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Kim KJ, Yun SG, Cho Y, Lee CK, Nam MH. Rapid Direct Identification of Microbial Pathogens and Antimicrobial Resistance Genes in Positive Blood Cultures Using a Fully Automated Multiplex PCR Assay. J Korean Med Sci 2024; 39:e157. [PMID: 38711319 DOI: 10.3346/jkms.2024.39.e157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/22/2024] [Indexed: 05/08/2024] Open
Abstract
This study assessed the performance of the BioFire Blood Culture Identification 2 (BCID2) panel in identifying microorganisms and antimicrobial resistance (AMR) profiles in positive blood cultures (BCs) and its influence on turnaround time (TAT) compared with conventional culture methods. We obtained 117 positive BCs, of these, 102 (87.2%) were correctly identified using BCID2. The discordance was due to off-panel pathogens detected by culture (n = 13), and additional pathogens identified by BCID2 (n = 2). On-panel pathogen concordance between the conventional culture and BCID2 methods was 98.1% (102/104). The conventional method detected 19 carbapenemase-producing organisms, 14 extended-spectrum beta-lactamase-producing Enterobacterales, 18 methicillin-resistant Staphylococcus spp., and four vancomycin-resistant Enterococcus faecium. BCID2 correctly predicted 53 (96.4%) of 55 phenotypic resistance patterns by detecting AMR genes. The TAT for BCID2 was significantly lower than that for the conventional method. BCID2 rapidly identifies pathogens and AMR genes in positive BCs.
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Affiliation(s)
- Keun Ju Kim
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Seung Gyu Yun
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Yunjung Cho
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Chang Kyu Lee
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Myung-Hyun Nam
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea.
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Chai MG, Tu Q, Cotta MO, Bauer MJ, Balch R, Okafor C, Comans T, Kruger P, Meyer J, Shekar K, Brady K, Fourie C, Sharp N, Vlad L, Whiley D, Ungerer JPJ, Mcwhinney BC, Farkas A, Paterson DL, Clark JE, Hajkowicz K, Raman S, Bialasiewicz S, Lipman J, Forde BM, Harris PNA, Schlapbach LJ, Coin L, Roberts JA, Irwin AD. Achievement of therapeutic antibiotic exposures using Bayesian dosing software in critically unwell children and adults with sepsis. Intensive Care Med 2024; 50:539-547. [PMID: 38478027 PMCID: PMC11018654 DOI: 10.1007/s00134-024-07353-3] [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: 10/29/2023] [Accepted: 02/11/2024] [Indexed: 03/26/2024]
Abstract
PURPOSE Early recognition and effective treatment of sepsis improves outcomes in critically ill patients. However, antibiotic exposures are frequently suboptimal in the intensive care unit (ICU) setting. We describe the feasibility of the Bayesian dosing software Individually Designed Optimum Dosing Strategies (ID-ODS™), to reduce time to effective antibiotic exposure in children and adults with sepsis in ICU. METHODS A multi-centre prospective, non-randomised interventional trial in three adult ICUs and one paediatric ICU. In a pre-intervention Phase 1, we measured the time to target antibiotic exposure in participants. In Phase 2, antibiotic dosing recommendations were made using ID-ODS™, and time to target antibiotic concentrations were compared to patients in Phase 1 (a pre-post-design). RESULTS 175 antibiotic courses (Phase 1 = 123, Phase 2 = 52) were analysed from 156 participants. Across all patients, there was no difference in the time to achieve target exposures (8.7 h vs 14.3 h in Phase 1 and Phase 2, respectively, p = 0.45). Sixty-one courses in 54 participants failed to achieve target exposures within 24 h of antibiotic commencement (n = 36 in Phase 1, n = 18 in Phase 2). In these participants, ID-ODS™ was associated with a reduction in time to target antibiotic exposure (96 vs 36.4 h in Phase 1 and Phase 2, respectively, p < 0.01). These patients were less likely to exhibit subtherapeutic antibiotic exposures at 96 h (hazard ratio (HR) 0.02, 95% confidence interval (CI) 0.01-0.05, p < 0.01). There was no difference observed in in-hospital mortality. CONCLUSIONS Dosing software may reduce the time to achieve target antibiotic exposures. It should be evaluated further in trials to establish its impact on clinical outcomes.
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Affiliation(s)
- Ming G Chai
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Quyen Tu
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
- Paediatric Intensive Care Unit, Queensland Children's Hospital, South Brisbane, QLD, Australia
| | - Menino O Cotta
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
- Herston Infectious Disease Institute, Metro North, QLD Health, Herston, QLD, Australia
| | - Michelle J Bauer
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Ross Balch
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Charles Okafor
- Centre for Health Services Research, The University of Queensland, Brisbane, Australia
| | - Tracy Comans
- Centre for Health Services Research, The University of Queensland, Brisbane, Australia
| | - Peter Kruger
- Intensive Care Unit, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Jason Meyer
- Intensive Care Unit, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Kiran Shekar
- Adult Intensive Care Services and Critical Care Research Group, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Kara Brady
- Adult Intensive Care Services and Critical Care Research Group, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Cheryl Fourie
- Department of Infectious Diseases, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Natalie Sharp
- Paediatric Intensive Care Unit, Queensland Children's Hospital, South Brisbane, QLD, Australia
| | - Luminita Vlad
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - David Whiley
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Jacobus P J Ungerer
- Department of Chemical Pathology, Pathology Queensland, Brisbane, QLD, Australia
- Faculty of Biomedical Science, University of Queensland, Brisbane, QLD, Australia
| | - Brett C Mcwhinney
- Department of Chemical Pathology, Pathology Queensland, Brisbane, QLD, Australia
| | - Andras Farkas
- Optimum Dosing Strategies, Bloomingdale, NJ, 07403, USA
- Department of Pharmacy, Saint Clare's Health, Denville, NJ, 07834, USA
| | - David L Paterson
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
- ADVANCE-ID, Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Julia E Clark
- Infection Management and Prevention Service, Queensland Children's Hospital, Brisbane, Australia
| | - Krispin Hajkowicz
- Department of Infectious Diseases, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Sainath Raman
- Paediatric Intensive Care Unit, Queensland Children's Hospital, South Brisbane, QLD, Australia
- Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Seweryn Bialasiewicz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jeffrey Lipman
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
- ICU and Jameson Trauma Institute, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
- Nimes University Hospital, University of Montpellier, Nimes, France
| | - Brian M Forde
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Patrick N A Harris
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
- Herston Infectious Disease Institute, Metro North, QLD Health, Herston, QLD, Australia
- Central Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Luregn J Schlapbach
- Paediatric Intensive Care Unit, Queensland Children's Hospital, South Brisbane, QLD, Australia
- Department of Pediatric and Neonatal Intensive Care, University Children's Hospital Zurich, Zurich, Switzerland
| | - Lachlan Coin
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Jason A Roberts
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
- Herston Infectious Disease Institute, Metro North, QLD Health, Herston, QLD, Australia
| | - Adam D Irwin
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia.
- Infection Management and Prevention Service, Queensland Children's Hospital, Brisbane, Australia.
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3
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Hsu PH, Chang R, Yin CH, Chen YS, Chen JS. Association between blood culture turnaround time and clinical prognosis in emergency department patients with community acquired bloodstream infection: A retrospective study based on electronic medical records. Heliyon 2024; 10:e27957. [PMID: 38532997 PMCID: PMC10963333 DOI: 10.1016/j.heliyon.2024.e27957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 02/16/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024] Open
Abstract
Importance Previous investigations have found that time to positive blood culture (TTP) is a prognostic factor for clinical outcomes. In fact, what the emergency physician sees from the medical information system is TAT (turnaround time) defined as time required to post a bacterial culture report. We propose a definition of blood culture TAT that more closely aligns with clinical considerations by measuring the time from starting specimen culture to the release of an official blood culture report.We were curious to know whether the duration of TAT is as intricately linked to the prognosis of bacteremia as TTP. Objectives To examine the association between TAT and outcomes of adult patients who present to the ED with community acquired bacteremia. Design Setting, and Participants: This retrospective study utilized electronic medical records from Kaohsiung Veterans General Hospital (KVGH), a 1000-bed tertiary medical center in Taiwan. Patients were adults aged 18 years and older who presented to ED (Emergency department) for initial diagnosis of community acquired bacteremia from January 1, 2016 to March 31, 2021. Data analysis was performed from December 2022 to January 2023.Main outcomes and measures.The primary outcomes included mortality in the ED, all-cause in-hospital mortality, length of hospital stay, and all-cause 30-day mortality in relation to the individual first report of positive blood culture TAT. Results A total of 4011 eligible patients with bacteremia were evaluated, of which 207 patients had a blood culture TAT of ≤48 h. The overall 30-day all-cause mortality rate was 13%. Contrary to expectation, no statistically significant differences were observed in clinical prognosis between the TAT groups (≤48 versus >48 h). Subgroup analyses indicated that the length of TAT did not have a significant effect on clinical prognosis in patients who underwent lactate level assessment. Furthermore, no difference in clinical outcome was noted between TAT groups (≤48 versus >48 h) in terms of Gram-negative bacilli or Gram-positive cocci bacteremia. However, in patients with delayed antibiotic treatment (>3 h), a shorter TAT was significantly associated with a fatal outcome. Conclusion In adults with community-acquired bacteremia, this study did not observe a significant association between blood culture TAT and clinical prognosis, except in cases of delayed antibiotic treatment.
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Affiliation(s)
- Po-Hsiang Hsu
- Department of Emergency, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Renin Chang
- Department of Emergency, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Chun-Hao Yin
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
- Institute of Health Care Management, National Sun Yat-sen University, Taiwan
| | - Yao-Shen Chen
- Department of Administration, Kaohsiung Veterans General Hospital, Taiwan
- Department of Internal Medicine, Kaohsiung Veterans General Hospital, Taiwan
| | - Jin-Shuen Chen
- Department of Administration, Kaohsiung Veterans General Hospital, Taiwan
- Department of Internal Medicine, Kaohsiung Veterans General Hospital, Taiwan
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Quarton S, McGee K, Cumley N, Behruznia M, Jeff C, Belchamber K, Cox M, Thickett D, Scott A, Parekh D, McNally A, Sapey E. Towards personalised anti-microbial and immune approaches to infections in acute care. Can real-time genomic-informed diagnosis of pathogens, and immune-focused therapies improve outcomes for patients? An observational, experimental study protocol. PLoS One 2024; 19:e0298425. [PMID: 38551904 PMCID: PMC10980213 DOI: 10.1371/journal.pone.0298425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/24/2024] [Indexed: 04/01/2024] Open
Abstract
INTRODUCTION Infection causes a vast burden of disease, with significant mortality, morbidity and costs to health-care systems. However, identifying the pathogen causative infection can be challenging, resulting in high use of broad-spectrum antibiotics, much of which may be inappropriate. Novel metagenomic methods have potential to rapidly identify pathogens, however their clinical utility for many infections is currently unclear. Outcome from infection is also impacted by the effectiveness of immune responses, which can be impaired by age, co-morbidity and the infection itself. The aims of this study are twofold: To compare diversity of organisms identified and time-to-result using metagenomic methods versus traditional culture -based techniques, to explore the potential clinical role of metagenomic approaches to pathogen identification in a range of infections.To characterise the ex vivo function of immune cells from patients with acute infection, exploring host and pathogen-specific factors which may affect immune function and overall outcomes. METHODS This is a prospective observational study of patients with acute infection. Patients with symptoms suggestive of an acute infection will be recruited, and blood and bodily fluid relevant to the site of infection collected (for example, sputum and naso-oropharyngeal swabs for respiratory tract infections, or urine for a suspected urinary tract infection). Metagenomic analysis of samples will be compared to traditional microbiology, alongside the antimicrobials received. Blood and respiratory samples such as bronchoalveolar lavage will be used to isolate immune cells and interrogate immune cell function. Where possible, similar samples will be collected from matched participants without a suspected infection to determine the impact of infection on both microbiome and immune cell function.
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Affiliation(s)
- Samuel Quarton
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Inflammation & Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Kirsty McGee
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Inflammation & Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Nicola Cumley
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Microbiology & Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Mahboobeh Behruznia
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Microbiology & Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Charlotte Jeff
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Kylie Belchamber
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Inflammation & Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Michael Cox
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Microbiology & Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - David Thickett
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Inflammation & Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Aaron Scott
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Inflammation & Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Dhruv Parekh
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Inflammation & Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Alan McNally
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Microbiology & Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Elizabeth Sapey
- Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Director of PIONEER: Health Data Research UK (HDRUK) Health Data Research Hub for Acute Care, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
- Patient Safety Research Collaborative, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
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Sinto R, Lie KC, Setiati S, Suwarto S, Nelwan EJ, Karyanti MR, Karuniawati A, Djumaryo DH, Prayitno A, Sumariyono S, Sharland M, Moore CE, Hamers RL, Day NPJ, Limmathurotsakul D. Diagnostic and antibiotic use practices among COVID-19 and non-COVID-19 patients in the Indonesian National Referral Hospital. PLoS One 2024; 19:e0297405. [PMID: 38452030 PMCID: PMC10919621 DOI: 10.1371/journal.pone.0297405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/26/2023] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Little is known about diagnostic and antibiotic use practices in low and middle-income countries (LMICs) before and during COVID-19 pandemic. This information is crucial for monitoring and evaluation of diagnostic and antimicrobial stewardships in healthcare facilities. METHODS We linked and analyzed routine databases of hospital admission, microbiology laboratory and drug dispensing of Indonesian National Referral Hospital from 2019 to 2020. Patients were classified as COVID-19 cases if their SARS-CoV-2 RT-PCR result were positive. Blood culture (BC) practices and time to discontinuation of parenteral antibiotics among inpatients who received a parenteral antibiotic for at least four consecutive days were used to assess diagnostic and antibiotic use practices, respectively. Fine and Grey subdistribution hazard model was used. RESULTS Of 1,311 COVID-19 and 58,917 non-COVID-19 inpatients, 333 (25.4%) and 18,837 (32.0%) received a parenteral antibiotic for at least four consecutive days. Proportion of patients having BC taken within ±1 calendar day of parenteral antibiotics being started was higher in COVID-19 than in non-COVID-19 patients (21.0% [70/333] vs. 18.7% [3,529/18,837]; p<0.001). Cumulative incidence of having a BC taken within 28 days was higher in COVID-19 than in non-COVID-19 patients (44.7% [149/333] vs. 33.2% [6,254/18,837]; adjusted subdistribution-hazard ratio [aSHR] 1.71, 95% confidence interval [CI] 1.47-1.99, p<0.001). The median time to discontinuation of parenteral antibiotics was longer in COVID-19 than in non-COVID-19 patients (13 days vs. 8 days; aSHR 0.73, 95%Cl 0.65-0.83, p<0.001). CONCLUSIONS Routine electronic data could be used to inform diagnostic and antibiotic use practices in LMICs. In Indonesia, the proportion of timely blood culture is low in both COVID-19 and non-COVID-19 patients, and duration of parenteral antibiotics is longer in COVID-19 patients. Improving diagnostic and antimicrobial stewardship is critically needed.
