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Si W, Chen W, Chen B, Zhou Y, Zhang H. Detection value of third-generation sequencing to identify the pathogenic organisms in prosthetic joint infection. Diagn Microbiol Infect Dis 2024; 109:116319. [PMID: 38669776 DOI: 10.1016/j.diagmicrobio.2024.116319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 04/03/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024]
Abstract
To compare the detection value of third-generation sequencing (TGS) with pathogenic microbial culture in prosthetic joint infection (PJI). Arthrocentesis was performed on 29 patients who underwent hip and knee revision surgeries. In the PJI group, TGS detected 85.71 % of positive cases, while pathogenic microbial culture detected only 42.85 %. TGS identified 17 different pathogenic microorganisms, including Staphylococcus epidermidis, Staphylococcus aureus, Streptococcus lactis, and Mycobacterium tuberculosis complex. In the loosening group, TGS was positive in one patient, while microbial culture was negative in all cases. TGS showed higher sensitivity (85.71 % vs. 42.85 %), comparable specificity (93.33 % vs. 100 %), and similar positive predictive value (92.31 % vs. 100 %) compared to culture.However, TGS had a higher negative predictive value (87.5 % vs. 65.22 %).Additionally, TGS provided faster results (mean time 23.8±3.6 h) compared to microbial culture (mean time 108.0±9.4 h).These findings suggest that TGS holds promise for detecting pathogenic microorganisms in PJI and has potential for clinical application.
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Affiliation(s)
- Wenteng Si
- Zhengzhou Orthopaedic Hospital of Joint Surgery, Zhengzhou 450052, China
| | - Wenzhong Chen
- Zhengzhou Orthopaedic Hospital of Joint Surgery, Zhengzhou 450052, China
| | - Bin Chen
- Zhengzhou Orthopaedic Hospital of Joint Surgery, Zhengzhou 450052, China
| | - Yu Zhou
- Zhengzhou Orthopaedic Hospital of Joint Surgery, Zhengzhou 450052, China
| | - Huaguo Zhang
- Department of Nursing, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China.
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2
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Neser E, Jung P, Halfmann A, Schröder M, Thurner L, Becker SL, Schneitler S. A multi-pronged approach to improve blood culture diagnostics in different clinical departments: a single-centre experience. Infection 2024; 52:183-195. [PMID: 37589812 PMCID: PMC10810936 DOI: 10.1007/s15010-023-02083-y] [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: 06/07/2023] [Accepted: 08/01/2023] [Indexed: 08/18/2023]
Abstract
PURPOSE Blood culture (BC) diagnostics are influenced by many factors. We performed a targeted interdisciplinary analysis to analyse effects of various measures on BC diagnostics performance. METHODS A diagnostic stewardship initiative was conducted at two intervention and two control wards in a German tertiary level hospital. The initiative comprised staff training on the correct indications and sampling for BC, implementation of information cards, labels to identify the collection site, regular BC bottle feedback including the number of bottles, filling volumes and identified pathogens; and the use of a specific sampling device (BD Vacutainer®). Before and after the interventions, two three-month measurement periods were performed, as well as a one-month follow-up period to assess the sustainability of the conducted measures. RESULTS In total, 9362 BC bottles from 787 patients were included in the analysis. The number of BCs obtained from peripheral venous puncture could be increased at both intervention wards (44.0 vs. 22.2%, 58.3 vs. 34.4%), while arterial sampling could be reduced (30.6 vs. 4.9%). A total of 134 staff members were fully trained. The intervention led to a considerable increase in BC knowledge (from 62.4 to 79.8% correct answers) with differences between the individual professional groups. Relevant reduced contamination rates could be detected at both intervention wards. CONCLUSIONS As knowledge on the correct BC sampling and strategies to reduce contamination varies considerably between clinical departments and healthcare professionals, a targeted training should be adapted to the specific needs of the individual professional groups. An additional filling device is not necessary.
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Affiliation(s)
- Elisabeth Neser
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Strasse, Building 43, 66421, Homburg/Saar, Germany
| | - Philipp Jung
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Strasse, Building 43, 66421, Homburg/Saar, Germany
| | - Alexander Halfmann
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Strasse, Building 43, 66421, Homburg/Saar, Germany
| | - Matthias Schröder
- Department of Anaesthesiology, Intensive Care and Analgesic Therapy, Saarland University, Homburg/Saar, Germany
| | - Lorenz Thurner
- Department of Internal Medicine Oncology, Haematology, Clinical Immunology and Rheumatology, Saarland University, Homburg/Saar, Germany
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Strasse, Building 43, 66421, Homburg/Saar, Germany
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Sophie Schneitler
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Strasse, Building 43, 66421, Homburg/Saar, Germany.
- Clinic for Pneumology and Allergology, Bethanien Hospital, Centre of Sleep Medicine and Respiratory Care, Institute of Pneumology at the University of Cologne, Solingen, Germany.
