a WHO-alerted multi-resistant pathogen of extreme importance as a cause of sepsis. Septicemia patients have significantly increased survival chances if sepsis is diagnosed in the early stages. Affinity materials can not only represent attractive tools for specific diagnostics of pathogens in the blood but can prospectively also serve as the technical foundation of therapeutic filtration devices. Based on the recently developed aptamers directed against P. aeruginosa, we here present aptamer-functionalized beads for specific binding of this pathogen in blood samples. These aptamer capture beads (ACBs) are manufactured by crosslinking bovine serum albumin (BSA) in an emulsion and subsequent functionalization with the amino-modified aptamers on the bead surface using the thiol- and amino-reactive bispecific crosslinker PEG4-SPDP. Specific and quantitative binding of P. aeruginosa as the dedicated target of the ACBs was demonstrated in serum and blood. These initial but promising results may open new routes for the development of ACBs as a platform technology for fast and reliable diagnosis of bloodstream infections and, in the long term, blood filtration techniques in the fight against sepsis.
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Affiliation(s)
- Markus Krämer
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (M.K.); (A.-K.K.); (H.F.R.); (H.X.); (D.K.)
| | - Ann-Kathrin Kissmann
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (M.K.); (A.-K.K.); (H.F.R.); (H.X.); (D.K.)
| | - Heinz Fabian Raber
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (M.K.); (A.-K.K.); (H.F.R.); (H.X.); (D.K.)
| | - Hu Xing
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (M.K.); (A.-K.K.); (H.F.R.); (H.X.); (D.K.)
| | - Patrizia Favella
- Department of Life Sciences, Albstadt-Sigmaringen University of Applied Sciences, 72488 Sigmaringen, Germany; (P.F.); (I.M.)
| | - Ingrid Müller
- Department of Life Sciences, Albstadt-Sigmaringen University of Applied Sciences, 72488 Sigmaringen, Germany; (P.F.); (I.M.)
| | - Barbara Spellerberg
- Institute for Medical Microbiology and Hygiene, University Hospital Ulm, 89081 Ulm, Germany;
| | - Tanja Weil
- Department Synthesis of Macromolecules, Max-Planck-Institute of Polymer Science, 55128 Mainz, Germany;
| | - Dennis Kubiczek
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (M.K.); (A.-K.K.); (H.F.R.); (H.X.); (D.K.)
| | - Susanne Sihler
- Institute of Organic Chemistry III-Macromolecular Chemistry and Organic Materials, Ulm University, 89081 Ulm, Germany; (S.S.); (U.Z.)
| | - Ulrich Ziener
- Institute of Organic Chemistry III-Macromolecular Chemistry and Organic Materials, Ulm University, 89081 Ulm, Germany; (S.S.); (U.Z.)
| | - Frank Rosenau
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (M.K.); (A.-K.K.); (H.F.R.); (H.X.); (D.K.)
- Department Synthesis of Macromolecules, Max-Planck-Institute of Polymer Science, 55128 Mainz, Germany;
- Correspondence:
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26
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Utility of P-SEP, sTREM-1 and suPAR as Novel Sepsis Biomarkers in SARS-CoV-2 Infection. Indian J Clin Biochem 2021; 37:131-138. [PMID: 34642555 PMCID: PMC8494168 DOI: 10.1007/s12291-021-01008-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/18/2021] [Indexed: 12/22/2022]
Abstract
The coronavirus disease 2019 is a highly contagious viral infection caused by SARS-CoV-2 virus, member of coronaviridae family. It causes life threatening complications due to complexity and rapid onset course of the disease. Early identification of high-risk patients who require close monitoring and aggressive treatment remains challengeable till date. Novel biomarkers which help to identify high risk patients at the early stage is high priority. Objective of this review to find utility of P-SEP, sTREM-1 and suPAR for diagnosis, risk stratification and prognosis of SARS-CoV-2 infected cases. Soluble receptors like, P-SEP, sTREM-1 and suPAR have been involved in immune regulation in SARS-CoV-2 infection and elevate more in severe cases. A comprehensive research of databases like PubMed, EMBASE, CNKI and Web of Science was performed for relevant studies. A total of nine out of fifteen research literature in initial screening were included for this review. Interestingly all studies have reported high levels of P-SEP, sTREM-1 and suPAR in SARS-CoV-2 infected cases and the biomarkers positively correlated with severity of infection. This implies that P-SEP, sTREM-1 and suPAR can be implemented as surrogate marker in blood profile for early diagnosis, risk stratification and prognosis in SARS-CoV-2 for better management in Indian population at the current situation.
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27
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Kondori N, Kurtovic A, Piñeiro-Iglesias B, Salvà-Serra F, Jaén-Luchoro D, Andersson B, Alves G, Ogurtsov A, Thorsell A, Fuchs J, Tunovic T, Kamenska N, Karlsson A, Yu YK, Moore ERB, Karlsson R. Mass Spectrometry Proteotyping-Based Detection and Identification of Staphylococcus aureus, Escherichia coli, and Candida albicans in Blood. Front Cell Infect Microbiol 2021; 11:634215. [PMID: 34381737 PMCID: PMC8350517 DOI: 10.3389/fcimb.2021.634215] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 07/09/2021] [Indexed: 12/12/2022] Open
Abstract
Bloodstream infections (BSIs), the presence of microorganisms in blood, are potentially serious conditions that can quickly develop into sepsis and life-threatening situations. When assessing proper treatment, rapid diagnosis is the key; besides clinical judgement performed by attending physicians, supporting microbiological tests typically are performed, often requiring microbial isolation and culturing steps, which increases the time required for confirming positive cases of BSI. The additional waiting time forces physicians to prescribe broad-spectrum antibiotics and empirically based treatments, before determining the precise cause of the disease. Thus, alternative and more rapid cultivation-independent methods are needed to improve clinical diagnostics, supporting prompt and accurate treatment and reducing the development of antibiotic resistance. In this study, a culture-independent workflow for pathogen detection and identification in blood samples was developed, using peptide biomarkers and applying bottom-up proteomics analyses, i.e., so-called "proteotyping". To demonstrate the feasibility of detection of blood infectious pathogens, using proteotyping, Escherichia coli and Staphylococcus aureus were included in the study, as the most prominent bacterial causes of bacteremia and sepsis, as well as Candida albicans, one of the most prominent causes of fungemia. Model systems including spiked negative blood samples, as well as positive blood cultures, without further culturing steps, were investigated. Furthermore, an experiment designed to determine the incubation time needed for correct identification of the infectious pathogens in blood cultures was performed. The results for the spiked negative blood samples showed that proteotyping was 100- to 1,000-fold more sensitive, in comparison with the MALDI-TOF MS-based approach. Furthermore, in the analyses of ten positive blood cultures each of E. coli and S. aureus, both the MALDI-TOF MS-based and proteotyping approaches were successful in the identification of E. coli, although only proteotyping could identify S. aureus correctly in all samples. Compared with the MALDI-TOF MS-based approaches, shotgun proteotyping demonstrated higher sensitivity and accuracy, and required significantly shorter incubation time before detection and identification of the correct pathogen could be accomplished.