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Affiliation(s)
- Robert Sinto
- Division of Tropical and Infectious Diseases, Department of Internal Medicine, Cipto Mangunkusumo National Hospital, Faculty of Medicine Universitas Indonesia, Jakarta Pusat, Jakarta, Indonesia
- Infection and Antimicrobial Resistance Control Committee, Cipto Mangunkusumo National Hospital, Jakarta Pusat, Jakarta, Indonesia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Internal Medicine, Cipto Mangunkusumo National Hospital, Faculty of Medicine Universitas Indonesia, Jakarta Pusat, Jakarta, Indonesia
| | - Khie Chen Lie
- Division of Tropical and Infectious Diseases, Department of Internal Medicine, Cipto Mangunkusumo National Hospital, Faculty of Medicine Universitas Indonesia, Jakarta Pusat, Jakarta, Indonesia
- Infection and Antimicrobial Resistance Control Committee, Cipto Mangunkusumo National Hospital, Jakarta Pusat, Jakarta, Indonesia
| | - Siti Setiati
- Department of Internal Medicine, Cipto Mangunkusumo National Hospital, Faculty of Medicine Universitas Indonesia, Jakarta Pusat, Jakarta, Indonesia
- Center for Clinical Epidemiology and Evidence Based Medicine, Faculty of Medicine Universitas Indonesia, Cipto Mangunkusumo National Hospital, Jakarta Pusat, Jakarta, Indonesia
| | - Suhendro Suwarto
- Division of Tropical and Infectious Diseases, Department of Internal Medicine, Cipto Mangunkusumo National Hospital, Faculty of Medicine Universitas Indonesia, Jakarta Pusat, Jakarta, Indonesia
| | - Erni J. Nelwan
- Division of Tropical and Infectious Diseases, Department of Internal Medicine, Cipto Mangunkusumo National Hospital, Faculty of Medicine Universitas Indonesia, Jakarta Pusat, Jakarta, Indonesia
- Infection and Antimicrobial Resistance Control Committee, Cipto Mangunkusumo National Hospital, Jakarta Pusat, Jakarta, Indonesia
| | - Mulya Rahma Karyanti
- Infection and Antimicrobial Resistance Control Committee, Cipto Mangunkusumo National Hospital, Jakarta Pusat, Jakarta, Indonesia
- Department of Child Health, Cipto Mangunkusumo National Hospital, Faculty of Medicine Universitas Indonesia, Jakarta Pusat, Jakarta, Indonesia
| | - Anis Karuniawati
- Infection and Antimicrobial Resistance Control Committee, Cipto Mangunkusumo National Hospital, Jakarta Pusat, Jakarta, Indonesia
- Department of Clinical Microbiology, Faculty of Medicine Universitas Indonesia, Cipto Mangunkusumo National Hospital, Jakarta Pusat, Jakarta, Indonesia
| | - Dean Handimulya Djumaryo
- Infection and Antimicrobial Resistance Control Committee, Cipto Mangunkusumo National Hospital, Jakarta Pusat, Jakarta, Indonesia
- Department of Clinical Pathology, Cipto Mangunkusumo National Hospital, Faculty of Medicine Universitas Indonesia, Jakarta Pusat, Jakarta, Indonesia
| | - Ari Prayitno
- Infection and Antimicrobial Resistance Control Committee, Cipto Mangunkusumo National Hospital, Jakarta Pusat, Jakarta, Indonesia
- Department of Child Health, Cipto Mangunkusumo National Hospital, Faculty of Medicine Universitas Indonesia, Jakarta Pusat, Jakarta, Indonesia
| | - Sumariyono Sumariyono
- Department of Internal Medicine, Cipto Mangunkusumo National Hospital, Faculty of Medicine Universitas Indonesia, Jakarta Pusat, Jakarta, Indonesia
- Board of Directors, Cipto Mangunkusumo National Hospital, Jakarta Pusat, Jakarta, Indonesia
| | - Mike Sharland
- Centre for Neonatal and Paediatric Infection, St George’s University of London, Cranmer Terrace, London, United Kingdom
| | - Catrin E. Moore
- Centre for Neonatal and Paediatric Infection, St George’s University of London, Cranmer Terrace, London, United Kingdom
| | - Raph L. Hamers
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford University Clinical Research Unit Indonesia, Faculty of Medicine Universitas Indonesia, Jakarta Pusat, Jakarta, Indonesia
| | - Nicholas P. J. Day
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Direk Limmathurotsakul
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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Kou X, Zhu D, Zhang Y, Huang L, Liang J, Wu Z, Liu Z, Guan C, Yu L. Development and clinical validation of a dual ddPCR assay for detecting carbapenem-resistant Acinetobacter baumannii in bloodstream infections. Front Microbiol 2024; 15:1338395. [PMID: 38591042 PMCID: PMC11000175 DOI: 10.3389/fmicb.2024.1338395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/13/2024] [Indexed: 04/10/2024] Open
Abstract
Objective Acinetobacter baumannii (A. baumannii, AB) represents a major species of Gram-negative bacteria involved in bloodstream infections (BSIs) and shows a high capability of developing antibiotic resistance. Especially, carbapenem-resistant Acinetobacter baumannii (CRAB) becomes more and more prevalent in BSIs. Hence, a rapid and sensitive CRAB detection method is of urgent need to reduce the morbidity and mortality due to CRAB-associated BSIs. Methods A dual droplet digital PCR (ddPCR) reaction system was designed for detecting the antibiotic resistance gene OXA-23 and AB-specific gene gltA. Then, the specificity of the primers and probes, limit of detection (LOD), linear range, and accuracy of the assay were evaluated. Furthermore, the established assay approach was validated on 37 clinical isolates and compared with blood culture and drug sensitivity tests. Results The dual ddPCR method established in this study demonstrated strong primer and probe specificity, distinguishing CRAB among 21 common clinical pathogens. The method showed excellent precision (3 × 10-4 ng/μL, CV < 25%) and linearity (OXA-23: y = 1.4558x + 4.0981, R2 = 0.9976; gltA: y = 1.2716x + 3.6092, R2 = 0.9949). While the dual qPCR LOD is 3 × 10-3 ng/μL, the dual ddPCR's LOD stands at 3 × 10-4 ng/μL, indicating a higher sensitivity in the latter. When applied to detect 35 patients with BSIs of AB, the results were consistent with clinical blood culture identification and drug sensitivity tests. Conclusion The dual ddPCR detection method for OXA-23 and gltA developed in this study exhibits good specificity, excellent linearity, and a higher LOD than qPCR. It demonstrates reproducibility even for minute samples, making it suitable for rapid diagnosis and precision treatment of CRAB in BSIs.
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Affiliation(s)
- Xiaoxia Kou
- Department of Laboratory, The Key Laboratory of Advanced Interdisciplinary Studies Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China
| | - Detu Zhu
- Biologics Test and Evaluation Center, Guangzhou Laboratory, Guangzhou, China
| | - Yandong Zhang
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China
| | - Liyan Huang
- Department of Laboratory, The Key Laboratory of Advanced Interdisciplinary Studies Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jiawei Liang
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China
| | - Ziman Wu
- Department of Laboratory, The Key Laboratory of Advanced Interdisciplinary Studies Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ze Liu
- Department of Laboratory, The Key Laboratory of Advanced Interdisciplinary Studies Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Chushi Guan
- Department of Laboratory, The Key Laboratory of Advanced Interdisciplinary Studies Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Lin Yu
- Department of Laboratory, The Key Laboratory of Advanced Interdisciplinary Studies Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China
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Pickens CI, Wunderink RG. Novel and Rapid Diagnostics for Common Infections in the Critically Ill Patient. Infect Dis Clin North Am 2024; 38:51-63. [PMID: 38280767 DOI: 10.1016/j.idc.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2024]
Abstract
There are several novel platforms that enhance detection of pathogens that cause common infections in the intensive care unit. These platforms have a sample to answer time of a few hours, are often higher yield than culture, and have the potential to improve antibiotic stewardship.
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Affiliation(s)
- Chiagozie I Pickens
- Department of Medicine, Pulmonary and Critical Care Division, Northwestern University Feinberg School of Medicine, 303 E. Superior Street Simpson Querrey 5th Floor, Suite 5-406, Chicago, IL 60611-2909, USA.
| | - Richard G Wunderink
- Department of Medicine, Pulmonary and Critical Care Division, Northwestern University Feinberg School of Medicine, 303 E. Superior Street Simpson Querrey 5th Floor, Suite 5-406, Chicago, IL 60611-2909, USA
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Falconer K, Hammond R, Parcell BJ, Gillespie SH. Rapid determination of antimicrobial susceptibility of Gram-negative bacteria from clinical blood cultures using a scattered light-integrated collection device. J Med Microbiol 2024; 73. [PMID: 38415707 DOI: 10.1099/jmm.0.001812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024] Open
Abstract
Background. A bloodstream infection (BSI) presents a complex and serious health problem, a problem that is being exacerbated by increasing antimicrobial resistance (AMR).Gap Statement. The current turnaround times (TATs) for most antimicrobial susceptibility testing (AST) methods offer results retrospective of treatment decisions, and this limits the impact AST can have on antibiotic prescribing and patient care. Progress must be made towards rapid BSI diagnosis and AST to improve antimicrobial stewardship and reduce preventable deaths from BSIs. To support the successful implementation of rapid AST (rAST) in hospital settings, a rAST method that is affordable, is sustainable and offers comprehensive AMR detection is needed.Aim. To evaluate a scattered light-integrated collection (SLIC) device against standard of care (SOC) to determine whether SLIC could accelerate the current TATs with actionable, accurate rAST results for Gram-negative BSIs.Methods. Positive blood cultures from a tertiary referral hospital were studied prospectively. Flagged positive Gram-negative blood cultures were confirmed by Gram staining and analysed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, Vitek 2, disc diffusion (ceftriaxone susceptibility only) and an SLIC device. Susceptibility to a panel of five antibiotics, as defined by European Committee on Antimicrobial Susceptibility Testing breakpoints, was examined using SLIC.Results. A total of 505 bacterial-antimicrobial combinations were analysed. A categorical agreement of 95.5 % (482/505) was achieved between SLIC and SOC. The 23 discrepancies that occurred were further investigated by the broth microdilution method, with 10 AST results in agreement with SLIC and 13 in agreement with SOC. The mean time for AST was 10.53±0.46 h and 1.94±0.02 h for Vitek 2 and SLIC, respectively. SLIC saved 23.96±1.47 h from positive blood culture to AST result.Conclusion. SLIC has the capacity to provide accurate AST 1 day earlier from flagged positive blood cultures than SOC. This significant time saving could accelerate time to optimal antimicrobial therapy, improving antimicrobial stewardship and management of BSIs.
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Affiliation(s)
- Kerry Falconer
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK
| | - Robert Hammond
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK
| | - Benjamin J Parcell
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK
- Ninewells Hospital and Medical School, Dundee, UK
| | - Stephen H Gillespie
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK
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9
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Aruhomukama D, Magiidu WT, Katende G, Ebwongu RI, Bulafu D, Kasolo R, Nakabuye H, Musoke D, Asiimwe B. Evaluation of three protocols for direct susceptibility testing for gram negative-Enterobacteriaceae from patient samples in Uganda with SMS reporting. Sci Rep 2024; 14:2730. [PMID: 38302620 PMCID: PMC10834995 DOI: 10.1038/s41598-024-53230-w] [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: 10/03/2023] [Accepted: 01/30/2024] [Indexed: 02/03/2024] Open
Abstract
In Uganda, the challenge of generating and timely reporting essential antimicrobial resistance (AMR) data has led to overreliance on empirical antibiotic therapy, exacerbating the AMR crisis. To address this issue, this study aimed to adapt a one-step AMR testing protocol alongside an SMS (Short Message Service) result relay system (SRRS), with the potential to reduce the turnaround time for AMR testing and result communication from 4 days or more to 1 day in Ugandan clinical microbiology laboratories. Out of the 377 samples examined, 54 isolates were obtained. Notably, E. coli (61%) and K. pneumoniae (33%) were the most frequently identified, majority testing positive for ESBL. Evaluation of three AMR testing protocols revealed varying sensitivity and specificity, with Protocol A (ChromID ESBL-based) demonstrating high sensitivity (100%) but no calculable specificity, Protocol B (ceftazidime-based) showing high sensitivity (100%) and relatively low specificity (7.1%), and Protocol C (cefotaxime-based) exhibiting high sensitivity (97.8%) but no calculable specificity. ESBL positivity strongly correlated with resistance to specific antibiotics, including cefotaxime, ampicillin, and aztreonam (100%), cefuroxime (96%), ceftriaxone (93%), and trimethoprim sulfamethoxazole (87%). The potential of integrating an SRRS underscored the crucial role this could have in enabling efficient healthcare communication in AMR management. This study underscores the substantial potential of the tested protocols for accurately detecting ESBL production in clinical samples, potentially, providing a critical foundation for predicting and reporting AMR patterns. Although considerations related to specificity warrant careful assessment before widespread clinical adoption.