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3
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Affiliation(s)
- Alexander Lawandi
- Division of Infectious Diseases, Department of Medicine, McGill University, Montreal, QC, Canada
- Department of Critical Care Medicine, McGill University, Montreal, QC, Canada
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4
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Peukert C, Popat Gholap S, Green O, Pinkert L, van den Heuvel J, van Ham M, Shabat D, Brönstrup M. Enzyme-Activated, Chemiluminescent Siderophore-Dioxetane Probes Enable the Selective and Highly Sensitive Detection of Bacterial Pathogens. Angew Chem Int Ed Engl 2022; 61:e202201423. [PMID: 35358362 PMCID: PMC9322335 DOI: 10.1002/anie.202201423] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Indexed: 12/18/2022]
Abstract
The sensitive detection of bacterial infections is a prerequisite for their successful treatment. The use of a chemiluminescent readout was so far hampered by an insufficient probe enrichment at the pathogens. We coupled siderophore moieties, that harness the unique iron transport system of bacteria, with enzyme‐activatable dioxetanes and obtained seven trifunctional probes with high signal‐to‐background ratios (S/B=426‐859). Conjugates with efficient iron transport capability into bacteria were identified through a growth recovery assay. All ESKAPE pathogens were labelled brightly by desferrioxamine conjugates, while catechols were weaker due to self‐quenching. Bacteria could also be detected inside lung epithelial cells. The best probe 8 detected 9.1×103 CFU mL−1 of S. aureus and 5.0×104 CFU mL−1 of P. aeruginosa, while the analogous fluorescent probe 10 was 205–305fold less sensitive. This qualifies siderophore dioxetane probes for the selective and sensitive detection of bacteria.
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Affiliation(s)
- Carsten Peukert
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Sachin Popat Gholap
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ori Green
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Lukas Pinkert
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Joop van den Heuvel
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Marco van Ham
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Doron Shabat
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
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5
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Peukert C, Gholap SP, Green O, Pinkert L, van den Heuvel J, van Ham M, Shabat D, Broenstrup M. Enzyme‐activated, Chemiluminescent Siderophore‐Dioxetane Probes Enable the Selective and Highly Sensitive Detection of Bacterial ESKAPE Pathogens. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Carsten Peukert
- Helmholtz-Zentrum für Infektionsforschung GmbH: Helmholtz-Zentrum fur Infektionsforschung GmbH Chemical Biology GERMANY
| | - Sachin Popat Gholap
- Tel Aviv University Raymond and Beverly Sackler Faculty of Exact Sciences School of Chemistry ISRAEL
| | - Ori Green
- Tel Aviv University Raymond and Beverly Sackler Faculty of Exact Sciences School of Chemistry ISRAEL
| | - Lukas Pinkert
- Helmholtz-Zentrum für Infektionsforschung GmbH: Helmholtz-Zentrum fur Infektionsforschung GmbH Chemical Biology GERMANY
| | - Joop van den Heuvel
- Helmholtz-Zentrum für Infektionsforschung GmbH: Helmholtz-Zentrum fur Infektionsforschung GmbH SFPR GERMANY
| | - Marco van Ham
- Helmholtz-Zentrum für Infektionsforschung GmbH: Helmholtz-Zentrum fur Infektionsforschung GmbH SFPR GERMANY
| | - Doron Shabat
- Tel Aviv University Raymond and Beverly Sackler Faculty of Exact Sciences School of Chemistry ISRAEL
| | - Mark Broenstrup
- Helmholtz-Zentrum fur Infektionsforschung GmbH Chemical Biology Inhoffenstraße 7 38124 Braunschweig GERMANY
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Garnica O, Gómez D, Ramos V, Hidalgo JI, Ruiz-Giardín JM. Diagnosing hospital bacteraemia in the framework of predictive, preventive and personalised medicine using electronic health records and machine learning classifiers. EPMA J 2021; 12:365-381. [PMID: 34484472 PMCID: PMC8405861 DOI: 10.1007/s13167-021-00252-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/30/2021] [Indexed: 12/12/2022]
Abstract
Background The bacteraemia prediction is relevant because sepsis is one of the most important causes of morbidity and mortality. Bacteraemia prognosis primarily depends on a rapid diagnosis. The bacteraemia prediction would shorten up to 6 days the diagnosis, and, in conjunction with individual patient variables, should be considered to start the early administration of personalised antibiotic treatment and medical services, the election of specific diagnostic techniques and the determination of additional treatments, such as surgery, that would prevent subsequent complications. Machine learning techniques could help physicians make these informed decisions by predicting bacteraemia using the data already available in electronic hospital records. Objective This study presents the application of machine learning techniques to these records to predict the blood culture's outcome, which would reduce the lag in starting a personalised antibiotic treatment and the medical costs associated with erroneous treatments due to conservative assumptions about blood culture outcomes. Methods Six supervised classifiers were created using three machine learning techniques, Support Vector Machine, Random Forest and K-Nearest Neighbours, on the electronic health records of hospital patients. The best approach to handle missing data was chosen and, for each machine learning technique, two classification models were created: the first uses the features known at the time of blood extraction, whereas the second uses four extra features revealed during the blood culture. Results The six classifiers were trained and tested using a dataset of 4357 patients with 117 features per patient. The models obtain predictions that, for the best case, are up to a state-of-the-art accuracy of 85.9%, a sensitivity of 87.4% and an AUC of 0.93. Conclusions Our results provide cutting-edge metrics of interest in predictive medical models with values that exceed the medical practice threshold and previous results in the literature using classical modelling techniques in specific types of bacteraemia. Additionally, the consistency of results is reasserted because the three classifiers' importance ranking shows similar features that coincide with those that physicians use in their manual heuristics. Therefore, the efficacy of these machine learning techniques confirms their viability to assist in the aims of predictive and personalised medicine once the disease presents bacteraemia-compatible symptoms and to assist in improving the healthcare economy.