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Affiliation(s)
- Nahid Kondori
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Amra Kurtovic
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Francisco Salvà-Serra
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Björn Andersson
- Bioinformatics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Gelio Alves
- National Center for Biotechnology Information (NCBI), Bethesda, MD, United States
| | - Aleksey Ogurtsov
- National Center for Biotechnology Information (NCBI), Bethesda, MD, United States
| | - Annika Thorsell
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Johannes Fuchs
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Timur Tunovic
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Nina Kamenska
- Norra-Älvsborgs-Länssjukhus (NÄL), Trollhättan, Sweden
| | | | - Yi-Kuo Yu
- National Center for Biotechnology Information (NCBI), Bethesda, MD, United States
| | - Edward R. B. Moore
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Roger Karlsson
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Nanoxis Consulting AB, Gothenburg, Sweden
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Grosso S, Pagani L, Tosoni N, Crapis M, Turrini E, Mannu F, Carta F, Rosa RD, Turrini F, Avolio M. A new molecular method for rapid etiological diagnosis of sepsis with improved performance. Future Microbiol 2021; 16:741-751. [PMID: 34082567 DOI: 10.2217/fmb-2020-0154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The value of blood cultures for confirming the clinical diagnosis of sepsis is suboptimal. There is growing interest in the potential of real-time PCR technology by detection of minute amounts of pathogen DNA in patient blood samples with results available within 4-6 h. Adopting a two-step approach, we evaluated the compliance of two versions of the MicrobScan assay on a total of 748 patients with suspected bloodstream infections. The results obtained with a second version of the MicrobScan assay are characterized by increased specificity (from 95.1 to 98.2%) and sensitivity (from 76.7 to 85.1), increased throughput and the possibility of simultaneously testing different kinds of samples collected from the potential sites of infection and utilizing different syndromic panels.
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Affiliation(s)
- Shamanta Grosso
- Microbiology & Virology Department, Azienda per l'Assistenza Sanitaria n 5 Friuli Occidentale, Via Montereale 24, Pordenone, 33170, Italy
| | - Lucia Pagani
- Microbiology & Virology Department, Azienda per l'Assistenza Sanitaria n 5 Friuli Occidentale, Via Montereale 24, Pordenone, 33170, Italy
| | - Nilla Tosoni
- Microbiology & Virology Department, Azienda per l'Assistenza Sanitaria n 5 Friuli Occidentale, Via Montereale 24, Pordenone, 33170, Italy
| | - Massimo Crapis
- Infectious Diseases Unit, Azienda per l'Assistenza Sanitaria n 5 Friuli Occidentale, Via Montereale 24, Pordenone, 33170, Italy
| | - Enrico Turrini
- Research Unit, Nurex Srl, Strada 3, Sassari, 07100, Italy
| | - Franca Mannu
- Research Unit, Nurex Srl, Strada 3, Sassari, 07100, Italy
| | - Franco Carta
- Research Unit, Nurex Srl, Strada 3, Sassari, 07100, Italy
| | - Rita De Rosa
- Microbiology & Virology Department, Azienda per l'Assistenza Sanitaria n 5 Friuli Occidentale, Via Montereale 24, Pordenone, 33170, Italy
| | - Francesco Turrini
- Department of Oncology, University of Torino, Via Santena 5, Torino, 10126, Italy
| | - Manuela Avolio
- Microbiology & Virology Department, Azienda per l'Assistenza Sanitaria n 5 Friuli Occidentale, Via Montereale 24, Pordenone, 33170, Italy
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29
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Mannino Avila E, Stucky Fisher E, Rhee K. True Versus False Bacteremia in Infants and Children Less Than 3 Years of Age. Pediatr Emerg Care 2021; 37:e307-e312. [PMID: 30106869 DOI: 10.1097/pec.0000000000001585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The objective of this study was to examine patient history as well as clinical and laboratory features associated with true bacteremia versus false bacteremia in previously healthy febrile children ages 0 to 36 months in the era of polyvalent conjugate pneumococcal immunization. METHODS Using retrospective chart review, we examined history, physical examination, and laboratory characteristics associated with true and false bacteremia. We included subjects under 3 years old, with a positive blood culture obtained in the emergency department or clinic from July 2011 to July 2013, and fever defined as a temperature of greater than or equal to 100.4°F by history or examination. We excluded those with a previously known underlying disease process that could increase the risk for positive blood culture, for example, immunodeficiency, cancer, cystic fibrosis, or significant skin disorders such as severe eczema, as well as patients with any indwelling central line, shunt, or other implanted device, or recent hospitalization for a febrile illness. RESULTS Thirty subjects (24%) had true bacteremia, and 97 (76%) had false bacteremia. In the multivariable logistic regression analysis, exposure to sick contacts (odds ratio, 0.1; 95% confidence interval, 0.01-0.6; P = 0.01) and increased hours to positive blood culture (odds ratio, 0.8; 95% confidence interval, 0.8-0.9; P < 0.001) remained significant factors associated with false bacteremia. Age, maximum reported temperature, and reported days of fever were not associated with true bacteremia. CONCLUSIONS We found that previously healthy children with true bacteremia are more likely to grow bacteria faster on blood culture and lack exposure to sick contacts than children with false bacteremia.
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Affiliation(s)
| | | | - Kyung Rhee
- Division of Academic General Pediatrics, San Diego/Rady Children's Hospital San Diego, University of California, San Diego, CA
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30
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The Development and Validation of a Machine Learning Model to Predict Bacteremia and Fungemia in Hospitalized Patients Using Electronic Health Record Data. Crit Care Med 2021; 48:e1020-e1028. [PMID: 32796184 DOI: 10.1097/ccm.0000000000004556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OBJECTIVES Bacteremia and fungemia can cause life-threatening illness with high mortality rates, which increase with delays in antimicrobial therapy. The objective of this study is to develop machine learning models to predict blood culture results at the time of the blood culture order using routine data in the electronic health record. DESIGN Retrospective analysis of a large, multicenter inpatient data. SETTING Two academic tertiary medical centers between the years 2007 and 2018. SUBJECTS All hospitalized patients who received a blood culture during hospitalization. INTERVENTIONS The dataset was partitioned temporally into development and validation cohorts: the logistic regression and gradient boosting machine models were trained on the earliest 80% of hospital admissions and validated on the most recent 20%. MEASUREMENTS AND MAIN RESULTS There were 252,569 blood culture days-defined as nonoverlapping 24-hour periods in which one or more blood cultures were ordered. In the validation cohort, there were 50,514 blood culture days, with 3,762 cases of bacteremia (7.5%) and 370 cases of fungemia (0.7%). The gradient boosting machine model for bacteremia had significantly higher area under the receiver operating characteristic curve (0.78 [95% CI 0.77-0.78]) than the logistic regression model (0.73 [0.72-0.74]) (p < 0.001). The model identified a high-risk group with over 30 times the occurrence rate of bacteremia in the low-risk group (27.4% vs 0.9%; p < 0.001). Using the low-risk cut-off, the model identifies bacteremia with 98.7% sensitivity. The gradient boosting machine model for fungemia had high discrimination (area under the receiver operating characteristic curve 0.88 [95% CI 0.86-0.90]). The high-risk fungemia group had 252 fungemic cultures compared with one fungemic culture in the low-risk group (5.0% vs 0.02%; p < 0.001). Further, the high-risk group had a mortality rate 60 times higher than the low-risk group (28.2% vs 0.4%; p < 0.001). CONCLUSIONS Our novel models identified patients at low and high-risk for bacteremia and fungemia using routinely collected electronic health record data. Further research is needed to evaluate the cost-effectiveness and impact of model implementation in clinical practice.