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Affiliation(s)
- Dickson Aruhomukama
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda.
| | - Walusimbi Talemwa Magiidu
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - George Katende
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Robert Innocent Ebwongu
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Douglas Bulafu
- Department of Disease Control and Environmental Health, School of Public Health, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Rajab Kasolo
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Hellen Nakabuye
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - David Musoke
- Department of Disease Control and Environmental Health, School of Public Health, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Benon Asiimwe
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
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10
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Bae S, Kwon KT, Hwang S, Kim Y, Chang HH, Kim SW, Lee NY, Kim YK, Lee JC. Analysis of microbiological tests in patients withholding or withdrawing life-sustaining treatment at the end stage of life in 2 Korean hospitals. Infect Control Hosp Epidemiol 2024; 45:201-206. [PMID: 37694735 PMCID: PMC10877534 DOI: 10.1017/ice.2023.191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/23/2023] [Accepted: 07/15/2023] [Indexed: 09/12/2023]
Abstract
OBJECTIVE We evaluated the adequacy of microbiological tests in patients withholding or withdrawing life-sustaining treatment (WLST) at the end stage of life. SETTING The study was conducted at 2 tertiary-care referral hospitals in Daegu, Republic of Korea. DESIGN Retrospective cross-sectional study. METHODS Demographic findings, clinical and epidemiological characteristics, statistics of microbiological tests, and microbial species isolated from patients within 2 weeks before death were collected in 2 tertiary-care referral hospitals from January to December 2018. We also reviewed the antimicrobial treatment that was given within 3 days of microbiological testing in patients on WLST. RESULTS Of the 1,187 hospitalized patients included, 905 patients (76.2%) had WLST. The number of tests per 1,000 patient days was higher after WLST than before WLST (242.0 vs 202.4). Among the category of microbiological tests, blood cultures were performed most frequently, and their numbers per 1,000 patient days before and after WLST were 95.9 and 99.0, respectively. The positive rates of blood culture before and after WLST were 17.2% and 18.0%, respectively. Candida spp. were the most common microbiological species in sputum (17.4%) and urine (48.2%), and Acinetobacter spp. were the most common in blood culture (17.3%). After WLST determination, 70.5% of microbiological tests did not lead to a change in antibiotic use. CONCLUSIONS Many unnecessary microbiological tests are being performed in patients with WLST within 2 weeks of death. Microbiological testing should be performed carefully and in accordance with the patient's treatment goals.
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Affiliation(s)
- Sohyun Bae
- Division of Infectious Diseases, Department of Internal Medicine, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Ki Tae Kwon
- Division of Infectious Diseases, Department of Internal Medicine, Kyungpook National University Chilgok Hospital, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Soyoon Hwang
- Division of Infectious Diseases, Department of Internal Medicine, Kyungpook National University Chilgok Hospital, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Yoonjung Kim
- Division of Infectious Diseases, Department of Internal Medicine, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Hyun-Ha Chang
- Division of Infectious Diseases, Department of Internal Medicine, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Shin-Woo Kim
- Division of Infectious Diseases, Department of Internal Medicine, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Nan Young Lee
- Department of Clinical Pathology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Yu Kyoung Kim
- Department of Clinical Pathology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Je Chul Lee
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
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11
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Overbeek R, Leitl CJ, Stoll SE, Wetsch WA, Kammerer T, Mathes A, Böttiger BW, Seifert H, Hart D, Dusse F. The Value of Next-Generation Sequencing in Diagnosis and Therapy of Critically Ill Patients with Suspected Bloodstream Infections: A Retrospective Cohort Study. J Clin Med 2024; 13:306. [PMID: 38256440 PMCID: PMC10816005 DOI: 10.3390/jcm13020306] [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: 12/13/2023] [Revised: 12/30/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Bloodstream infection (BSI), a frequent cause of severe sepsis, is a life-threatening complication in critically ill patients and still associated with a high mortality rate. Rapid pathogen identification from blood is crucial for an early diagnosis and the treatment of patients with suspected BSI. For this purpose, novel diagnostic tools on the base of genetic analysis have emerged for clinical application. The aim of this study was to assess the diagnostic value of additional next-generation sequencing (NGS) pathogen test for patients with suspected BSI in a surgical ICU and its potential impact on antimicrobial therapy. In this retrospective single-centre study, clinical data and results from blood culture (BC) and NGS pathogen diagnostics were analysed for ICU patients with suspected BSI. Consecutive changes in antimicrobial therapy and diagnostic procedures were evaluated. Results: 41 cases with simultaneous NGS and BC sampling were assessed. NGS showed a statistically non-significant higher positivity rate than BC (NGS: 58.5% (24/41 samples) vs. BC: 21.9% (9/41); p = 0.056). NGS detected eight different potentially relevant bacterial species, one fungus and six different viruses, whereas BC detected four different bacterial species and one fungus. NGS results affected antimicrobial treatment in 7.3% of cases. Conclusions: NGS-based diagnostics have the potential to offer a higher positivity rate than conventional culture-based methods in patients with suspected BSI. Regarding the high cost, their impact on anti-infective therapy is currently limited. Larger randomized prospective clinical multicentre studies are required to assess the clinical benefit of this novel diagnostic technology.
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Affiliation(s)
- Remco Overbeek
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Christoph J. Leitl
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Sandra E. Stoll
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Wolfgang A. Wetsch
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Tobias Kammerer
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Alexander Mathes
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Bernd W. Böttiger
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50935 Cologne, Germany
| | - Dominique Hart
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Fabian Dusse
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
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12
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Liu W, Liao K, Wu J, Liu S, Zheng X, Wen W, Fu L, Fan X, Yang X, Hu X, Jiang Y, Wu K, Guo Z, Li Y, Liu W, Cai M, Guo Z, Guo X, Lu J, Chen E, Zhou H, Chen D. Blood culture quality and turnaround time of clinical microbiology laboratories in Chinese Teaching Hospitals: A multicenter study. J Clin Lab Anal 2024; 38:e25008. [PMID: 38235610 PMCID: PMC10829685 DOI: 10.1002/jcla.25008] [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: 10/04/2023] [Revised: 12/10/2023] [Accepted: 01/06/2024] [Indexed: 01/19/2024] Open
Abstract
PURPOSE Blood culture (BC) remains the gold standard for the diagnosis of bloodstream infections. Improving the quality of clinical BC samples, optimizing BC performance, and accelerating antimicrobial susceptibility test (AST) results are essential for the early detection of bloodstream infections and specific treatments. METHODS We conducted a retrospective multicenter study using 450,845 BC specimens from clinical laboratories obtained from 19 teaching hospitals between 1 January 2021 and 31 December 2021. We evaluated key performance indicators (KPIs), turnaround times (TATs), and frequency distributions of processing in BC specimens. We also evaluated the AST results of clinically significant isolates for four different laboratory workflow styles. RESULTS Across the 10 common bacterial isolates (n = 16,865) and yeast isolates (n = 1011), the overall median (interquartile range) TATs of AST results were 2.67 (2.05-3.31) and 3.73 (2.98-4.64) days, respectively. The specimen collections mainly occurred between 06:00 and 24:00, and specimen reception and loadings mainly between 08:00 and 24:00. Based on the laboratory workflows of the BCs, 16 of the 19 hospitals were divided into four groups. Time to results (TTRs) from specimen collection to the AST reports were 2.35 (1.95-3.06), 2.61 (1.98-3.32), 2.99 (2.60-3.87), and 3.25 (2.80-3.98) days for groups I, II, III, and IV, respectively. CONCLUSION This study shows the related BC KPIs and workflows in different Chinese hospitals, suggesting that laboratory workflow optimization can play important roles in shortening time to AST reports and initiation of appropriate timely treatment.
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Affiliation(s)
- Wanting Liu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Kang Liao
- Department of Laboratory MedicineThe First Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Jinsong Wu
- Department of Laboratory MedicineShenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology)ShenzhenGuangdongChina
| | - Suling Liu
- Department of Clinical Laboratory, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouGuangdongChina
| | - Xin Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouGuangdongChina
| | - Weihong Wen
- Department of Laboratory MedicineThe Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's HospitalQingyuanGuangdongChina
| | - Liang Fu
- Department of Laboratory MedicineThe Fifth Affiliated Hospital, Southern Medical UniversityGuangzhouGuangdongChina
| | - Xiaoyi Fan
- The Clinical Microbiological LaboratoryThe First Affiliated Hospital of Jinan UniversityGuangzhouGuangdongChina
| | - Xiao Yang
- Department of Laboratory MedicineGuangzhou First People's HospitalGuangzhouGuangdongChina
| | - Xiumei Hu
- Department of Laboratory MedicineNanfang Hospital, Southern Medical UniversityGuangzhouGuangdongChina
| | - Yueting Jiang
- Department of Laboratory MedicineThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdongChina
| | - Kuihai Wu
- Department of Laboratory MedicineThe First People's Hospital of FoshanFoshanGuangdongChina
| | - Zhusheng Guo
- Clinical Microbiology LaboratoryDepartment of Dongguan Tungwah HospitalDongguanGuangdongChina
| | - Yang Li
- Department of Laboratory MedicineZhongshan City People's HospitalZhongshanGuangdongChina
| | - Weiyang Liu
- Clinical LaboratoryThe Third People's Hospital of HuizhouHuizhouGuangdongChina
| | - Mufa Cai
- The Center for Laboratory MedicineAffiliated Hospital of Guangdong Medical UniversityZhanjiangGuangdongChina
| | - Zhaowang Guo
- Clinical LaboratoryThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhaiGuangdongChina
| | - Xuguang Guo
- Department of Clinical Laboratory MedicineThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdongChina
| | - Jinghui Lu
- Laboratory Medicine DepartmentThe First Affiliated Hospital (School of Clinical Medicine), Guangdong Pharmaceutical UniversityGuangzhouGuangdongChina
| | - Enzhong Chen
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Hongwei Zhou
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
| | - Dingqiang Chen
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang HospitalSouthern Medical UniversityGuangzhouGuangdongChina
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13
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Chotiprasitsakul D, Trirattanapikul A, Namsiripongpun W, Chaihongsa N, Santanirand P. From Epidemiology of Community-Onset Bloodstream Infections to the Development of Empirical Antimicrobial Treatment-Decision Algorithm in a Region with High Burden of Antimicrobial Resistance. Antibiotics (Basel) 2023; 12:1699. [PMID: 38136733 PMCID: PMC10740575 DOI: 10.3390/antibiotics12121699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/14/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Antimicrobial-resistant (AMR) infections have increased in community settings. Our objectives were to study the epidemiology of community-onset bloodstream infections (BSIs), identify risk factors for AMR-BSI and mortality-related factors, and develop the empirical antimicrobial treatment-decision algorithm. All adult, positive blood cultures at the emergency room and outpatient clinics were evaluated from 08/2021 to 04/2022. AMR was defined as the resistance of organisms to an antimicrobial to which they were previously sensitive. A total of 1151 positive blood cultures were identified. There were 450 initial episodes of bacterial BSI, and 114 BSIs (25%) were AMR-BSI. Non-susceptibility to ceftriaxone was detected in 40.9% of 195 E. coli isolates and 16.4% among 67 K. pneumoniae isolates. A treatment-decision algorithm was developed using the independent risk factors for AMR-BSI: presence of multidrug-resistant organisms (MDROs) within 90 days (aOR 3.63), prior antimicrobial exposure within 90 days (aOR 1.94), and urinary source (aOR 1.79). The positive and negative predictive values were 53.3% and 83.2%, respectively. The C-statistic was 0.73. Factors significantly associated with 30-day all-cause mortality were Pitt bacteremia score (aHR 1.39), solid malignancy (aHR 2.61), and urinary source (aHR 0.30). In conclusion, one-fourth of community-onset BSI were antimicrobial-resistant, and one-third of Enterobacteriaceae were non-susceptible to ceftriaxone. Treatment-decision algorithms may reduce overly broad antimicrobial treatment.
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Affiliation(s)
- Darunee Chotiprasitsakul
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (A.T.); (W.N.)
| | - Akeatit Trirattanapikul
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (A.T.); (W.N.)
| | - Warunyu Namsiripongpun
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (A.T.); (W.N.)
| | - Narong Chaihongsa
- Microbiology Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.C.); (P.S.)
| | - Pitak Santanirand
- Microbiology Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.C.); (P.S.)
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14
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Baillie VL, Madhi SA, Ahyong V, Olwagen CP. Metagenomic sequencing of post-mortem tissue samples for the identification of pathogens associated with neonatal deaths. Nat Commun 2023; 14:5373. [PMID: 37666833 PMCID: PMC10477270 DOI: 10.1038/s41467-023-40958-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 08/17/2023] [Indexed: 09/06/2023] Open
Abstract
Postmortem minimally invasive tissue sampling together with the detailed review of clinical records has been shown to be highly successful in determining the cause of neonatal deaths. However, conventional tests including traditional culture methods and nucleic acid amplification tests have periodically proven to be insufficient to detect the causative agent in the infectious deaths. In this study, metagenomic next generation sequencing was used to explore for putative pathogens associated with neonatal deaths in post-mortem blood and lung tissue samples, in Soweto, South Africa. Here we show that the metagenomic sequencing results corroborate the findings using conventional methods of culture and nucleic acid amplifications tests on post-mortem samples in detecting the pathogens attributed in the causal pathway of death in 90% (18/20) of the decedents. Furthermore, metagenomic sequencing detected a putative pathogen, including Acinetobacter baumannii, Klebsiella pneumoniae, Escherichia coli, and Serratia marcescens, in a further nine of 11 (81%) cases where no causative pathogen was identified. The antimicrobial susceptibility profile was also determined by the metagenomic sequencing for all pathogens with numerous multi drug resistant organism identified. In conclusion, metagenomic sequencing is able to successfully identify pathogens contributing to infection associated deaths on postmortem blood and tissue samples.