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Affiliation(s)
- Oscar Garnica
- Departamento de Arquitectura de Computadores, Universidad Complutense de Madrid, Madrid, Spain
| | - Diego Gómez
- Universidad Complutense de Madrid, Madrid, Spain
| | - Víctor Ramos
- Universidad Complutense de Madrid, Madrid, Spain
| | - J. Ignacio Hidalgo
- Departamento de Arquitectura de Computadores, Universidad Complutense de Madrid, Madrid, Spain
| | - José M. Ruiz-Giardín
- Departamento de Medicina Interna, Hospital Universitario de Fuenlabrada, Madrid, Spain
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7
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Giordano L, Liotti FM, Menchinelli G, De Angelis G, D'Inzeo T, Morandotti GA, Sanguinetti M, Spanu T, Posteraro B. Simulated Pediatric Blood Cultures to Assess the Inactivation of Clinically Relevant Antimicrobial Drug Concentrations in Resin-Containing Bottles. Front Cell Infect Microbiol 2021; 11:649769. [PMID: 33869081 PMCID: PMC8044943 DOI: 10.3389/fcimb.2021.649769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/01/2021] [Indexed: 01/20/2023] Open
Abstract
The bacteremia level as well as the administration of antibiotics before blood collection may significantly affect the recovery of bacterial pathogens from pediatric blood cultures in BacT/Alert Virtuo or Bactec FX BC systems, which remain the common techniques to diagnose bacteremia in pediatric patients. We simulated pediatric blood cultures with low or intermediate bacteremia level to evaluate BacT/Alert PF Plus and Bactec Peds Plus blood culture bottles for resin-based inactivation of 16 antibiotic-bacterium combinations. Overall, 105/192 (54.7%) of BacT/Alert PF Plus bottles and 69/192 (36.0%) of Bactec Peds Plus bottles allowed organisms to grow when exposed to antibiotics. In particular, both BacT/Alert PF Plus and Bactec Peds Plus bottles proved to be effective with piperacillin/tazobactam and Pseudomonas aeruginosa or with oxacillin and methicillin-susceptible Staphylococcus aureus (100% growth), whereas no effectiveness was apparent with ceftriaxone and Escherichia coli, Streptococcus agalactiae, or Streptococcus pneumoniae or with cefepime and E. coli (0% growth). In some relevant instances (e.g., with vancomycin and methicillin-resistant S. aureus or Streptococcus pneumoniae), BacT/Alert PF Plus bottles were superior to Bactec Peds Plus bottles. Together, these findings underscore the potentiality of resin-containing bottles to enhance diagnosis of bacteremia in pediatric patients on antimicrobial therapy. This is particularly true with one of the evaluated BC systems and with simulated intermediate bacteremia level only.
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Affiliation(s)
- Liliana Giordano
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Flora Marzia Liotti
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giulia Menchinelli
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giulia De Angelis
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Tiziana D'Inzeo
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Grazia Angela Morandotti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Maurizio Sanguinetti
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Teresa Spanu
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Brunella Posteraro
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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8
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Verkaik N, Yusuf E, Croughs P. Re: 'Critical factors in the recovery of pathogenic microorganisms in blood' by Wilson et al. Clin Microbiol Infect 2020; 26:1423. [DOI: 10.1016/j.cmi.2020.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 10/24/2022]
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9
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Bordetella pertussis DNA detected in a tracheostomized child blood before seroconversion. Eur J Clin Microbiol Infect Dis 2020; 40:205-208. [PMID: 32661807 DOI: 10.1007/s10096-020-03988-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/06/2020] [Indexed: 10/23/2022]
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10
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Wilson M. Development of new methods for detecting bloodstream pathogens. Clin Microbiol Infect 2020; 26:319-324. [DOI: 10.1016/j.cmi.2019.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 07/31/2019] [Accepted: 08/03/2019] [Indexed: 11/25/2022]
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11
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Bacterial bloodstream infection. Clin Microbiol Infect 2020; 26:140-141. [DOI: 10.1016/j.cmi.2019.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/29/2019] [Accepted: 10/02/2019] [Indexed: 12/31/2022]
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