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Hu B, Tao Y, Shao Z, Zheng Y, Zhang R, Yang X, Liu J, Li X, Sun R. A Comparison of Blood Pathogen Detection Among Droplet Digital PCR, Metagenomic Next-Generation Sequencing, and Blood Culture in Critically Ill Patients With Suspected Bloodstream Infections. Front Microbiol 2021; 12:641202. [PMID: 34079528 PMCID: PMC8165239 DOI: 10.3389/fmicb.2021.641202] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 04/12/2021] [Indexed: 12/12/2022] Open
Abstract
Metagenomic next-generation sequencing (mNGS) and droplet digital PCR (ddPCR) have recently demonstrated a great potential for pathogen detection. However, few studies have been undertaken to compare these two nucleic acid detection methods for identifying pathogens in patients with bloodstream infections (BSIs). This prospective study was thus conducted to compare these two methods for diagnostic applications in a clinical setting for critically ill patients with suspected BSIs. Upon suspicion of BSIs, whole blood samples were simultaneously drawn for ddPCR covering 20 common isolated pathogens and four antimicrobial resistance (AMR) genes, mNGS, and blood culture. Then, a head-to-head comparison was performed between ddPCR and mNGS. A total of 60 episodes of suspected BSIs were investigated in 45 critically ill patients, and ddPCR was positive in 50 (83.3%), mNGS in 41 (68.3%, not including viruses), and blood culture in 10 (16.7%) episodes. Of the 10 positive blood cultures, nine were concordantly identified by both mNGS and ddPCR methods. The head-to-head comparison showed that ddPCR was more rapid (~4 h vs. ~2 days) and sensitive (88 vs. 53 detectable pathogens) than mNGS within the detection range of ddPCR, while mNGS detected a broader range of pathogens (126 vs. 88 detectable pathogens, including viruses) than ddPCR. In addition, a total of 17 AMR genes, including 14 blaKPC and 3 mecA genes, were exclusively identified by ddPCR. Based on their respective limitations and strengths, the ddPCR method is more useful for rapid detection of common isolated pathogens as well as AMR genes in critically ill patients with suspected BSI, whereas mNGS testing is more appropriate for the diagnosis of BSI where classic microbiological or molecular diagnostic approaches fail to identify causative pathogens.
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Affiliation(s)
- Bangchuan Hu
- Intensive Care Unit, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Yue Tao
- The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Ziqiang Shao
- Intensive Care Unit, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Yang Zheng
- Intensive Care Unit, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Run Zhang
- Intensive Care Unit, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Xuejing Yang
- The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Jingquan Liu
- Intensive Care Unit, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Xi Li
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Renhua Sun
- Intensive Care Unit, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
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Grumaz C, Hoffmann A, Vainshtein Y, Kopp M, Grumaz S, Stevens P, Decker SO, Weigand MA, Hofer S, Brenner T, Sohn K. Rapid Next-Generation Sequencing-Based Diagnostics of Bacteremia in Septic Patients. J Mol Diagn 2021; 22:405-418. [PMID: 32146977 DOI: 10.1016/j.jmoldx.2019.12.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 11/18/2019] [Accepted: 12/11/2019] [Indexed: 01/23/2023] Open
Abstract
The increasing incidence of bloodstream infections including sepsis is a major challenge in intensive care units worldwide. However, current diagnostics for pathogen identification mainly depend on culture- and molecular-based approaches, which are not satisfactory regarding specificity, sensitivity, and time to diagnosis. Herein, we established a complete diagnostic workflow for real-time high-throughput sequencing of cell-free DNA from plasma based on nanopore sequencing for the detection of the causative agents, which was applied to the analyses of eight samples from four septic patients and three healthy controls, and subsequently validated against standard next-generation sequencing results. By optimization of library preparation protocols for short fragments with low input amounts, a 3.5-fold increase in sequencing throughput could be achieved. With tailored bioinformatics workflows, all eight septic patient samples were found to be positive for relevant pathogens. When considering time to diagnosis, pathogens were identified within minutes after start of sequencing. Moreover, an extrapolation of real-time sequencing performance on a cohort of 239 septic patient samples revealed that more than 90% of pathogen hits would have also been detected using the optimized MinION workflow. Reliable identification of pathogens based on circulating cell-free DNA sequencing using optimized workflows and real-time nanopore-based sequencing can be accomplished within 5 to 6 hours following blood draw. Therefore, this approach might provide therapy-relevant results in a clinically critical timeframe.
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Affiliation(s)
- Christian Grumaz
- Department of in-Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
| | - Anne Hoffmann
- Department of in-Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
| | - Yevhen Vainshtein
- Department of in-Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
| | - Maria Kopp
- Department of in-Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
| | - Silke Grumaz
- Department of in-Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
| | | | - Sebastian O Decker
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Markus A Weigand
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan Hofer
- Westpfalz-Klinikum GmbH, Kaiserslautern, Germany
| | - Thorsten Brenner
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Kai Sohn
- Department of in-Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany.
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Wang Q, Shen X, Qiu T, Wu W, Li L, Wang Z, Shou H. Evaluation and application of an efficient plant DNA extraction protocol for laboratory and field testing. J Zhejiang Univ Sci B 2021; 22:99-111. [PMID: 33615751 DOI: 10.1631/jzus.b2000465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Nucleic acids in plant tissue lysates can be captured quickly by a cellulose filter paper and prepared for amplification after a quick purification. In this study, a published filter paper strip method was modified by sticking the filter paper on a polyvinyl chloride resin (PVC) sheet. This modified method is named EZ-D, for EASY DNA extraction. Compared with the original cetyl trimethylammonium bromide (CTAB) method, DNA extracted by EZ-D is more efficient in polymerase chain reaction (PCR) amplification due to the more stable performance of the EZ-D stick. The EZ-D method is also faster, easier, and cheaper. PCR analyses showed that DNA extracted from several types of plant tissues by EZ-D was appropriate for specific identification of biological samples. A regular PCR reaction can detect the EZ-D-extracted DNA template at concentration as low as 0.1 ng/μL. Evaluation of the EZ-D showed that DNA extracts could be successfully amplified by PCR reaction for DNA fragments up to 3000 bp in length and up to 80% in GC content. EZ-D was successfully used for DNA extraction from a variety of plant species and plant tissues. Moreover, when EZ-D was combined with the loop-mediated isothermal amplification (LAMP) method, DNA identification of biological samples could be achieved without the need for specialized equipment. As an optimized DNA purification method, EZ-D shows great advantages in application and can be used widely in laboratories where equipment is limited and rapid results are required.
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Affiliation(s)
- Qi Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaoxia Shen
- Zhejiang Institute of Chinese Medicine, Hangzhou 310023, China
| | - Tian Qiu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wei Wu
- Shanghai YouLong Biotech Co., Ltd., Shanghai 200063, China
| | - Lin Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhi'an Wang
- Zhejiang Institute of Chinese Medicine, Hangzhou 310023, China
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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Yochpaz S, Friedman N, Zirkin S, Blumovich A, Mandel D, Marom R. C-reactive protein in early-onset neonatal sepsis - a cutoff point for CRP value as a predictor of early-onset neonatal sepsis in term and late preterm infants early after birth? J Matern Fetal Neonatal Med 2020; 35:4552-4557. [PMID: 33280469 DOI: 10.1080/14767058.2020.1856068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
OBJECTIVE To identify whether the first plasma C-reactive protein values taken 6-8 h postpartum are predictive of the clinical early-onset neonatal sepsis (cEONS). STUDY DESIGN We retrospectively analyzed C-reactive protein (CRP) values of 400 neonates, including 28 with cEONS, who underwent plasma CRP measurements as part of sepsis work-up. To determine whether the first CRP measurement is predictive of cEONS, logistic regression was used with CRP as an independent variable and cEONS (yes/no) as a dependent variable. RESULT A moderate predictive ability of the first CRP measurement (odds ratio 1.4, CI: [1.13, 1.76], p=.003) was revealed, at a 5.3 mg/L threshold. However, it resulted in poor sensitivity of 50%, and a false positive rate of 30%. Increasing the sensitivity to 75% or 90% lead to increased false-positive rates of 55% and 75%, respectively. CONCLUSIONS Our findings suggest that the first CRP value taken in neonates is a weak predictor of cEONS.