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Affiliation(s)
- Vicky L Baillie
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa.
- Wits Infectious Diseases and Oncology Research Institute, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa.
| | - Shabir A Madhi
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa
- Wits Infectious Diseases and Oncology Research Institute, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa
| | - Vida Ahyong
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA, 94158, USA
| | - Courtney P Olwagen
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa
- Wits Infectious Diseases and Oncology Research Institute, University of the Witwatersrand, Faculty of Health Science, Johannesburg, South Africa
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15
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Choi DH, Lim MH, Kim KH, Shin SD, Hong KJ, Kim S. Development of an artificial intelligence bacteremia prediction model and evaluation of its impact on physician predictions focusing on uncertainty. Sci Rep 2023; 13:13518. [PMID: 37598221 PMCID: PMC10439897 DOI: 10.1038/s41598-023-40708-2] [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: 06/14/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023] Open
Abstract
Prediction of bacteremia is a clinically important but challenging task. An artificial intelligence (AI) model has the potential to facilitate early bacteremia prediction, aiding emergency department (ED) physicians in making timely decisions and reducing unnecessary medical costs. In this study, we developed and externally validated a Bayesian neural network-based AI bacteremia prediction model (AI-BPM). We also evaluated its impact on physician predictive performance considering both AI and physician uncertainties using historical patient data. A retrospective cohort of 15,362 adult patients with blood cultures performed in the ED was used to develop the AI-BPM. The AI-BPM used structured and unstructured text data acquired during the early stage of ED visit, and provided both the point estimate and 95% confidence interval (CI) of its predictions. High AI-BPM uncertainty was defined as when the predetermined bacteremia risk threshold (5%) was included in the 95% CI of the AI-BPM prediction, and low AI-BPM uncertainty was when it was not included. In the temporal validation dataset (N = 8,188), the AI-BPM achieved area under the receiver operating characteristic curve (AUC) of 0.754 (95% CI 0.737-0.771), sensitivity of 0.917 (95% CI 0.897-0.934), and specificity of 0.340 (95% CI 0.330-0.351). In the external validation dataset (N = 7,029), the AI-BPM's AUC was 0.738 (95% CI 0.722-0.755), sensitivity was 0.927 (95% CI 0.909-0.942), and specificity was 0.319 (95% CI 0.307-0.330). The AUC of the post-AI physicians predictions (0.703, 95% CI 0.654-0.753) was significantly improved compared with that of the pre-AI predictions (0.639, 95% CI 0.585-0.693; p-value < 0.001) in the sampled dataset (N = 1,000). The AI-BPM especially improved the predictive performance of physicians in cases with high physician uncertainty (low subjective confidence) and low AI-BPM uncertainty. Our results suggest that the uncertainty of both the AI model and physicians should be considered for successful AI model implementation.
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Affiliation(s)
- Dong Hyun Choi
- Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, South Korea
| | - Min Hyuk Lim
- Transdisciplinary Department of Medicine and Advanced Technology, Seoul National University Hospital, Seoul, South Korea
- Innovative Medical Technology Research Institute, Seoul National University Hospital, Seoul, South Korea
- Institute of Medical and Biological Engineering, Seoul National University, Seoul, South Korea
| | - Ki Hong Kim
- Department of Emergency Medicine, Seoul National University Hospital, Seoul, South Korea
- Department of Emergency Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Laboratory of Emergency Medical Services, Seoul National University Hospital Biomedical Research Institute, Seoul, South Korea
| | - Sang Do Shin
- Department of Emergency Medicine, Seoul National University Hospital, Seoul, South Korea
- Department of Emergency Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Laboratory of Emergency Medical Services, Seoul National University Hospital Biomedical Research Institute, Seoul, South Korea
| | - Ki Jeong Hong
- Department of Emergency Medicine, Seoul National University Hospital, Seoul, South Korea.
- Department of Emergency Medicine, Seoul National University College of Medicine, Seoul, South Korea.
- Laboratory of Emergency Medical Services, Seoul National University Hospital Biomedical Research Institute, Seoul, South Korea.
| | - Sungwan Kim
- Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, South Korea.
- Institute of Bioengineering, Seoul National University, Seoul, South Korea.
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16
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Hisada A, Matsumoto E, Hirano R, Konomi M, Bou Khalil JY, Raoult D, Ominami Y. Detection of antimicrobial impact on gram-negative bacterial cell envelope based on single-cell imaging by scanning electron microscopy. Sci Rep 2023; 13:11258. [PMID: 37438469 DOI: 10.1038/s41598-023-38198-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/05/2023] [Indexed: 07/14/2023] Open
Abstract
Rapid determination of drug efficacy against bacterial pathogens is needed to detect potentially resistant bacteria and allow for more rational use of antimicrobials. As an indicator of the antimicrobial effect for rapid detection, we found changes in image brightness in antimicrobial-affected bacteria by scanning electron microscopy (SEM). The cell envelopes of unaffected bacteria were stained with phosphotungstic acid (PTA), whereas the entire cells of affected bacteria were stained. Since tungsten density increases backscattered electron intensity, brighter bacterial images indicate lethal damage. We propose a simplified method for determining antimicrobial efficacy by detecting damage that occurs immediately after drug administration using tabletop SEM. This method enabled the visualization of microscopic deformations while distinguishing bacterial-cell-envelope damage on gram-negative bacteria due to image-brightness change. Escherichia coli, Acinetobacter baumannii, Enterobacter cloacae, Klebsiella pneumoniae, and Pseudomonas aeruginosa were exposed to imipenem and colistin, which affect the cell envelope through different mechanisms. Classification of single-cell images based on brightness was quantified for approximately 500 bacteria per sample, and the bright images predominated within 5 to 60 min of antimicrobial treatment, depending on the species. Using intracellular PTA staining and characteristic deformations as indicators, it was possible to determine the efficacy of antimicrobials in causing bacterial-cell-envelope damage.
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Affiliation(s)
- Akiko Hisada
- Healthcare Innovation Center, Research and Development Group, Hitachi, Ltd., 1-280, Higashi-Koigakubo, Kokubunji-shi, Tokyo, 185-8601, Japan.
| | - Erino Matsumoto
- Healthcare Innovation Center, Research and Development Group, Hitachi, Ltd., 1-280, Higashi-Koigakubo, Kokubunji-shi, Tokyo, 185-8601, Japan
| | - Ryo Hirano
- Core Technology and Solutions Group, Hitachi High-Tech Corporation, Tokyo, 105-6409, Japan
| | - Mami Konomi
- Core Technology and Solutions Group, Hitachi High-Tech Corporation, Tokyo, 105-6409, Japan
| | | | - Didier Raoult
- Consulting Infection Marseille, 13008, Marseille, France
| | - Yusuke Ominami
- Core Technology and Solutions Group, Hitachi High-Tech Corporation, Tokyo, 105-6409, Japan
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Mencacci A, De Socio GV, Pirelli E, Bondi P, Cenci E. Laboratory automation, informatics, and artificial intelligence: current and future perspectives in clinical microbiology. Front Cell Infect Microbiol 2023; 13:1188684. [PMID: 37441239 PMCID: PMC10333692 DOI: 10.3389/fcimb.2023.1188684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/05/2023] [Indexed: 07/15/2023] Open
Abstract
Clinical diagnostic laboratories produce one product-information-and for this to be valuable, the information must be clinically relevant, accurate, and timely. Although diagnostic information can clearly improve patient outcomes and decrease healthcare costs, technological challenges and laboratory workflow practices affect the timeliness and clinical value of diagnostics. This article will examine how prioritizing laboratory practices in a patient-oriented approach can be used to optimize technology advances for improved patient care.
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Affiliation(s)
- Antonella Mencacci
- Microbiology and Clinical Microbiology, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
- Microbiology, Perugia General Hospital, Perugia, Italy
| | | | - Eleonora Pirelli
- Microbiology and Clinical Microbiology, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Paola Bondi
- Microbiology and Clinical Microbiology, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Elio Cenci
- Microbiology and Clinical Microbiology, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
- Microbiology, Perugia General Hospital, Perugia, Italy
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18
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Chen Y, Dai Y, Zhou Y, Huang Y, Jin Y, Geng Y, Ji B, Xu R, Zhu W, Hu S, Li Z, Liang J, Xiao Y. Improving Blood Culture Quality with a Medical Staff Educational Program: A Prospective Cohort Study. Infect Drug Resist 2023; 16:3607-3617. [PMID: 37309379 PMCID: PMC10257920 DOI: 10.2147/idr.s412348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/24/2023] [Indexed: 06/14/2023] Open
Abstract
Purpose Blood cultures (BCs) are essential laboratory tests for diagnosing blood stream infections. BC diagnostic improvement depends on several factors during the preanalytical phase outside of innovative technologies. In order to evaluate the impact of an educational program on BC quality improvement, a total of 11 hospitals across China were included from June 1st 2020 to January 31st 2021. Methods Each hospital recruited 3 to 4 wards to participate. The project was divided into three different periods, pre-implementation (baseline), implementation (educational activities administered to the medical staff) and post-implementation (experimental group). The educational program was led by hospital microbiologists and included professional presentations, morning meetings, academic salons, seminars, posters and procedural feedback. Results The total number of valid BC case report forms was 6299, including 2739 sets during the pre-implementation period and 3560 sets during the post-implementation period. Compared with the pre-implementation period, some indicators, such as the proportion of patients who had 2 sets or more, volume of blood cultured, and BC sets per 1000 patient days, were improved in the post-implementation period (61.2% vs 49.8%, 18.56 vs 16.09 sets, and 8.0 vs 9.0mL). While BC positivity and contamination rates did not change following the educational intervention (10.44% vs 11.97%, 1.86% vs 1.94%, respectively), the proportion of coagulase negative staphylococci-positive samples decreased in BSI patients (6.87% vs 4.28%). Conclusion Therefore, medical staff education can improve BC quality, especially increasing volume of blood cultured as the most important variable to determine BC positivity, which may lead to improved BSI diagnosis.
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Affiliation(s)
- Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People’s Republic of China
| | - Yuanyuan Dai
- Clinical Laboratory, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, People’s Republic of China
| | - Yizheng Zhou
- Clinical Laboratory, Jingzhou Central Hospital, Jingzhou, People’s Republic of China
| | - Ying Huang
- Clinical Laboratory, First Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
| | - Yan Jin
- Clinical Laboratory, Shandong Provincial Hospital, Jinan, People’s Republic of China
| | - Yan Geng
- Clinical Laboratory, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, People’s Republic of China
| | - Bing Ji
- Clinical Laboratory, Affiliated Hospital of Binzhou Medical College, Binzhou, People’s Republic of China
| | - Rong Xu
- Clinical Laboratory, People’s Hospital of Yichun City, Yichun, People’s Republic of China
| | - Wencheng Zhu
- Clinical Laboratory, Lu’an Civil Hospital, Lu’an, People’s Republic of China
| | - Shuyan Hu
- Clinical Laboratory, People’s Hospital of Qingyang, Qingyang, People’s Republic of China
| | - Zhuo Li
- Clinical Laboratory, The First Affiliated Hospital of Xi’an Medical University, Xi’an, People’s Republic of China
| | - Jinhua Liang
- Clinical Laboratory, The Affiliated Hongqi Hospital of Mudanjiang Medicine College, Mudanjiang, People’s Republic of China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People’s Republic of China
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19
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Chokkalla AK, Tam E, Liang R, Cruz AT, Devaraj S. Validation of a Multi-Analyte Immunoassay for Distinguishing Bacterial vs. Viral Infections in a Pediatric Cohort. Clin Chim Acta 2023; 546:117387. [PMID: 37201742 DOI: 10.1016/j.cca.2023.117387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/10/2023] [Accepted: 05/03/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND Clinical presentation of viral and bacterial infections or co-infections overlaps significantly. Pathogen identification is the gold standard for appropriate treatment. Recently, FDA cleared a multivariate index test called MeMed-BV that distinguishes viral and bacterial infections based on the differential expression of 3 host proteins. Here, we sought to validate MeMed-BV immunoassay on MedKey analyzer in our pediatric hospital following guidelines from the Clinical and Laboratory Standards Institute. METHODS The analytical performance of the MeMed-BV test was evaluated with precision (intra- and inter-assay), method comparison and interference studies. The clinical performance (diagnostic sensitivity and specificity) of the MeMed-BV test was assessed by conducting a retrospective cohort study (n=60) using plasma samples from pediatric patients with acute febrile illness who visited the emergency department of our hospital. RESULTS MeMed-BV showed acceptable intra- and inter-assay precision with a range of <3 score units in both the high-score bacterial as well as the low-score viral controls. Diagnostic accuracy studies revealed a sensitivity of 94% and specificity of 88% for identifying bacterial infections or co-infections. Our MeMed-BV results showed an excellent agreement (R=0.998) with manufacturer's laboratory data and compared well with ELISA studies. Gross hemolysis and icterus did not affect the assay, but gross lipemia showed a considerable bias in samples with moderate likelihood of viral infection. Importantly, the MeMed-BV test performed better than routinely measured infection-related biomarkers like white blood cell counts, procalcitonin and C-reactive protein in classifying bacterial infections. CONCLUSION MeMed-BV immunoassay demonstrated acceptable analytical performance and is reliable for distinguishing viral and bacterial infections or co-infections in pediatric patients. Future studies are warranted to examine the clinical utility, especially with respect to reducing the need for blood cultures and time to treatment for the patient.
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Affiliation(s)
- Anil K Chokkalla
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA; Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - Estella Tam
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - Rommel Liang
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - Andrea T Cruz
- Divisions of Emergency Medicine and Infectious Diseases, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Sridevi Devaraj
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA; Department of Pathology, Texas Children's Hospital, Houston, TX, USA.
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20
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Kim KJ, Yun SG, Cho Y, Nam MH, Ko YJ, Lee CK. Evaluation of a sterile, filter-based, in-house method for rapid direct bacterial identification and antimicrobial susceptibility testing using positive blood culture. Eur J Clin Microbiol Infect Dis 2023; 42:691-700. [PMID: 37012540 DOI: 10.1007/s10096-023-04592-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023]
Abstract
This study aimed to assess the performance of our in-house method for rapid direct bacterial identification (ID) and antimicrobial susceptibility testing (AST) using a positive blood culture (BC) broth. For Gram-negative bacteria, 4 mL of BC broth was aspirated and passed through a Sartorius Minisart syringe filter with a pore size of 5 µm. The filtrate was then centrifuged and washed. A small volume of the pellet was used for ID, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and for AST, using automated broth microdilution. For Gram-positive cocci, 4 mL of BC broth was passed through the Minisart syringe filter. Then, 4 mL of sterile distilled water was injected in the direction opposite to that of the filtration to collect the bacterial residue trapped in the filter. Compared with the conventional method performed with pure colonies on agar plates, 94.0% (234/249) were correctly identified using the in-house method, with rates of 91.4% (127/139) and 97.3% (107/110) for Gram-positive and Gram-negative isolates, respectively. Of 234 correctly identified isolates, 230 were assessed by AST. Categorical agreement and essential agreement were 93.3% and 94.5%, respectively, with a minor error rate of 3.8%, a major error rate of 3.4%, and a very major error rate of 1.6%. Our in-house preparation method showed good performance in rapid direct ID and AST using positive BC broths compared to the conventional method. This simple method can shorten the conventional turnaround time for ID and AST by at least 1 day, potentially contributing to better patient management.
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Affiliation(s)
- Keun Ju Kim
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Seung Gyu Yun
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Yunjung Cho
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Myung-Hyun Nam
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Young Jin Ko
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwangju, Korea
| | - Chang Kyu Lee
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Korea.
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21
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Da Prat V, Galli L, Cichero P, Castiglioni B, Oltolini C, Tassan Din C, Andolina A, Bruzzesi E, Poli A, Moro M, Mancini N, Clementi M, Tresoldi M, Castagna A, Scarpellini P, Ripa M. Antibiotic appropriateness for Gram-negative bloodstream infections: impact of infectious disease consultation. Infect Dis (Lond) 2023; 55:255-262. [PMID: 36694444 DOI: 10.1080/23744235.2023.2169345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND We investigated the role of infectious disease consultation (IDC) on therapeutic appropriateness in Gram-negative bloodstream infections (GNBSIs) in a setting with a high proportion of antibiotic resistance. Secondary outcomes were in-hospital mortality and the impact of rapid diagnostic tests (RDTs). METHODS Retrospective study on hospitalised patients with GNBSIs. Therapy was deemed appropriate if it had the narrowest spectrum considering infection and patients' characteristics. Interventional-IDC (I-IDC) group included patients with IDC-advised first appropriate or last non-appropriate therapy. Time to first appropriate therapy and survival were evaluated by Kaplan-Meier curves. Factors associated with therapy appropriateness were assessed by multivariate Cox proportional-hazard models. RESULTS 471 patients were included. High antibiotic resistance rates were detected: quinolones 45.5%, third-generation cephalosporins 37.4%, carbapenems 7.9%. I-IDC was performed in 31.6% of patients (149/471), RDTs in 70.7% (333/471). The 7-day probability of appropriate treatment was 91.9% (95% confidence interval [95%CI]: 86.4-95.8%) vs. 75.8% (95%CI: 70.9-80.4%) with and without I-IDC, respectively (p-value = 0.0495); 85.5% (95%CI: 81.3-89.1%) vs. 69.4% (95%CI: 61.3-77.2%) with and without RDTs, respectively (p-value = 0.0023). Compared to RDTs alone, the combination with I-IDC was associated with a higher proportion of appropriate therapies at day 7: 81.9% (95%CI: 76.4-86.7%) vs. 92.6% (95%CI: 86.3-96.7%). At multivariate analysis, I-IDC and RDTs were associated with time to first appropriate therapy [adjusted hazard-ratio 1.292 (95%CI: 1.014-1.647) and 1.383 (95%CI: 1.080-1.771), respectively], with no impact on mortality. CONCLUSIONS In a setting with a high proportion of antibiotic resistance, IDC and RDTs were associated with earlier prescription of appropriate therapy in GNBSIs, without impact on mortality.
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Affiliation(s)
- Valentina Da Prat
- General Medicine and Advanced Care Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Laura Galli
- Unit of Infectious and Tropical Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paola Cichero
- Microbiology and Virology Department, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Barbara Castiglioni
- Unit of Infectious and Tropical Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Oltolini
- Unit of Infectious and Tropical Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Tassan Din
- Unit of Infectious and Tropical Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Andolina
- Unit of Infectious and Tropical Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Andrea Poli
- Unit of Infectious and Tropical Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Moro
- Hospital Management, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Nicasio Mancini
- Microbiology and Virology Department, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Massimo Clementi
- Microbiology and Virology Department, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Moreno Tresoldi
- General Medicine and Advanced Care Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Antonella Castagna
- Unit of Infectious and Tropical Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Paolo Scarpellini
- Unit of Infectious and Tropical Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marco Ripa
- Unit of Infectious and Tropical Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
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22
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Nanopore-Targeted Sequencing Improves the Diagnosis and Treatment of Patients with Serious Infections. mBio 2023; 14:e0305522. [PMID: 36651731 PMCID: PMC9979620 DOI: 10.1128/mbio.03055-22] [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] [Indexed: 01/19/2023] Open
Abstract
Serious infections are characterized by rapid progression, poor prognosis, and difficulty in diagnosis. Recently, a new technique known as nanopore-targeted sequencing (NTS) was developed that facilitates the rapid and accurate detection of pathogenic microorganisms and is extremely suitable for patients with serious infections. The aim of our study was to evaluate the clinical application of NTS in the diagnosis and treatment of patients with serious infections. We developed an NTS technology that could detect microorganisms within a 6-h window based on the amplification of the 16S rRNA gene of bacteria, the internal transcribed spacer region of fungi, and the rpoB gene of Mycobacterium. The NTS detection results were compared with those of blood cultures and anal swabs from 50 patients with blood diseases suffering serious infections. The patient's condition before and after NTS was compared. The response rate and the infection-related mortality after the adjustment of antibiotics based on NTS were calculated. The positivity rate of pathogens was highest in NTS (90%), followed by blood culture (32.6%) and anal swabs (14.6%). After adjusting antibiotics for bacteria and fungi detected by NTS, the patients' condition improved significantly. Moreover, the response rate of anti-infective treatment based on NTS was 93.02% (40/43), and infection-related mortality was reduced to 0. NTS is an effective method to identify pathogens in the blood specimens of patients with serious infections and can guide anti-infection treatment and reduce infection-related mortality. IMPORTANCE We introduce the application of NTS in blood samples of patients with serious infections and expound the efficiency and accuracy of NTS in detecting pathogenic microorganisms. Our work builds on the considerable interest of the scientific community in the management of serious infection. This issue is becoming more pressing, especially since the incidence of blood diseases is increasing year by year and hematopoietic stem cell transplantation (HSCT) has been widely used in benign and malignant blood diseases in recent years. The infection progression of these patients is faster, and the study further demonstrates the effectiveness of NTS in guiding the diagnosis and treatment of patients with severe infections. We firmly believe that this method will guide clinicians to adjust anti-infection strategies and bring significant benefits to patients, and our study will have implications for the future clinical application of NTS in all kinds of patients with serious infections.
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23
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Wenzler E, Maximos M, Asempa TE, Biehle L, Schuetz AN, Hirsch EB. Antimicrobial susceptibility testing: An updated primer for clinicians in the era of antimicrobial resistance: Insights from the Society of Infectious Diseases Pharmacists. Pharmacotherapy 2023; 43:264-278. [PMID: 36825480 DOI: 10.1002/phar.2781] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/15/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023]
Abstract
Antimicrobial susceptibility testing (AST) is a critical function of the clinical microbiology laboratory and is essential for optimizing care of patients with infectious diseases, monitoring antimicrobial resistance (AMR) trends, and informing public health initiatives. Several methods are available for performing AST including broth microdilution, agar dilution, and disk diffusion. Technological advances such as the development of commercial automated susceptibility testing platforms and the advent of rapid diagnostic tests have improved the rapidity, robustness, and clinical application of AST. Numerous accrediting and regulatory agencies are involved in the process of AST and setting and revising breakpoints, including the U.S. Food and Drug Administration and the Clinical and Laboratory Standards Institute. Challenges to optimizing AST include the emergence of new resistance mechanisms, the development of new antimicrobial agents, and generation of new data requiring updates and revisions to established methods and breakpoints. Together, the challenges in AST methods and their interpretation create important opportunities for well-informed clinicians to improve patient outcomes and provide value to antimicrobial stewardship programs, especially in the setting of rapidly changing and increasing AMR. Addressing AST challenges will involve continued development of new technologies along with collaboration between clinicians and the laboratory to facilitate optimal antimicrobial use, combat the increasing burden of AMR, and inform the development of novel antimicrobials. This updated primer serves to reinforce important principles of AST, and to provide guidance on their implementation and optimization.
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Affiliation(s)
- Eric Wenzler
- College of Pharmacy, University of Illinois Chicago, Chicago, Illinois, USA
| | - Mira Maximos
- School of Pharmacy, University of Waterloo, Kitchener, Ontario, Canada.,Women's College Hospital, Toronto, Ontario, Canada
| | - Tomefa E Asempa
- Center for Anti-Infective Research and Development, Hartford Hospital, Hartford, Connecticut, USA
| | - Lauren Biehle
- School of Pharmacy, University of Wyoming, Laramie, Wyoming, USA
| | - Audrey N Schuetz
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
| | - Elizabeth B Hirsch
- Department of Experimental and Clinical Pharmacology, University of Minnesota College of Pharmacy, Minneapolis, Minnesota, USA
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24
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Caméléna F, Péan de Ponfilly G, Pailhoriès H, Bonzon L, Alanio A, Poncin T, Lafaurie M, Dépret F, Cambau E, Godreuil S, Chenouard R, Le Monnier A, Jacquier H, Berçot B. Multicenter Evaluation of the FilmArray Blood Culture Identification 2 Panel for Pathogen Detection in Bloodstream Infections. Microbiol Spectr 2023; 11:e0254722. [PMID: 36519852 PMCID: PMC9927563 DOI: 10.1128/spectrum.02547-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022] Open
Abstract
The FilmArray Blood Culture Identification 2 panel (BCID2; bioMérieux) is a fully automated PCR-based assay for identifying bacteria, fungi, and bacterial resistance markers in positive blood cultures (BC) in about 1 h. In this multicenter study, we evaluated the performance of the BCID2 panel for pathogen detection in positive BC. Conventional culture and BCID2 were performed in parallel at four tertiary-care hospitals. We included 152 positive BC-130 monomicrobial and 22 polymicrobial cultures-in this analysis. The BCID2 assay correctly identified 90% (88/98) of Gram-negative and 89% (70/79) of Gram-positive bacteria. Five bacterial isolates targeted by the BCID2 panel and recovered from five positive BC, including three polymicrobial cultures, were missed by the BCID2 assay. Fifteen isolates were off-panel organisms, accounting for 8% (15/182) of the isolates obtained from BC. The mean positive percent agreement between the BCID2 assay and standard culture was 97% (95% confidence interval, 95 to 99%), with agreement ranging from 67% for Candida albicans to 100% for 17 targets included in the BCID2 panel. BCID2 also identified the blaCTX-M gene in seven BC, including one for which no extended-spectrum β-lactamase (ESBL)-producing isolate was obtained in culture. However, it failed to detect ESBL-encoding genes in three BC. Two of the 18 mecA/C genes detected by the BCID2 were not confirmed. No carbapenemase, mecA/C, or MREJ targets were detected. The median turnaround time was significantly shorter for BCID2 than for culture. The BCID2 panel may facilitate faster pathogen identification in bloodstream infections. IMPORTANCE Rapid molecular diagnosis combining the identification of pathogens and the detection of antibiotic resistance genes from positive blood cultures (BC) can improve the outcome for patients with bloodstream infections. The FilmArray BCID2 panel, an updated version of the original BCID, can detect 11 Gram-positive bacteria, 15 Gram-negative bacteria, 7 fungal pathogens, and 10 antimicrobial resistance genes directly from a positive BC. Here, we evaluated the real-life microbiological performance of the BCID2 assay in comparison to the results of standard methods used in routine practice at four tertiary care hospitals.