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Affiliation(s)
- Sivan Yochpaz
- Department of Neonatology, Faculty of Medicine, Dana Dwek Children's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel
| | - Nati Friedman
- Department of Neonatology, Faculty of Medicine, Dana Dwek Children's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel
| | - Semyon Zirkin
- Department of Neonatology, Faculty of Medicine, Dana Dwek Children's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel
| | - Amit Blumovich
- Department of Neonatology, Faculty of Medicine, Dana Dwek Children's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel
| | - Dror Mandel
- Department of Neonatology, Faculty of Medicine, Dana Dwek Children's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel
| | - Ronella Marom
- Department of Neonatology, Faculty of Medicine, Dana Dwek Children's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel
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35
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Cenci E, Paggi R, Socio GVD, Bozza S, Camilloni B, Pietrella D, Mencacci A. Accelerate Pheno™ blood culture detection system: a literature review. Future Microbiol 2020; 15:1595-1605. [PMID: 33215528 DOI: 10.2217/fmb-2020-0177] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Accelerate Pheno™ (ACC) is a fully automated system providing rapid identification of a panel of bacteria and yeasts, and antimicrobial susceptibility testing of common bacterial pathogens responsible for bloodstream infections and sepsis. Diagnostic accuracy for identification ranges from 87.9 to 100%, and antimicrobial susceptibility testing categorical agreement is higher than 91%. The present review includes peer-reviewed studies on ACC published to date. Both interventional and hypothetical studies evidenced the potential positive clinical role of ACC in the management and therapy of patients with bloodstream infections and sepsis, due to the important reduction in time to report, suggesting a crucial impact on the therapeutic management of these patients, provided the presence of a hospital antimicrobial stewardship program, a 24/7 laboratory operating time and a strict collaboration between clinical microbiologist and clinician. Further prospective multicenter studies are necessary to explore the impact of this system on mortality, length of stay and spread of multidrug-resistant organisms.
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Affiliation(s)
- Elio Cenci
- Department of Medicine, Medical Microbiology, University of Perugia, Perugia, Italy.,Microbiology, Perugia General Hospital, Perugia, Italy
| | - Riccardo Paggi
- Department of Medicine, Medical Microbiology, University of Perugia, Perugia, Italy
| | | | - Silvia Bozza
- Department of Medicine, Medical Microbiology, University of Perugia, Perugia, Italy.,Microbiology, Perugia General Hospital, Perugia, Italy
| | - Barbara Camilloni
- Department of Medicine, Medical Microbiology, University of Perugia, Perugia, Italy.,Microbiology, Perugia General Hospital, Perugia, Italy
| | - Donatella Pietrella
- Department of Medicine, Medical Microbiology, University of Perugia, Perugia, Italy.,Microbiology, Perugia General Hospital, Perugia, Italy
| | - Antonella Mencacci
- Department of Medicine, Medical Microbiology, University of Perugia, Perugia, Italy.,Microbiology, Perugia General Hospital, Perugia, Italy
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36
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Yoshida J, Tamura T, Otani K, Inoue M, Miyatake E, Ishimitsu T, Nakahara C, Tanaka M. Mortality related to drug-resistant organisms in surgical sepsis-3: an 8-year time trend study using sequential organ failure assessment scores. Eur J Clin Microbiol Infect Dis 2020; 40:535-540. [PMID: 32954476 PMCID: PMC7892503 DOI: 10.1007/s10096-020-04037-w] [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: 05/25/2020] [Accepted: 09/10/2020] [Indexed: 11/04/2022]
Abstract
The difference in sequential organ failure assessment (SOFA) scores from the baseline to sepsis is a known predictor of sepsis-3 outcome, but the prognostic value of drug-resistant organisms for mortality is unexplained. We employed sepsis stewardship and herein report an observational study. Study subjects were patients admitted to the Departments of Surgery/Chest Surgery from 2011 through 2018 with a diagnosis of sepsis and a SOFA score of 2 or more. Our sepsis stewardship methods included antimicrobial and diagnostic stewardship and infection control. We determined the primary endpoint as in-hospital death and the secondary endpoint as the annual trend of the risk-adjusted mortality ratio (RAMR). For mortality, we performed logistic regression analysis based on SOFA score, age, sex, comorbid disease, and the presence of methicillin-resistant Staphylococcus aureus (MRSA) and extended-spectrum beta-lactamase inhibitor–producing bacteria. In a total of 457 patients, two factors were significant predictors for fatality, i.e., SOFA score of 9 or more with an odds ratio (OR) 4.921 and 95% confidence interval [95% CI] 1.968–12.302 (P = 0.001) and presence of MRSA with an OR 1.83 and 95% CI 1.003–3.338 (P = 0.049). RAMR showed a decrease during the study years (P < 0.05). Early detection of MRSA may help patients survive surgical sepsis-3. Thus, MRSA-oriented diagnosis may play a role in expediting treatment with anti-MRSA antimicrobials.
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Affiliation(s)
- Junichi Yoshida
- Department of Surgery/Chest Surgery, Shimonoseki City Hospital, 1-13-1 Koyo-cho, Shimonoseki, 750-8520, Japan.
| | - Tetsuro Tamura
- Department of Surgery/Chest Surgery, Shimonoseki City Hospital, 1-13-1 Koyo-cho, Shimonoseki, 750-8520, Japan
| | - Kazuhiro Otani
- Department of Surgery/Chest Surgery, Shimonoseki City Hospital, 1-13-1 Koyo-cho, Shimonoseki, 750-8520, Japan
| | - Masaaki Inoue
- Department of Surgery/Chest Surgery, Shimonoseki City Hospital, 1-13-1 Koyo-cho, Shimonoseki, 750-8520, Japan
| | - Eiji Miyatake
- Department of Surgery/Chest Surgery, Shimonoseki City Hospital, 1-13-1 Koyo-cho, Shimonoseki, 750-8520, Japan
| | - Toshiyuki Ishimitsu
- Department of Surgery/Chest Surgery, Shimonoseki City Hospital, 1-13-1 Koyo-cho, Shimonoseki, 750-8520, Japan
| | - Chihiro Nakahara
- Department of Surgery/Chest Surgery, Shimonoseki City Hospital, 1-13-1 Koyo-cho, Shimonoseki, 750-8520, Japan
| | - Masao Tanaka
- Department of Surgery/Chest Surgery, Shimonoseki City Hospital, 1-13-1 Koyo-cho, Shimonoseki, 750-8520, Japan
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Hedde PN, Bouzin M, Abram TJ, Chen X, Toosky MN, Vu T, Li Y, Zhao W, Gratton E. Rapid isolation of rare targets from large fluid volumes. Sci Rep 2020; 10:12458. [PMID: 32719382 PMCID: PMC7385493 DOI: 10.1038/s41598-020-69315-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/26/2020] [Indexed: 11/24/2022] Open
Abstract
Rapidly isolating rare targets from larger, clinically relevant fluid volumes remains an unresolved problem in biomedicine and diagnosis. Here, we describe how 3D particle sorting can enrich targets at ultralow concentrations over 100-fold within minutes not possible with conventional approaches. Current clinical devices based on biochemical extraction and microfluidic solutions typically require high concentrations and/or can only process sub-milliliter volumes in time. In a proof-of-concept application, we isolated bacteria from whole blood as demanded for rapid sepsis diagnosis where minimal numbers of bacteria need to be found in a 1–10 mL blood sample. After sample encapsulation in droplets and target enrichment with the 3D particle sorter within a few minutes, downstream analyses were able to identify bacteria and test for antibiotic susceptibility, information which is critical for successful treatment of bloodstream infections.
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Affiliation(s)
- Per Niklas Hedde
- Department of Biomedical Engineering, University of California, Irvine, CA, USA. .,Department of Biochemistry, University of Hawaii at Manoa, Manoa, HI, USA.
| | - Margaux Bouzin
- Department of Biomedical Engineering, University of California, Irvine, CA, USA.,Physics Department, Università degli Studi di Milano-Bicocca, Milan, Italy
| | | | - Xiaoming Chen
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
| | | | - Tam Vu
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
| | - Yiyan Li
- Department of Physics and Engineering, Fort Lewis College, Durango, CO, USA
| | - Weian Zhao
- Department of Biomedical Engineering, University of California, Irvine, CA, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA.,Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA.,Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA.,Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, USA.,Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California, Irvine, CA, USA
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Lara MO, Lucas TC, Kalapothakis E, Thomasini RL, Machado CJ. Molecular tracking of pathogens in central venous catheter. J Vasc Access 2020; 22:209-217. [PMID: 32588732 DOI: 10.1177/1129729820934354] [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] Open
Abstract
BACKGROUND Central venous catheter-related bloodstream infection is an important adverse event in health care. Molecular methods are not yet substitutive of microbiological in the detection of the pathogens responsible for the infection, but they can help in the epidemiological characterization. AIM To detect bacteria by polymerase chain reaction, from material extracted from the tip of central catheters of patients suspected of infection at the intensive care unit. METHODS Catheters (n = 34) of patients suspected of central venous catheter-related infection were analyzed by polymerase chain reaction. The findings were compared with culture of catheter tip and blood cultures performed by the hospital. FINDINGS The prevalence of bacteria was Staphylococcus aureus (50%), Enterococcus faecalis (41.2%), Klebsiella pneumoniae (32.4), Pseudomonas aeruginosa (20.6%), Acinetobacter baumannii (38.2%), Escherichia coli (2.9%), and Enterobacter cloacae (0%). No blood culture showed bacterial growth, the culture of catheter tip revealed bacteria in 21 (61.8%) and the polymerase chain reaction had positivity in 31 (91.2%) of the catheters. The mean central venous catheter time was 11 days, and the jugular vein was the site of insertion. CONCLUSION The molecular method identified more bacteria than microbiological methods and revealed colonization of the catheters. The most commonly found bacteria are in the environment and in the microbiota of the skin, which suggests contamination by the hands of health professionals and points out the need for more efforts in preventive strategies.
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Affiliation(s)
- Maristela Oliveira Lara
- Nursing Department, Federal University of Jequitinhonha and Mucuri Valleys, Diamantina, MG, Brazil
| | - Thabata Coaglio Lucas
- Nursing Department, Federal University of Jequitinhonha and Mucuri Valleys, Diamantina, MG, Brazil
| | - Evanguedes Kalapothakis
- Laboratory of Biotechnology and Molecular Markers, General Biology Department, Institute of Basic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ronaldo Luis Thomasini
- Faculty of Medicine, Federal University of Jequitinhonha and Mucuri Valleys, Diamantina, MG, Brazil
| | - Carla Jorge Machado
- Department of Social and Preventive Medicine, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
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Multicenter Evaluation of the BioFire FilmArray Pneumonia/Pneumonia Plus Panel for Detection and Quantification of Agents of Lower Respiratory Tract Infection. J Clin Microbiol 2020; 58:JCM.00128-20. [PMID: 32350043 PMCID: PMC7315029 DOI: 10.1128/jcm.00128-20] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/01/2020] [Indexed: 01/05/2023] Open
Abstract
The ability to provide timely identification of the causative agents of lower respiratory tract infections can promote better patient outcomes and support antimicrobial stewardship efforts. Current diagnostic testing options include culture, molecular testing, and antigen detection. These methods may require collection of various specimens, involve extensive sample treatment, and can suffer from low sensitivity and long turnaround times. This study assessed the performance of the BioFire FilmArray Pneumonia Panel (PN panel) and Pneumonia Plus Panel (PNplus panel), an FDA-cleared sample-to-answer assay that enables the detection of viruses, atypical bacteria, bacteria, and antimicrobial resistance marker genes from lower respiratory tract specimens (sputum and bronchoalveolar lavage [BAL] fluid). Semiquantitative results are also provided for the bacterial targets. This paper describes selected analytical and clinical studies that were conducted to evaluate performance of the panel for regulatory clearance. Prospectively collected respiratory specimens (846 BAL and 836 sputum specimens) evaluated with the PN panel were also tested by quantitative reference culture and molecular methods for comparison. The PN panel showed a sensitivity of 100% for 15/22 etiologic targets using BAL specimens and for 10/24 using sputum specimens. All other targets had sensitivities of ≥75% or were unable to be calculated due to low prevalence in the study population. Specificity for all targets was ≥87.2%, with many false-positive results compared to culture that were confirmed by alternative molecular methods. Appropriate adoption of this test could provide actionable diagnostic information that is anticipated to impact patient care and antimicrobial stewardship decisions.
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Berger J, Valera E, Jankelow A, Garcia C, Akhand M, Heredia J, Ghonge T, Liu C, Font-Bartumeus V, Oshana G, Tiao J, Bashir R. Simultaneous electrical detection of IL-6 and PCT using a microfluidic biochip platform. Biomed Microdevices 2020; 22:36. [PMID: 32419087 DOI: 10.1007/s10544-020-00492-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Sepsis, a life-threatening organ dysfunction caused by a dysregulated host response, leads the U.S in both mortality rate and cost of treatment. Sepsis treatment protocols currently rely on broad and non-specific parameters like heart and respiration rate, and temperature; however, studies show that biomarkers Interlukin-6 (IL-6) and Procalcitonin (PCT) correlate to sepsis progression and response to treatment. Prior work also suggests that using multi-parameter predictive analytics with biomarkers and clinical information can inform treatment to improve outcome. A point-of-care (POC) platform that provides information for multiple biomarkers can aid in the diagnosis and prognosis of potentially septic patients. Using impedance cytometry, microbead immunoassays, and biotin-streptavidin binding, we report a microfluidic POC system that correlates microbead capture to IL-6 and PCT concentrations. A multiplexed microbead immunoassay is developed and validated for simultaneous detection of both IL-6 and PCT from human plasma samples. Using the POC platform, we quantified plasma samples containing healthy, medium (~103pg/ml) and high (~105pg/ml) IL-6 and PCT concentrations with various levels of significance (P < 0.05-P < 0.00001) and validated the concept of this device as a POC platform for sepsis biomarkers.
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Affiliation(s)
- Jacob Berger
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1102 Everitt Lab, MC 278, 1406 W. Green St, Urbana, IL, 61801, USA.,Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, 208 N. Wright St., Urbana, IL, 61801, USA.,Biomedical Research Center, Carle Foundation Hospital, 509 W University Ave., Urbana, IL, 61801, USA
| | - Enrique Valera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1102 Everitt Lab, MC 278, 1406 W. Green St, Urbana, IL, 61801, USA.,Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, 208 N. Wright St., Urbana, IL, 61801, USA.,Biomedical Research Center, Carle Foundation Hospital, 509 W University Ave., Urbana, IL, 61801, USA
| | - Aaron Jankelow
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1102 Everitt Lab, MC 278, 1406 W. Green St, Urbana, IL, 61801, USA.,Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, 208 N. Wright St., Urbana, IL, 61801, USA.,Biomedical Research Center, Carle Foundation Hospital, 509 W University Ave., Urbana, IL, 61801, USA
| | - Carlos Garcia
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1102 Everitt Lab, MC 278, 1406 W. Green St, Urbana, IL, 61801, USA.,Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, 208 N. Wright St., Urbana, IL, 61801, USA.,Biomedical Research Center, Carle Foundation Hospital, 509 W University Ave., Urbana, IL, 61801, USA
| | - Manik Akhand
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1102 Everitt Lab, MC 278, 1406 W. Green St, Urbana, IL, 61801, USA.,Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, 208 N. Wright St., Urbana, IL, 61801, USA
| | - John Heredia
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1102 Everitt Lab, MC 278, 1406 W. Green St, Urbana, IL, 61801, USA.,Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, 208 N. Wright St., Urbana, IL, 61801, USA
| | - Tanmay Ghonge
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1102 Everitt Lab, MC 278, 1406 W. Green St, Urbana, IL, 61801, USA.,Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, 208 N. Wright St., Urbana, IL, 61801, USA.,Biomedical Research Center, Carle Foundation Hospital, 509 W University Ave., Urbana, IL, 61801, USA.,Illumina, San Diego, CA, USA
| | - Cynthia Liu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1102 Everitt Lab, MC 278, 1406 W. Green St, Urbana, IL, 61801, USA.,Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, 208 N. Wright St., Urbana, IL, 61801, USA
| | - Victor Font-Bartumeus
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1102 Everitt Lab, MC 278, 1406 W. Green St, Urbana, IL, 61801, USA.,Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, 208 N. Wright St., Urbana, IL, 61801, USA
| | - Gina Oshana
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1102 Everitt Lab, MC 278, 1406 W. Green St, Urbana, IL, 61801, USA.,Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, 208 N. Wright St., Urbana, IL, 61801, USA
| | - Justin Tiao
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1102 Everitt Lab, MC 278, 1406 W. Green St, Urbana, IL, 61801, USA.,Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, 208 N. Wright St., Urbana, IL, 61801, USA
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1102 Everitt Lab, MC 278, 1406 W. Green St, Urbana, IL, 61801, USA. .,Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, 208 N. Wright St., Urbana, IL, 61801, USA. .,Biomedical Research Center, Carle Foundation Hospital, 509 W University Ave., Urbana, IL, 61801, USA. .,Carle Illinois College of Medicine, 807 South Wright St., Urbana, IL, 61801, USA.