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Affiliation(s)
- François Caméléna
- Département de Bactériologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
| | - Gauthier Péan de Ponfilly
- Service de Microbiologie clinique, Groupe hospitalier Paris Saint Joseph, Paris, France
- Institut Micalis UMR 1319, Université Paris-Saclay, INRAe, AgroParisTech, Châtenay Malabry, France
| | - Hélène Pailhoriès
- Laboratoire de Bactériologie, Institut de Biologie en Santé, Centre Hospitalier Universitaire d’Angers, Laboratoire HIFIH, UPRES EA3859, SFR ICAT 4208, Université d’Angers, Angers, France
| | - Lucas Bonzon
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier et MIVEGEC, UMR IRD-CNRS-Université de Montpellier, Montpellier, France
| | - Alexandre Alanio
- Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
- Institut Pasteur, Université Paris Cité, CNRS, Unité de Mycologie Moléculaire, UMR2000, Paris, France
| | - Thibaut Poncin
- Département de Bactériologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
| | - Matthieu Lafaurie
- Département des Maladies Infectieuses et Tropicales, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - François Dépret
- Département d’Anesthésie et Réanimation chirurgicale et brûlés, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Emmanuel Cambau
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
- Laboratoire de mycobactériologie spécialisée et de référence, Laboratoire associé du Centre National de Référence des mycobactéries et résistance des mycobactéries aux antituberculeux, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sylvain Godreuil
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier et MIVEGEC, UMR IRD-CNRS-Université de Montpellier, Montpellier, France
| | - Rachel Chenouard
- Laboratoire de Bactériologie, Institut de Biologie en Santé, Centre Hospitalier Universitaire d’Angers, Laboratoire HIFIH, UPRES EA3859, SFR ICAT 4208, Université d’Angers, Angers, France
| | - Alban Le Monnier
- Service de Microbiologie clinique, Groupe hospitalier Paris Saint Joseph, Paris, France
- Institut Micalis UMR 1319, Université Paris-Saclay, INRAe, AgroParisTech, Châtenay Malabry, France
| | - Hervé Jacquier
- Département de Bactériologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
| | - Béatrice Berçot
- Département de Bactériologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand Widal, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
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25
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Metagenomic Antimicrobial Susceptibility Testing from Simulated Native Patient Samples. Antibiotics (Basel) 2023; 12:antibiotics12020366. [PMID: 36830277 PMCID: PMC9952719 DOI: 10.3390/antibiotics12020366] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Genomic antimicrobial susceptibility testing (AST) has been shown to be accurate for many pathogens and antimicrobials. However, these methods have not been systematically evaluated for clinical metagenomic data. We investigate the performance of in-silico AST from clinical metagenomes (MG-AST). Using isolate sequencing data from a multi-center study on antimicrobial resistance (AMR) as well as shotgun-sequenced septic urine samples, we simulate over 2000 complicated urinary tract infection (cUTI) metagenomes with known resistance phenotype to 5 antimicrobials. Applying rule-based and machine learning-based genomic AST classifiers, we explore the impact of sequencing depth and technology, metagenome complexity, and bioinformatics processing approaches on AST accuracy. By using an optimized metagenomics assembly and binning workflow, MG-AST achieved balanced accuracy within 5.1% of isolate-derived genomic AST. For poly-microbial infections, taxonomic sample complexity and relatedness of taxa in the sample is a key factor influencing metagenomic binning and downstream MG-AST accuracy. We show that the reassignment of putative plasmid contigs by their predicted host range and investigation of whole resistome capabilities improved MG-AST performance on poly-microbial samples. We further demonstrate that machine learning-based methods enable MG-AST with superior accuracy compared to rule-based approaches on simulated native patient samples.
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Fast Track Diagnostic Tools for Clinical Management of Sepsis: Paradigm Shift from Conventional to Advanced Methods. Diagnostics (Basel) 2023; 13:diagnostics13020277. [PMID: 36673087 PMCID: PMC9857847 DOI: 10.3390/diagnostics13020277] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/24/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Sepsis is one of the deadliest disorders in the new century due to specific limitations in early and differential diagnosis. Moreover, antimicrobial resistance (AMR) is becoming the dominant threat to human health globally. The only way to encounter the spread and emergence of AMR is through the active detection and identification of the pathogen along with the quantification of resistance. For better management of such disease, there is an essential requirement to approach many suitable diagnostic techniques for the proper administration of antibiotics and elimination of these infectious diseases. The current method employed for the diagnosis of sepsis relies on the conventional culture of blood suspected infection. However, this method is more time consuming and generates results that are false negative in the case of antibiotic pretreated samples as well as slow-growing microbes. In comparison to the conventional method, modern methods are capable of analyzing blood samples, obtaining accurate results from the suspicious patient of sepsis, and giving all the necessary information to identify the pathogens as well as AMR in a short period. The present review is intended to highlight the culture shift from conventional to modern and advanced technologies including their limitations for the proper and prompt diagnosing of bloodstream infections and AMR detection.
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Epidemiology and Economic Outcomes Associated with Timely versus Delayed Receipt of Appropriate Antibiotic Therapy among US Patients Hospitalized for Native Septic Arthritis: A Retrospective Cohort Study. Antibiotics (Basel) 2022; 11:antibiotics11121732. [PMID: 36551387 PMCID: PMC9774525 DOI: 10.3390/antibiotics11121732] [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: 10/18/2022] [Revised: 11/17/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022] Open
Abstract
Timely administration of appropriate antibiotic therapy is associated with better patient outcomes and lower costs of care compared to delayed appropriate therapy, yet initial treatment is often empiric since causal pathogens are typically unknown upon presentation. The challenge for clinicians is balancing selection of adequate coverage treatment regimens, adherence to antimicrobial stewardship principles to deter resistance, and financial constraints. This retrospective cohort study aimed to assess the magnitude and impact of delayed appropriate antibiotic therapy among patients hospitalized with septic arthritis (SA) in the U.S. from 2017 to 2019 using healthcare encounter data. Timely appropriate therapy was defined as the receipt of antibiotic(s) with in vitro activity against identified pathogens within two days of admission; all other patients were assumed to have received delayed appropriate therapy. Of the 517 patients admitted to hospital for SA who met all selection criteria, 26 (5.0%) received delayed appropriate therapy. In inverse-probability-treatment-weighting-adjusted analyses, the receipt of delayed appropriate therapy was associated with an additional 1.1 days of antibiotic therapy, 1.4 days in length of stay, and $3531 in hospital costs (all vs. timely appropriate therapy; all p ≤ 0.02). Timely appropriate therapy was associated with a twofold increased likelihood of antibiotic de-escalation during the SA admission.
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Alkhawaldeh R, Abu Farha R, Abu Hammour K, Alefishat E. Optimizing antimicrobial therapy in urinary tract infections: A focus on urine culture and sensitivity testing. Front Pharmacol 2022; 13:1058669. [PMID: 36532780 PMCID: PMC9748416 DOI: 10.3389/fphar.2022.1058669] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/15/2022] [Indexed: 09/29/2023] Open
Abstract
Objectives: This cross-sectional study was conducted at Jordan university hospital to evaluate the impact of microbial culture data and sensitivity results on optimizing UTI treatment. Methods: All positive urine cultures requested for adult patients (≥18 years) admitted to Jordan University Hospital (JUH) within the period from January 2019-July 2021 were evaluated. The antibiotics prescribed before and after culture data and sensitivity results were compared to evaluate the impact of these diagnostic measures on optimizing UTI treatment. Results: During the study period, 2400 urine cultures revealed positive results. Among those patients, 1,600 (66.7%) were discharged before the availability of culture results and excluded. Of the remaining 800 patients, 701 patients (87.6%) received empiric treatment. After culture and sensitivity results were available, overall, 84 (10.5%) patients had optimization (improvement) in their UTI management after culture results were known, while 6 (0.8%) patients had a worsening in their treatments. Based on the culture results, we found that only 12.4% of patients were appropriately treated before and after the culture results. Moreover, our results revealed that 31.9% were inappropriately treated for their UTIs before and after culture results. Conclusion: This study revealed an alarmingly high rate of inappropriate treatment of UTIs despite the availability of urine culture and sensitivity data, and that culture results were not used to optimize treatment strategies for UTI. This practice can potentially result in poor health-related outcomes and adversely affects efforts to battle AMR. Multifaceted strategies must be implemented to help clinicians follow the best current evidence and current guidelines in their selection of antibiotics for the management of UTIs.
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Affiliation(s)
- Rama Alkhawaldeh
- Department of Clinical Pharmacy, Faculty of Pharmacy, Applied Science Private University, Amman, Jordan
| | - Rana Abu Farha
- Department of Clinical Pharmacy, Faculty of Pharmacy, Applied Science Private University, Amman, Jordan
| | - Khawla Abu Hammour
- Department Biopharmaceutics and Clinical Pharmacy, Faculty of Pharmacy, The University of Jordan, Amman, Jordan
| | - Eman Alefishat
- Department Biopharmaceutics and Clinical Pharmacy, Faculty of Pharmacy, The University of Jordan, Amman, Jordan
- Department of Pharmacology, College of Medicine and Health Science, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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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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Temkin E, Biran D, Braun T, Schwartz D, Carmeli Y. Analysis of Blood Culture Collection and Laboratory Processing Practices in Israel. JAMA Netw Open 2022; 5:e2238309. [PMID: 36282502 PMCID: PMC9597385 DOI: 10.1001/jamanetworkopen.2022.38309] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
IMPORTANCE Blood culturing is a critical diagnostic procedure affecting patient outcomes and antibiotic stewardship. Although there are standards for blood culturing, the process is not often measured. OBJECTIVES To evaluate processes related to the diagnosis of bloodstream infection and compare them with best practices. DESIGN, SETTING, AND PARTICIPANTS A quality improvement study using laboratory data from January 1 to June 30, 2019, was conducted in 28 (96.6%) Israeli acute care hospitals. All blood cultures (BCs) performed on samples from adults and children in a period of 147 hospital-months were analyzed. Data analysis was performed from April 12, 2021, to September 9, 2022. MAIN OUTCOMES AND MEASURES True pathogen detection rate, contamination rate, proportion of adults with blood cultures performed, proportion of adult culturing episodes with only 1 set or bottle used, and median time of steps from sample collection to pathogen identification. RESULTS The data set consisted of 348 987 BC bottles. Bloodstream infection was detected in a median of 6.7% (IQR, 5.8%-8.2%) of adult culturing episodes and 1.1% (IQR, 0.7%-1.9%) of pediatric episodes. Eleven of 27 hospitals (40.7%) with adult patients met the standard of a contamination rate of less than 3% and only 2 hospitals (7.4%) met the more stringent standard of less than or equal to 1% contamination rate. The percentage of adults with blood cultures ranged from 2.7% to 29.0% (mean [SD], 15.7% [6.0%]). There was an association between sampling rate and pathogen detection until BCs were performed in 17% of adult admissions. The percentage of solitary BCs ranged from 47.8% to 94.4%. An estimated 1745 of 7436 (23.5%) adult bloodstream infections went undetected because solitary BCs were performed, anaerobic bottles were not used, or BCs were not performed. Median processing time was 51.2 (IQR, 33.9-78.0) hours, 3 times the optimal time: 4.4 (IQR, 1.7-12.5) hours for the preanalytical stage, 15.9 (IQR, 10.2-23.6) hours from incubation to growth detection, 4.5 (IQR, 1.5-10.7) hours from detection to Gram stain, and 30.9 (IQR, 22.0-41.9) hours from detection to isolate identification. An 8.6-hour delay was related to off-hours operating of laboratories. CONCLUSIONS AND RELEVANCE The findings of this study suggest that the multistep process of blood culturing is not managed comprehensively in Israel, leading to poor clinical practices and delayed results.
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Affiliation(s)
- Elizabeth Temkin
- National Institute for Antibiotic Resistance and Infection Control, Israel Ministry of Health, Tel Aviv, Israel
| | - Dikla Biran
- National Institute for Antibiotic Resistance and Infection Control, Israel Ministry of Health, Tel Aviv, Israel
| | - Tali Braun
- National Institute for Antibiotic Resistance and Infection Control, Israel Ministry of Health, Tel Aviv, Israel
| | - David Schwartz
- National Institute for Antibiotic Resistance and Infection Control, Israel Ministry of Health, Tel Aviv, Israel
| | - Yehuda Carmeli
- National Institute for Antibiotic Resistance and Infection Control, Israel Ministry of Health and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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Chotiprasitsakul D, Bruminhent J, Watcharananan SP. Current state of antimicrobial stewardship and organ transplantation in Thailand. Transpl Infect Dis 2022; 24:e13877. [DOI: 10.1111/tid.13877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 01/15/2023]
Affiliation(s)
- Darunee Chotiprasitsakul
- Department of Medicine Faculty of Medicine Ramathibodi Hospital, Mahidol University Bangkok Thailand
| | - Jackrapong Bruminhent
- Department of Medicine Faculty of Medicine Ramathibodi Hospital, Mahidol University Bangkok Thailand
| | - Siriorn P. Watcharananan
- Department of Medicine Faculty of Medicine Ramathibodi Hospital, Mahidol University Bangkok Thailand
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Michel LV, Gaborski T. Outer Membrane Vesicles as Molecular Biomarkers for Gram-negative Sepsis: Taking Advantage of Nature's Perfect Packages. J Biol Chem 2022; 298:102483. [PMID: 36108741 PMCID: PMC9576880 DOI: 10.1016/j.jbc.2022.102483] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 07/13/2022] [Accepted: 09/08/2022] [Indexed: 11/18/2022] Open
Abstract
Sepsis is an often life-threatening response to infection, occurring when host pro-inflammatory immune responses become abnormally elevated and dysregulated. To diagnose sepsis, the patient must have a confirmed or predicted infection, as well as other symptoms associated with the pathophysiology of sepsis. However, a recent study found that a specific causal organism could not be determined in the majority (70.1%) of sepsis cases, likely due to aggressive antibiotics or localized infections. The timing of a patient's sepsis diagnosis is often predictive of their clinical outcome, underlining the need for a more definitive molecular diagnostic test. Here, we outline the advantages and challenges to using bacterial outer membrane vesicles (OMVs), nanoscale spherical buds derived from the outer membrane of Gram-negative bacteria, as a diagnostic biomarker for Gram-negative sepsis. Advantages include OMV abundance, their robustness in the presence of antibiotics, and their unique features derived from their parent cell that could allow for differentiation between bacterial species. Challenges include the rigorous purification methods required to isolate OMVs from complex biofluids and the additional need to separate OMVs from similarly-sized extracellular vesicles, which can share physical properties with OMVs.
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Affiliation(s)
- Lea Vacca Michel
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York, USA.
| | - Thomas Gaborski
- Department of Biomedical Engineering, Rochester Institute of Technology, Rochester, New York, USA
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33
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Pickens CI, Wunderink RG. Novel and Rapid Diagnostics for Common Infections in the Critically Ill Patient. Clin Chest Med 2022; 43:401-410. [PMID: 36116810 DOI: 10.1016/j.ccm.2022.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
There are several novel platforms that enhance detection of pathogens that cause common infections in the intensive care unit. These platforms have a sample to answer time of a few hours, are often higher yield than culture, and have the potential to improve antibiotic stewardship.