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41
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Burklund A, Petryk JD, Hoopes PJ, Zhang JXJ. Microfluidic enrichment of bacteria coupled to contact-free lysis on a magnetic polymer surface for downstream molecular detection. BIOMICROFLUIDICS 2020; 14:034115. [PMID: 32642021 PMCID: PMC7316515 DOI: 10.1063/5.0011908] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/28/2020] [Indexed: 05/02/2023]
Abstract
We report on a microsystem that couples high-throughput bacterial immunomagnetic capture to contact-free cell lysis using an alternating current magnetic field (AMF) to enable downstream molecular characterization of bacterial nucleic acids. Traditional methods for cell lysis rely on either dilutive chemical methods, expensive biological reagents, or imprecise physical methods. We present a microchip with a magnetic polymer substrate (Mag-Polymer microchip), which enables highly controlled, on-chip heating of biological targets following exposure to an AMF. First, we present a theoretical framework for the quantitation of power generation for single-domain magnetic nanoparticles embedded in a polymer matrix. Next, we demonstrate successful bacterial DNA recovery by coupling (1) high-throughput, sensitive microfluidic immunomagnetic capture of bacteria to (2) on-chip, contact-free bacterial lysis using an AMF. The bacterial capture efficiency exceeded 76% at 50 ml/h at cell loads as low as ∼10 CFU/ml, and intact DNA was successfully recovered at starting bacterial concentrations as low as ∼1000 CFU/ml. Using the presented methodology, cell lysis becomes non-dilutive, temperature is precisely controlled, and potential contamination risks are eliminated. This workflow and substrate modification could be easily integrated in a range of micro-scale diagnostic systems for infectious disease.
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Affiliation(s)
- Alison Burklund
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755, USA
| | - James D. Petryk
- Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire 03755, USA
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42
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Wouters Y, Dalloyaux D, Christenhusz A, Roelofs HMJ, Wertheim HF, Bleeker‐Rovers CP, te Morsche RH, Wanten GJA. Droplet digital polymerase chain reaction for rapid broad-spectrum detection of bloodstream infections. Microb Biotechnol 2020; 13:657-668. [PMID: 31605465 PMCID: PMC7111091 DOI: 10.1111/1751-7915.13491] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 08/21/2019] [Accepted: 09/17/2019] [Indexed: 11/30/2022] Open
Abstract
The droplet digital polymerase chain reaction (ddPCR) is a novel molecular technique that allows rapid quantification of rare target DNA sequences. Aim of this study was to explore the feasibility of the ddPCR technique to detect pathogen DNA in whole blood and to assess the diagnostic accuracy of ddPCR to detect bloodstream infections (BSIs), benchmarked against blood cultures. Broad-range primers and probes were designed to detect bacterial 16S rRNA (and Gram stain for differentiation) and fungal 28S rRNA. To determine the detection limit of ddPCR, 10-fold serial dilutions of E. coli and C. albicans were spiked in both PBS and whole blood. The diagnostic accuracy of ddPCR was tested in historically collected frozen blood samples from adult patients suspected of a BSI and compared with blood cultures. Analyses were independently performed by two research analysts. Outcomes included sensitivity and specificity of ddPCR. Within 4 h, blood samples were drawn, and DNA was isolated and analysed. The ddPCR detection limit was approximately 1-2 bacteria or fungi per ddPCR reaction. In total, 45 blood samples were collected from patients, of which 15 (33%) presented with positive blood cultures. The overall sensitivity of ddPCR was 80% (95% CI 52-96) and specificity 87% (95% CI 69-96). In conclusion, the ddPCR technique has considerable potential and is able to detect very low amounts of pathogen DNA in whole blood within 4 h. Currently, ddPCR has a reasonable sensitivity and specificity, but requires further optimization to make it more useful for clinical practice.
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Affiliation(s)
- Yannick Wouters
- Intestinal Failure UnitDepartment of Gastroenterology and HepatologyRadboud University Medical CentreNijmegenThe Netherlands
| | - Daisy Dalloyaux
- Intestinal Failure UnitDepartment of Gastroenterology and HepatologyRadboud University Medical CentreNijmegenThe Netherlands
| | - Anke Christenhusz
- Intestinal Failure UnitDepartment of Gastroenterology and HepatologyRadboud University Medical CentreNijmegenThe Netherlands
| | - Hennie M. J. Roelofs
- Intestinal Failure UnitDepartment of Gastroenterology and HepatologyRadboud University Medical CentreNijmegenThe Netherlands
| | - Heiman F. Wertheim
- Department of Medical MicrobiologyRadboud University Medical CentreNijmegenThe Netherlands
| | - Chantal P. Bleeker‐Rovers
- Department of Internal Medicine and Infectious DiseasesRadboud University Medical CentreNijmegenThe Netherlands
| | - René H. te Morsche
- Intestinal Failure UnitDepartment of Gastroenterology and HepatologyRadboud University Medical CentreNijmegenThe Netherlands
| | - Geert J. A. Wanten
- Intestinal Failure UnitDepartment of Gastroenterology and HepatologyRadboud University Medical CentreNijmegenThe Netherlands
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43
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Mishra D, Satpathy G, Wig N, Fazal F, Ahmed NH, Panda SK. Evaluation of 16S rRNA broad range PCR assay for microbial detection in serum specimens in sepsis patients. J Infect Public Health 2020; 13:998-1002. [PMID: 32061569 DOI: 10.1016/j.jiph.2020.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 12/23/2019] [Accepted: 01/15/2020] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Early and accurate laboratory diagnosis and appropriate management of infection improves the survival rate in sepsis. In this study we evaluated broad range 16S rRNA and 16 S-23 S intergenic spacer region (ISR) PCR assays followed by nucleotide sequencing directly from patients' serum and automated blood culture for laboratory diagnosis in admitted sepsis patients. METHODS A broad range 16S rRNA PCR and 16 S-23 S ISR PCR assay followed by nucleotide sequencing was used directly from patients' serum in hospital admitted patients in 62 sepsis and 16 suspected blood stream infection (sBSI) patients. Automated blood culture was also used in the same patients. Nucleotide sequences were analyzed against NCBI Genbank database and organisms were identified using CLSI MM18A guidelines. RESULTS Bacterial culture were positive in 10/62 (16.12%) sepsis and 3/16 (18.75%) suspected BSI patients along with 3 detected fungi (2 in sepsis and 1 in suspected BSI group). PCR assay was positive in 36/62 (58.06%) sepsis and 6/16 (37.5%) suspected BSI patients respectively. All but 2 bacteria (both from culture negative patients) detected by PCR assay could be identified from nucleotide sequencing. Survival in sepsis patients was 77%. PCR assay could detect bacteria in 9/14 (64.28%) of sepsis patients with death. CONCLUSION Broad range PCR assay was far superior for early diagnosis of infection. The bacteria which could not be detected by culture and were not commonly reported from this centre, were detected by the broad range PCR assays. Detection of these rare bacteria/fungi had significant clinical correlation with patient's underlying clinical conditions, immune status and prognosis. The tests could provide definitive diagnosis of infection in >58% of sepsis patients, which helped in patient management and better survival.
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Affiliation(s)
- Deepanshi Mishra
- Ocular Microbiology, Dr. R.P.Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - Gita Satpathy
- Ocular Microbiology, Dr. R.P.Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India; Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India.
| | - Naveet Wig
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Farhan Fazal
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Nishat Hussain Ahmed
- Ocular Microbiology, Dr. R.P.Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - Subrat Kumar Panda
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
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44
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Arena F, Argentieri M, Bernaschi P, Fortina G, Kroumova V, Pecile P, Rassu M, Spanu T, Rossolini GM, Fontana C. Compliance of clinical microbiology laboratories with recommendations for the diagnosis of bloodstream infections: Data from a nationwide survey in Italy. Microbiologyopen 2020; 9:e1002. [PMID: 32012494 PMCID: PMC7142361 DOI: 10.1002/mbo3.1002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 01/09/2020] [Accepted: 01/09/2020] [Indexed: 12/17/2022] Open
Abstract
In 2014, the Italian Working Group for Infections in Critically Ill Patient of the Italian Association of Clinical Microbiologists updated the recommendations for the diagnostic workflow for bloodstream infections (BSI). Two years after publication, a nationwide survey was conducted to assess the compliance with the updated recommendations by clinical microbiology laboratories. A total of 168 microbiologists from 168 laboratories, serving 204 acute care hospitals and postacute care facilities, were interviewed during the period January–October 2016 using a questionnaire consisting of nineteen questions which assessed the level of adherence to various recommendations. The most critical issues were as follows: (a) The number of sets of blood cultures (BC) per 1,000 hospitalization days was acceptable in only 11% of laboratories; (b) the minority of laboratories (42%) was able to monitor whether BCs were over or under‐inoculated; (c) among the laboratories monitoring BC contamination (80%), the rate of contaminated samples was acceptable in only 12% of cases;(d) the Gram‐staining results were reported within 1 hr since BC positivity in less than 50% of laboratories. By contrast, most laboratories received vials within 2–4 hr from withdrawal (65%) and incubated vials as soon as they were received in the laboratory (95%). The study revealed that compliance with the recommendations is still partial. Further surveys will be needed to monitor the situation in the future.
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Affiliation(s)
- Fabio Arena
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy.,IRCCS Don Carlo Gnocchi Foundation, Florence, Italy
| | - Marta Argentieri
- Microbiology Unit, Children's Hospital Bambino Gesù, Rome, Italy
| | - Paola Bernaschi
- Microbiology Unit, Children's Hospital Bambino Gesù, Rome, Italy
| | - Giacomo Fortina
- Italian Work Group for Infections in Critically Ill Patient (GliPac-AMCLI), Milan, Italy
| | - Vesselina Kroumova
- Infection Control Unit, University Hospital "Maggiore della Carità", Novara, Italy
| | - Patrizia Pecile
- Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Mario Rassu
- Microbiology and Virology Lab, AULS 8 Berica, S. Bortolo Hospital, Vicenza, Italy
| | - Teresa Spanu
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Gian Maria Rossolini
- Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy.,Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Carla Fontana
- Department Experimental Medicine, University of Rome Tor Vergata, Rome, Italy.,Microbiology and Virology Lab, Tor Vergata University Hospital, Rome, Italy
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45
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Cherkaoui A, Renzi G, Azam N, Schorderet D, Vuilleumier N, Schrenzel J. Rapid identification by MALDI-TOF/MS and antimicrobial disk diffusion susceptibility testing for positive blood cultures after a short incubation on the WASPLab. Eur J Clin Microbiol Infect Dis 2020; 39:1063-1070. [PMID: 31965365 DOI: 10.1007/s10096-020-03817-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/12/2020] [Indexed: 12/19/2022]
Abstract
The objectives of this study were to define the shortest incubation times on the WASPLab for reliable MALDI-TOF/MS-based species identification and for the preparation of a 0.5 McFarland suspension for antimicrobial disk diffusion susceptibility testing using short subcultures growing on solid culture media inoculated by positive blood cultures spiked with a wide range of pathogens associated with bloodstream infections. The 520 clinical strains (20 × 26 different species) included in this study were obtained from a collection of non-consecutive and non-duplicate pathogens identified at Geneva University Hospitals. After 4 h of incubation on the WASPLab, microorganisms' growth allowed accurate identification of 73% (380/520) (95% CI, 69.1-76.7%) of the strains included in this study. The identification rate increased to 85% (440/520) (95% CI, 81.3-87.5%) after 6-h incubation. When excluding Corynebacterium and Candida spp., the microbial growth was sufficient to permit accurate identification of all tested species (100%, 460/460) (95% CI, 99.2-100%) after 8-h incubation. With the exception of Burkholderia cepacia and Haemophilus influenzae, AST by disk diffusion could be performed for Enterobacterales and non-fermenting Gram-negative bacilli after only 4 h of growth in the WASPLab. The preparation of a 0.5 McFarland suspension for Gram-positive bacteria required incubation times ranging between 3 and 8 h according to the bacterial species. Only Corynebacterium spp. required incubation times as long as 16 h. The WASPLab enables rapid pathogen identification as well as swift comprehensive AST from positive blood cultures that can be implemented without additional costs nor hands-on time by defining optimal time points for image acquisition.
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Affiliation(s)
- Abdessalam Cherkaoui
- Department of Diagnostics, Bacteriology Laboratory, Division of Laboratory Medicine, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland.
| | - Gesuele Renzi
- Department of Diagnostics, Bacteriology Laboratory, Division of Laboratory Medicine, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland
| | - Nouria Azam
- Department of Diagnostics, Bacteriology Laboratory, Division of Laboratory Medicine, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland
| | - Didier Schorderet
- Department of Diagnostics, Bacteriology Laboratory, Division of Laboratory Medicine, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland
| | - Nicolas Vuilleumier
- Department of Diagnostics, Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland.,Department of Medical Specialities, Division of Laboratory Medicine, Faculty of Medicine, Geneva, Switzerland
| | - Jacques Schrenzel
- Department of Diagnostics, Bacteriology Laboratory, Division of Laboratory Medicine, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland.,Department of Medicine, Genomic Research Laboratory, Division of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
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46
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Samuel L. Direct Detection of Pathogens in Bloodstream During Sepsis: Are We There Yet? J Appl Lab Med 2019; 3:631-642. [DOI: 10.1373/jalm.2018.028274] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/07/2018] [Indexed: 12/22/2022]
Abstract
Abstract
Background
Advances in medicine have improved our understanding of sepsis, but it remains a major cause of morbidity and mortality. The detection of pathogens that cause sepsis remains a challenge for clinical microbiology laboratories.
Content
Routine blood cultures are time-consuming and are negative in a large proportion of cases, leading to excessive use of broad-spectrum antimicrobials. Molecular testing direct from patient blood without the need for incubation has the potential to fill the gaps in our diagnostic armament and complement blood cultures to provide results in a timely manner. Currently available platforms show promise but have yet to definitively address gaps in sensitivity and specificity.
Summary
Significant strides have been made in the detection of pathogens directly from blood. A number of hurdles, however, remain before this technology can be adapted for routine use.