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Affiliation(s)
- Chiagozie I Pickens
- Department of Medicine, Pulmonary and Critical Care Division, Northwestern University Feinberg School of Medicine, 303 E. Superior Street Simpson Querrey 5th Floor, Suite 5-406, Chicago, IL 60611-2909, USA.
| | - Richard G Wunderink
- Department of Medicine, Pulmonary and Critical Care Division, Northwestern University Feinberg School of Medicine, 303 E. Superior Street Simpson Querrey 5th Floor, Suite 5-406, Chicago, IL 60611-2909, USA
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Blood Culture Headspace Gas Analysis Enables Early Detection of Escherichia coli Bacteremia in an Animal Model of Sepsis. Antibiotics (Basel) 2022; 11:antibiotics11080992. [PMID: 35892382 PMCID: PMC9331843 DOI: 10.3390/antibiotics11080992] [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: 06/24/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 12/04/2022] Open
Abstract
(1) Background: Automated blood culture headspace analysis for the detection of volatile organic compounds of microbial origin (mVOC) could be a non-invasive method for bedside rapid pathogen identification. We investigated whether analyzing the gaseous headspace of blood culture (BC) bottles through gas chromatography-ion mobility spectrometry (GC-IMS) enables differentiation of infected and non-infected; (2) Methods: BC were gained out of a rabbit model, with sepsis induced by intravenous administration of E. coli (EC group; n = 6) and control group (n = 6) receiving sterile LB medium intravenously. After 10 h, a pair of blood cultures was obtained and incubated for 36 h. The headspace from aerobic and anaerobic BC was sampled every two hours using an autosampler and analyzed using a GC-IMS device. MALDI-TOF MS was performed to confirm or exclude microbial growth in BCs; (3) Results: Signal intensities (SI) of 113 mVOC peak regions were statistically analyzed. In 24 regions, the SI trends differed between the groups and were considered to be useful for differentiation. The principal component analysis showed differentiation between EC and control group after 6 h, with 62.2% of the data variance described by the principal components 1 and 2. Single peak regions, for example peak region P_15, show significant SI differences after 6 h in the anaerobic environment (p < 0.001) and after 8 h in the aerobic environment (p < 0.001); (4) Conclusions: The results are promising and warrant further evaluation in studies with an extended microbial panel and indications concerning its transferability to human samples.
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Performance Evaluation of the Quantamatrix QMAC-dRAST System for Rapid Antibiotic Susceptibility Testing Directly from Blood Cultures. Microorganisms 2022; 10:microorganisms10061212. [PMID: 35744730 PMCID: PMC9229829 DOI: 10.3390/microorganisms10061212] [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: 06/03/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 02/01/2023] Open
Abstract
Objectives: Rapid antibiotic susceptibility testing (AST) for positive blood cultures can improve patient clinical outcomes if the time to an effective antimicrobial therapy is shortened. In this study, we tested the Quantamatrix dRAST system (QMAC-dRAST), a rapid AST system based on time-lapse microscopic imagery of bacterial colony formation in agarose. Methods: Evaluation of the QMAC-dRAST was performed from 250 monobacterial blood cultures including 130 Enterobacterales, 20 non-fermentative Gram-negative bacteria, 69 staphylococci and 31 enterococci. Blood cultures were recovered from anonymous patients or from spiking experiments to enrich our study with bacterial species and resistant strains. Categorical agreement (CA), minor errors (me), major errors (ME) and very major errors (VME) were calculated in comparison to the results obtained from the BD Phoenix™ M50. Discrepancies between the Phoenix™ M50 and QMAC-dRAST results were investigated using the gradient strip method. The repeatability and reproducibility performance of the QMAC-dRAST was assessed for 16 strains, each strain being tested five times from a spiked blood culture. Results: The overall CAs for Enterobacterales, non-fermentative Gram-negative bacteria, staphylococci and enterococci were 95.1%, 91.2%, 93.4% and 94.5%, respectively. The VME percentage was below 4% for all the groups except for staphylococci, which showed a VME rate of 7%. The median time to result was 6.7 h (range: 4.7–7.9). Repeatability and reproducibility assays showed a high reliability of AST results with best and worst ratios of 98.8% and 99.6% and 95.0% and 98.3%, respectively. Conclusions: The QMAC-dRAST is a fast and reliable system to determine AST directly from monobacterial blood cultures with a major TAT reduction compared to conventional AST testing.
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36
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Du Y, Li X, Liu Y, Mu S, Shen D, Fan S, Lou Z, Zhang S, Xia H, Yuan Y, Wang S. The Species Identification and Genomic Analysis of Haemobacillus shengwangii: A Novel Pathogenic Bacterium Isolated From a Critically Ill Patient With Bloodstream Infection. Front Microbiol 2022; 13:919169. [PMID: 35774464 PMCID: PMC9237643 DOI: 10.3389/fmicb.2022.919169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/17/2022] [Indexed: 11/17/2022] Open
Abstract
Since the first strain related to Thermicanaceae was reported in 1999, almost no literature on Thermicanaceae is available, particularly its genomics. We recently isolated a novel pathogenic bacterium, the △ strain DYY3, from the blood sample of a critically ill patient. The morphological, physiological, and biochemical characteristics of △ strain DYY3 were presented in this study, and the virulence factor genes and antibiotic resistance of DYY3 were also determined. Interestingly, the average nucleotide identity (ANI) and core-genes average amino acid identity (cAAI) analysis indicated that △ strain DYY3 was genus novel and species novel. Moreover, phylogenetic analysis based on both 16S rRNA gene and whole genomic core gene sequences suggested that △ strain DYY3 belonged to the family Thermicanaceae, and this novel taxon was thus named Haemobacillus shengwangii gen. nov., sp. nov. Besides, both the whole genome-based phylogenetic tree and amino acid identity analysis indicated that Thermicanus aegyptius, Hydrogenibacillus schlegelii, Brockia lithotrophica, and the newly discovered species H. shengwangii should belong to Thermicanaceae at the family level, and T. aegyptius was the closest species to H. shengwangii. We also constructed the first high-quality genome in the family Thermicanaceae using the next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing technologies, which certainly contributed to further genomics studies and metagenomic-based pathogenic detection in the future.
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Affiliation(s)
- Yingying Du
- Department of Critical Care Medicine, School of Medicine, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, China
| | - Xuming Li
- Department of Scientific Affairs, Hugo Biotech Co., Ltd., Beijing, China
| | - Yuhao Liu
- Department of Critical Care Medicine, School of Medicine, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, China
| | - Shikui Mu
- Department of Critical Care Medicine, School of Medicine, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, China
| | - Dandan Shen
- Department of Clinical Microbiology, School of Medicine, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, China
| | - Shu Fan
- Department of Scientific Affairs, Hugo Biotech Co., Ltd., Beijing, China
| | - Zheng Lou
- Department of Scientific Affairs, Hugo Biotech Co., Ltd., Beijing, China
| | - Shouqin Zhang
- Department of Critical Care Medicine, School of Medicine, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, China
| | - Han Xia
- Department of Scientific Affairs, Hugo Biotech Co., Ltd., Beijing, China
- *Correspondence: Han Xia,
| | - Yinghua Yuan
- Department of Clinical Microbiology, School of Medicine, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, China
- Yinghua Yuan,
| | - Sheng Wang
- Department of Critical Care Medicine, School of Medicine, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, China
- Sheng Wang,
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Kong PH, Chiang CH, Lin TC, Kuo SC, Li CF, Hsiung CA, Shiue YL, Chiou HY, Wu LC, Tsou HH. Discrimination of Methicillin-resistant Staphylococcus aureus by MALDI-TOF Mass Spectrometry with Machine Learning Techniques in Patients with Staphylococcus aureus Bacteremia. Pathogens 2022; 11:pathogens11050586. [PMID: 35631107 PMCID: PMC9143686 DOI: 10.3390/pathogens11050586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/29/2022] Open
Abstract
Early administration of proper antibiotics is considered to improve the clinical outcomes of Staphylococcus aureus bacteremia (SAB), but routine clinical antimicrobial susceptibility testing takes an additional 24 h after species identification. Recent studies elucidated matrix-assisted laser desorption/ionization time-of-flight mass spectra to discriminate methicillin-resistant strains (MRSA) or even incorporated with machine learning (ML) techniques. However, no universally applicable mass peaks were revealed, which means that the discrimination model might need to be established or calibrated by local strains’ data. Here, a clinically feasible workflow was provided. We collected mass spectra from SAB patients over an 8-month duration and preprocessed by binning with reference peaks. Machine learning models were trained and tested by samples independently of the first six months and the following two months, respectively. The ML models were optimized by genetic algorithm (GA). The accuracy, sensitivity, specificity, and AUC of the independent testing of the best model, i.e., SVM, under the optimal parameters were 87%, 75%, 95%, and 87%, respectively. In summary, almost all resistant results were truly resistant, implying that physicians might escalate antibiotics for MRSA 24 h earlier. This report presents an attainable method for clinical laboratories to build an MRSA model and boost the performance using their local data.
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Affiliation(s)
- Po-Hsin Kong
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan; (P.-H.K.); (Y.-L.S.)
- Center for Precision Medicine, Chi Mei Medical Center, Tainan 71004, Taiwan;
| | - Cheng-Hsiung Chiang
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan; (C.-H.C.); (C.A.H.); (H.-Y.C.)
| | - Ting-Chia Lin
- Center for Precision Medicine, Chi Mei Medical Center, Tainan 71004, Taiwan;
- Institute of Precision Medicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Shu-Chen Kuo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan;
| | - Chien-Feng Li
- Department of Medical Research, Chi Mei Medical Center, Tainan 71004, Taiwan;
| | - Chao A. Hsiung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan; (C.-H.C.); (C.A.H.); (H.-Y.C.)
| | - Yow-Ling Shiue
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan; (P.-H.K.); (Y.-L.S.)
- Institute of Precision Medicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Hung-Yi Chiou
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan; (C.-H.C.); (C.A.H.); (H.-Y.C.)
- School of Public Health, College of Public Health, Taipei Medical University, Taipei 11031, Taiwan
- Master’s Program in Applied Epidemiology, College of Public Health, Taipei Medical University, Taipei 11031, Taiwan
| | - Li-Ching Wu
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan; (P.-H.K.); (Y.-L.S.)
- Center for Precision Medicine, Chi Mei Medical Center, Tainan 71004, Taiwan;
- Correspondence: (L.-C.W.); (H.-H.T.)
| | - Hsiao-Hui Tsou
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan; (C.-H.C.); (C.A.H.); (H.-Y.C.)
- Graduate Institute of Biostatistics, College of Public Health, China Medical University, Taichung 40402, Taiwan
- Correspondence: (L.-C.W.); (H.-H.T.)
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Alkhawaldeh R, Abu Farha R, Abu Hammour K, Alefishat E. The Appropriateness of Empiric Treatment of Urinary Tract Infections in a Tertiary Teaching Hospital in Joran: A Cross-Sectional Study. Antibiotics (Basel) 2022; 11:antibiotics11050629. [PMID: 35625272 PMCID: PMC9137745 DOI: 10.3390/antibiotics11050629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 04/23/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
This is a cross-sectional study that was conducted at Jordan University Hospital (JUH) to evaluate the appropriateness of Urinary Tract Infection (UTI) empiric treatment based on microbial culture data and susceptibility testing. All urine cultures requested for adult patients (≥18 years) admitted to JUH within the period from January 2019–July 2021 were reviewed and only those cultures with positive episodes of infection were considered. In this study, 6950 urine culture episodes were screened; among them, 34.5% (n = 2400) revealed positive results. Among those patients with positive culture episodes, 1600 patients (66.7%) were discharged before the availability of culture results and were excluded. Of the remaining eligible 800 patients, 701 (87.6%) received empiric treatment. In 26.8% of the eligible cases (n = 214), the prescribed empiric agents failed to have appropriate coverage of the identified pathogens, and in 14.6% of the cases (n = 117) the identified microorganisms were reported as resistant to the prescribed empiric agents. Furthermore, only 13.4% of the patients (n = 107) were appropriately treated for their UTI with empiric antibacterial agents. We were not able to judge the appropriateness of UTI treatment for one third (n = 263, 32.9%) of the patients, because they did not have susceptibility reports performed. This study revealed an alarmingly high rate of inappropriate treatment of UTIs, which encourages the emergence of bacterial resistance and affects health-related outcomes negatively. Therefore, antimicrobial stewardship programs must be applied to optimize antibiotic consumption in hospital settings.
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Affiliation(s)
- Rama Alkhawaldeh
- Department of Clinical Pharmacy, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan; (R.A.); (R.A.F.)
| | - Rana Abu Farha
- Department of Clinical Pharmacy, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan; (R.A.); (R.A.F.)
| | - Khawla Abu Hammour
- Department Biopharmaceutics and Clinical Pharmacy, Faculty of Pharmacy, The University of Jordan, Amman 11942, Jordan;
| | - Eman Alefishat
- Department Biopharmaceutics and Clinical Pharmacy, Faculty of Pharmacy, The University of Jordan, Amman 11942, Jordan;
- Department of Pharmacology, College of Medicine and Health Science, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
- Correspondence: ; Tel.: +97-15-018-466
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Corbin CK, Sung L, Chattopadhyay A, Noshad M, Chang A, Deresinksi S, Baiocchi M, Chen JH. Personalized antibiograms for machine learning driven antibiotic selection. COMMUNICATIONS MEDICINE 2022; 2:38. [PMID: 35603264 PMCID: PMC9053259 DOI: 10.1038/s43856-022-00094-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 02/25/2022] [Indexed: 11/09/2022] Open
Abstract
Abstract
Background
The Centers for Disease Control and Prevention identify antibiotic prescribing stewardship as the most important action to combat increasing antibiotic resistance. Clinicians balance broad empiric antibiotic coverage vs. precision coverage targeting only the most likely pathogens. We investigate the utility of machine learning-based clinical decision support for antibiotic prescribing stewardship.
Methods
In this retrospective multi-site study, we developed machine learning models that predict antibiotic susceptibility patterns (personalized antibiograms) using electronic health record data of 8342 infections from Stanford emergency departments and 15,806 uncomplicated urinary tract infections from Massachusetts General Hospital and Brigham & Women’s Hospital in Boston. We assessed the trade-off between broad-spectrum and precise antibiotic prescribing using linear programming.