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Affiliation(s)
- Linoj Samuel
- Department of Pathology and Laboratory Medicine, Clinical Microbiology Division, Henry Ford Health System, Detroit, MI
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47
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Trung NT, Thau NS, Bang MH, Song LH. PCR-based Sepsis@Quick test is superior in comparison with blood culture for identification of sepsis-causative pathogens. Sci Rep 2019; 9:13663. [PMID: 31541157 PMCID: PMC6754458 DOI: 10.1038/s41598-019-50150-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 09/05/2019] [Indexed: 12/17/2022] Open
Abstract
Sepsis is an acute, often fatal syndrome that requires early diagnosis and proper treatment. Blood culture (BC) is the gold standard for the identification of pathogens, however it has marked limitations, including that it is time-consuming (delaying treatment) and can only detect microbes that readily grow under culture conditions. Alternatively, non-culture-based methodologies like polymerase chain reaction (PCR) are faster but also have limitations; e.g., the reaction is often inhibited by the abundance of human DNA and thus can only detect limited known target pathogens. In our previous publication, we have demonstrated a proof-of-concept of a simple pre-analytical tool to remove human DNA from patients’ blood specimens, hence allowing downstream PCRs to detect rare bacterial genetic materials. In the current study, we reported a better performance of a novel prototype diagnosis kit named Sepsis@Quick that combines human DNA removal step with real-time PCRs compared to blood-culture for identifying sepsis causative bacteria. Our data showed that Sepsis@Quick is superior to blood culture in which the novel diagnostic kit could identify more pathogens and even polymicrobial infection, faster and less influenced by the empirical administration of broad spectrum antibiotic therapy (single administration or combination of cephalosporin III and fluoroquinolon). Additionally, for the first time, we demonstrated that positive results achieved by Sepsis@Quick are significantly associated with a reduction of sepsis-related mortality.
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Affiliation(s)
- Ngo Tat Trung
- Vietnamese-German Center for Medical Research (VG-CARE), 108 Military Central Hospital, Hà Nội, Vietnam. .,Centre for Genetic Consultation and Cancer Screening, 108 Military Central Hospital, Hà Nội, Vietnam. .,Department of Molecular Biology, 108 Military Central Hospital, Hà Nội, Vietnam.
| | - Nguyen Sy Thau
- Vietnamese-German Center for Medical Research (VG-CARE), 108 Military Central Hospital, Hà Nội, Vietnam.,Faculty of Tropical and Infectious Diseases, 108 Military Central Hospital, Hà Nội, Vietnam
| | - Mai Hong Bang
- Vietnamese-German Center for Medical Research (VG-CARE), 108 Military Central Hospital, Hà Nội, Vietnam
| | - Le Huu Song
- Vietnamese-German Center for Medical Research (VG-CARE), 108 Military Central Hospital, Hà Nội, Vietnam. .,Faculty of Tropical and Infectious Diseases, 108 Military Central Hospital, Hà Nội, Vietnam.
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48
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Djuric O, Markovic-Denic L, Jovanovic B, Bumbasirevic V. High incidence of multiresistant bacterial isolates from bloodstream infections in trauma emergency department and intensive care unit in Serbia. Acta Microbiol Immunol Hung 2019; 66:307-325. [PMID: 30786727 DOI: 10.1556/030.66.2019.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We investigated the incidence of bloodstream infections (BSIs) in trauma emergency department (ED) and intensive care unit (ICU), to assess ED- and ICU-related predictors of BSI and to describe the most common bacteria causing BSI and their antimicrobial resistance markers. A prospective study was conducted in two trauma ICUs of the ED of Clinical Center of Serbia. Overall, 62 BSIs were diagnosed in 406 patients, of which 13 were catheter-related BSI (3.0/1,000 CVC-days) and 30 BSIs of unknown origin, while 15% were attributed to ED CVC exposure. Lactate ≥2 mmol/L and SOFA score were independent ED-related predictors of BSI, while CVC in place for >7 days and mechanical ventilation >7 days were significant ICU-related predictors. The most common bacteria recovered were Acinetobacter spp., Klebsiella spp., and Pseudomonas aeruginosa. All Staphylococcus aureus and coagulase-negative staphylococci isolates were methicillin-resistant, whereas 66% of Enterococcus spp. were vancomycin-resistant. All isolates of Enterobacteriaceae were resistant to third-generation cephalosporins, whereas 87.5% of P. aeruginosa and 95.8% of Acinetobacter spp. isolates were resistant to carbapenems. ED BSI contributes substantially to overall ICU incidence of BSI. Lactate level and SOFA score can help to identify patients with higher risk of developing BSI. Better overall and CVC-specific control measures in patients with trauma are needed.
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Affiliation(s)
- Olivera Djuric
- 1 Faculty of Medicine, University of Belgrade, Belgrade, Serbia
- 2 Institute of Epidemiology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Ljiljana Markovic-Denic
- 1 Faculty of Medicine, University of Belgrade, Belgrade, Serbia
- 2 Institute of Epidemiology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Bojan Jovanovic
- 1 Faculty of Medicine, University of Belgrade, Belgrade, Serbia
- 3 Center for Anaesthesiology, Emergency Center, Clinical Center of Serbia, Belgrade, Serbia
| | - Vesna Bumbasirevic
- 1 Faculty of Medicine, University of Belgrade, Belgrade, Serbia
- 3 Center for Anaesthesiology, Emergency Center, Clinical Center of Serbia, Belgrade, Serbia
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49
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Yoon SH, Kim EH, Kim HY, Ahn JG. Presepsin as a diagnostic marker of sepsis in children and adolescents: a systemic review and meta-analysis. BMC Infect Dis 2019; 19:760. [PMID: 31470804 PMCID: PMC6717384 DOI: 10.1186/s12879-019-4397-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/23/2019] [Indexed: 12/15/2022] Open
Abstract
Background Early diagnosis of sepsis in pediatric patients is vital but remains a major challenge. Previous studies showed that presepsin is potentially a reliable diagnostic biomarker for sepsis in adult and neonates. However, there is no pooled analysis of its efficacy as a diagnostic biomarker for sepsis in children. The aims of the present meta-analysis were to assess the overall diagnostic accuracy of presepsin in pediatric sepsis and compare it to those for C-reactive protein (CRP) and procalcitonin (PCT). Methods A systematic literature search was performed in Medline/Pubmed, Embase, the Cochrane Library, and ISI Web of Science to identify relevant studies reporting the diagnostic accuracy of presepsin in patients with pediatric sepsis. Sensitivities and specificities were pooled by bivariate meta-analysis. Heterogeneity was evaluated by χ2 test. Results We identified 129 studies in total. Most were disqualified on the basis of their titles/abstracts and duplication. Four studies were included in the final analysis. They comprised 308 patients aged between 1 mo and 18 y. The pooled diagnostic sensitivity and specificity of presepsin were 0.94 (95% confidence interval [CI]: 0.74–0.99) and 0.71 (95% CI: 0.35–0.92), respectively. The pooled diagnostic odds ratio, positive likelihood ratio (LR), and negative LR of presepsin were 32.87 (95% CI: 2.12–510.09), 3.24 (95% CI, 1.14–12.38), and 0.08 (95% CI, 0.01–0.74), respectively. Heterogeneity was found in both sensitivity (χ2 = 11.17; P = 0.011) and specificity (χ2 = 65.78; P < 0.001). No threshold effect was identified among the studies (r = − 0.938). The pooled sensitivity of presepsin (0.94) was higher than that of CRP (0.51) and PCT (0.76), whereas the overall specificity of presepsin (0.71) was lower than that of CRP (0.81) and PCT (0.76). The AUC of presepsin (0.925) was higher than that of CRP (0.715) and PCT (0.820). Conclusion Currently available evidence indicates that presepsin has higher sensitivity and diagnostic accuracy, but lower specificity, than PCT or CRP in detecting sepsis in children. However, these results must be carefully interpreted as the number of studies included was small and the studies were statistically heterogeneous. Electronic supplementary material The online version of this article (10.1186/s12879-019-4397-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Seo Hee Yoon
- Department of Pediatrics, Severance Children's Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Eun Hwa Kim
- Biostatistics Collaboration Unit, Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Korea
| | - Ha Yan Kim
- Biostatistics Collaboration Unit, Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Korea
| | - Jong Gyun Ahn
- Department of Pediatrics, Severance Children's Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
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50
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Sweeney TE, Liesenfeld O, May L. Diagnosis of bacterial sepsis: why are tests for bacteremia not sufficient? Expert Rev Mol Diagn 2019; 19:959-962. [PMID: 31446810 DOI: 10.1080/14737159.2019.1660644] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | | | - Larissa May
- Department of Emergency Medicine, Davis School of Medicine, University of California Davis Health , Sacramento , CA , USA
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