Results
We find in Stanford data that personalized antibiograms reallocate clinician antibiotic selections with a coverage rate (fraction of infections covered by treatment) of 85.9%; similar to clinician performance (84.3% p = 0.11). In the Boston dataset, the personalized antibiograms coverage rate is 90.4%; a significant improvement over clinicians (88.1% p < 0.0001). Personalized antibiograms achieve similar coverage to the clinician benchmark with narrower antibiotics. With Stanford data, personalized antibiograms maintain clinician coverage rates while narrowing 69% of empiric vancomycin+piperacillin/tazobactam prescriptions to piperacillin/tazobactam. In the Boston dataset, personalized antibiograms maintain clinician coverage rates while narrowing 48% of ciprofloxacin to trimethoprim/sulfamethoxazole.
Conclusions
Precision empiric antibiotic prescribing with personalized antibiograms could improve patient safety and antibiotic stewardship by reducing unnecessary use of broad-spectrum antibiotics that breed a growing tide of resistant organisms.
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40
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Saving Time in Blood Culture Diagnostics: a Prospective Evaluation of the Qvella FAST-PBC Prep Application on the Fast System. J Clin Microbiol 2022; 60:e0253321. [PMID: 35387489 DOI: 10.1128/jcm.02533-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Time to results for identification (ID) and antimicrobial susceptibility testing (AST) from blood cultures is an important factor impacting outcome in sepsis. In this study we evaluated a novel device, the FAST™ system from Qvella that concentrates microbial biomass from positive blood culture flasks with the FAST-PBC Prep™ cartridge thereby producing a liquid colony™ (LC), which can be used immediately in standard laboratory downstream applications. We tested 250 positive blood culture bottles collected from January 2021 to May 2021. Results were obtained either with LC or from bacterial overnight cultures using Bruker's MALDI Biotyper™ and bioMérieux's Vitek 2. We compared ID and AST results obtained by both methods and evaluated turnaround times. Two-hundred and fourteen blood cultures could be included in the analysis. In 94% of the cases (n = 201) identification was obtained directly from the LC with concordant results compared to the standard workflow. No discordant results were observed. AST results could be analyzed for 175 samples. Using categorical analysis, concordant agreement was 97.4% of 1,676 AST results for Gram positive bacteria. Agreement for Gram negative bacteria was 98.5% of 980 AST results. Times-to-result were 36.9 h versus 12.8 h for ID and 52.9 h versus 26.8 h for AST in routine workflow vs FASTTM system, respectively. The FASTTM system gives reliable results for ID and AST directly from positive blood cultures and allows for significant time savings in blood culture diagnostics.
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Mponponsuo K, Leal J, Spackman E, Somayaji R, Gregson D, Rennert-May E. Mathematical model of the cost-effectiveness of the BioFire FilmArray Blood Culture Identification (BCID) Panel molecular rapid diagnostic test compared with conventional methods for identification of Escherichia coli bloodstream infections. J Antimicrob Chemother 2021; 77:507-516. [PMID: 34734238 DOI: 10.1093/jac/dkab398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/05/2021] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Gram-negative pathogens, such as Escherichia coli, are common causes of bloodstream infections (BSIs) and increasingly demonstrate antimicrobial resistance. Molecular rapid diagnostic tests (mRDTs) offer faster pathogen identification and susceptibility results, but higher costs compared with conventional methods. We determined the cost-effectiveness of the BioFire FilmArray Blood Culture Identification (BCID) Panel, as a type of mRDT, compared with conventional methods in the identification of E. coli BSIs. METHODS We constructed a decision analytic model comparing BCID with conventional methods in the identification and susceptibility testing of hospitalized patients with E. coli BSIs from the perspective of the public healthcare payer. Model inputs were obtained from published literature. Cost-effectiveness was calculated by determining the per-patient admission cost, the QALYs garnered and the incremental cost-effectiveness ratios (ICERs) where applicable. Monte Carlo probabilistic sensitivity analyses and one-way sensitivity analyses were conducted to assess the robustness of the model. All costs reflect 2019 Canadian dollars. RESULTS The Monte Carlo probabilistic analyses resulted in cost savings ($27 070.83 versus $35 649.81) and improved QALYs (8.65 versus 7.10) in favour of BCID. At a willingness to pay up to $100 000, BCID had a 72.6%-83.8% chance of being cost-effective. One-way sensitivity analyses revealed length of stay and cost per day of hospitalization to have the most substantial impact on costs and QALYs. CONCLUSIONS BCID was found to be cost-saving when used to diagnose E. coli BSI compared with conventional testing. Cost savings were most influenced by length of stay and cost per day of hospitalization.
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Affiliation(s)
- Kwadwo Mponponsuo
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jenine Leal
- Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Alberta, Canada.,Infection Prevention and Control, Alberta Health Services, Calgary, Alberta, Canada.,O'Brien Institute for Public Health, University of Calgary and Alberta Health Services, Calgary, Alberta, Canada
| | - Eldon Spackman
- Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada.,O'Brien Institute for Public Health, University of Calgary and Alberta Health Services, Calgary, Alberta, Canada
| | - Ranjani Somayaji
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Alberta, Canada.,O'Brien Institute for Public Health, University of Calgary and Alberta Health Services, Calgary, Alberta, Canada.,Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Daniel Gregson
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada.,Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada.,Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada.,Alberta Precision Laboratories, University of Calgary, Calgary, Alberta, Canada
| | - Elissa Rennert-May
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Alberta, Canada.,O'Brien Institute for Public Health, University of Calgary and Alberta Health Services, Calgary, Alberta, Canada.,Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
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Zheng Y, Jin J, Shao Z, Liu J, Zhang R, Sun R, Hu B. Development and clinical validation of a droplet digital PCR assay for detecting Acinetobacter baumannii and Klebsiella pneumoniae in patients with suspected bloodstream infections. Microbiologyopen 2021; 10:e1247. [PMID: 34964298 PMCID: PMC8594765 DOI: 10.1002/mbo3.1247] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 10/20/2021] [Indexed: 12/11/2022] Open
Abstract
The relatively long turnaround time and low sensitivity of traditional blood culture-based diagnosis may delay effective antibiotic therapy for patients with bloodstream infections (BSIs). A rapid and sensitive pathogen detection method is urgently required to reduce the morbidity and mortality associated with BSIs. Acinetobacter baumannii and Klebsiella pneumoniae are two major microorganisms that cause BSIs. Here we report a novel droplet digital polymerase chain reaction (ddPCR) assay that can detect A. baumannii and K. pneumoniae in blood samples within 4 h, with a specificity of 100% for each strain and a limit of detection at 0.93 copies/μl for A. baumannii and 0.27 copies/μl for K. pneumoniae. Clinical validation of 170 patients with suspected BSIs showed that compared to blood cultures that detected four (2.4%) A. baumannii cases and seven (4.1%) K. pneumoniae cases, ddPCR detected 23 (13.5%) A. baumannii cases, 26 (15.3%) K. pneumoniae cases, and four (2.4%) co-infection cases, including the 11 cases detected via blood culture. In addition, patients who tested positive via ddPCR alone (n = 42) had significantly lower serum concentrations of procalcitonin and lactate, SOFA and APACHE II scores, and 28-day mortality than those reported positive via both blood culture and ddPCR (n = 11), suggesting that patients with less severe symptoms can potentially benefit from ddPCR-based diagnosis. In conclusion, our study suggests that ddPCR represents a sensitive and rapid method for identifying causal pathogens in blood samples and guiding treatment decisions in the early stages of BSIs.
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Affiliation(s)
- Yang Zheng
- Intensive Care UnitZhejiang Provincial People’s HospitalPeople’s Hospital of Hangzhou Medical CollegeHangzhouChina
| | - Jun Jin
- Intensive Care UnitZhejiang Provincial People’s HospitalPeople’s Hospital of Hangzhou Medical CollegeHangzhouChina
| | - Ziqiang Shao
- Intensive Care UnitZhejiang Provincial People’s HospitalPeople’s Hospital of Hangzhou Medical CollegeHangzhouChina
| | - Jingquan Liu
- Intensive Care UnitZhejiang Provincial People’s HospitalPeople’s Hospital of Hangzhou Medical CollegeHangzhouChina
| | - Run Zhang
- Intensive Care UnitZhejiang Provincial People’s HospitalPeople’s Hospital of Hangzhou Medical CollegeHangzhouChina
| | - Renhua Sun
- Intensive Care UnitZhejiang Provincial People’s HospitalPeople’s Hospital of Hangzhou Medical CollegeHangzhouChina
| | - Bangchuan Hu
- Intensive Care UnitZhejiang Provincial People’s HospitalPeople’s Hospital of Hangzhou Medical CollegeHangzhouChina
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Puzniak L, Gupta V, Yu KC, Ye G, Outterson K. The impact of infections on reimbursement in 92 US hospitals, 2015-2018. Am J Infect Control 2021; 49:1275-1280. [PMID: 33891989 DOI: 10.1016/j.ajic.2021.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND The diagnosis-related group (DRG) is a payment system introduced to standardize healthcare costs. However, reimbursement for treatment of infections does not always cover costs. METHODS We used 2015-2018 data from 92 US hospitals in the Becton Dickinson Insights Research Database to compare the financial burden of hospital admissions within non-infection DRGs for patients with a bacterial infection (INF+) versus those without an infection (INF-). Included patients were adults with a hospital length of stay (LOS) ≥3 days and evidence of infection. Multi-variable adjusted analyses via generalized linear mixed models were used to evaluate the impact of an infection on outcomes. RESULTS We analyzed data from 133,423 INF+ admissions and 170,531 INF- admissions. Infections were associated with an approximately two-fold increase in model-estimated LOS (9.2 vs 4.8 d; P < .001) and intensive care unit LOS (5.1 vs 2.8 d; P < .001). The average additional hospital cost for INF+ versus INF- admissions was $10,326 per admission (P < .001) and the average loss after reimbursement was $1,067 (P = .006). Only private insurance payers had a positive margin. CONCLUSIONS Current reimbursement options for infections result in significant hospital financial burden. Reimbursement models should be reconsidered to enable adoption of costlier diagnostics and antimicrobials.
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Russo A, Venditti M, Ceccarelli G, Mastroianni CM, d'Ettorre G. Early antibiotic treatment in emergency department: the critical balance. Intern Emerg Med 2021; 16:1743-1745. [PMID: 34091840 DOI: 10.1007/s11739-021-02779-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 05/26/2021] [Indexed: 12/01/2022]
Affiliation(s)
- Alessandro Russo
- Infectious and Tropical Disease Unit, Department of Medical and Surgical Sciences, "Magna Graecia" University of Catanzaro, Viale Europa, 88100, Catanzaro, Italy.
| | - Mario Venditti
- Department of Public Health and Infectious Diseases, Policlinico "Umberto I", "Sapienza" University of Rome, Rome, Italy
| | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, Policlinico "Umberto I", "Sapienza" University of Rome, Rome, Italy
| | - Claudio Maria Mastroianni
- Department of Public Health and Infectious Diseases, Policlinico "Umberto I", "Sapienza" University of Rome, Rome, Italy
| | - Gabriella d'Ettorre
- Department of Public Health and Infectious Diseases, Policlinico "Umberto I", "Sapienza" University of Rome, Rome, Italy
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Shortening the Time of the Identification and Antimicrobial Susceptibility Testing on Positive Blood Cultures with MALDI-TOF MS. Diagnostics (Basel) 2021; 11:diagnostics11081514. [PMID: 34441448 PMCID: PMC8391154 DOI: 10.3390/diagnostics11081514] [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: 07/12/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 12/29/2022] Open
Abstract
The current processes used in clinical microbiology laboratories take ~24 h for incubation to identify the bacteria after the blood culture has been confirmed as positive and fa further ~24 h to report the results of antimicrobial susceptibility tests (ASTs). Patients with suspected bloodstream infection are treated with empiric broad-spectrum antibiotics but delayed targeted antimicrobial therapy. This study aimed to develop a method with a significantly shortened turnaround time for clinical application by identifying the optimal incubation period of a subculture. A total of 188 positive blood culture samples obtained from Nov. 2019 to Aug. 2020 were included. Compared to the conventional 24-h incubation for bacterial identification, our approach achieved 96.1% and 97.4% identification accuracy after shortening the incubation time to 4.5 and 3.5 h for gram-positive (GP) and gram-negative (GN) bacterial samples, respectively. Samples from short-term incubation without any intermediate step or process were directly subjected to analysis with the Phoenix M50 AST. Compared to the conventional disk diffusion AST, the category agreements for GP (excluding Streptococcus spp.), Streptococcus spp., and GN bacterial samples were 91.8%, 97.5%, and 92.7%, respectively. Our approach significantly reduced the average turnaround time from 48 h to 28 h for reporting bacterial identity and decreased average AST from 72 h to 50.3 h compared to the conventional methods. Accordingly, this approach allows a physician to prescribe the appropriate antibiotic(s) ~21.7 h earlier, thereby improving patient outcomes.
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Identification of volatile compounds from bacteria by spectrometric methods in medicine diagnostic and other areas: current state and perspectives. Appl Microbiol Biotechnol 2021; 105:6245-6255. [PMID: 34415392 PMCID: PMC8377328 DOI: 10.1007/s00253-021-11469-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 10/25/2022]
Abstract
Diagnosis of bacterial infections until today mostly relies on conventional microbiological methods. The resulting long turnaround times can lead to delayed initiation of adequate antibiotic therapy and prolonged periods of empiric antibiotic therapy (e.g., in intensive care medicine). Therewith, they contribute to the mortality of bacterial infections and the induction of multidrug resistances. The detection of species specific volatile organic compounds (VOCs) emitted by bacteria has been proposed as a possible diagnostic approach with the potential to serve as an innovative point-of-care diagnostic tool with very short turnaround times. A range of spectrometric methods are available which allow the detection and quantification of bacterial VOCs down to a range of part per trillion. This narrative review introduces the application of spectrometric analytical methods for the purpose of detecting VOCs of bacterial origin and their clinical use for diagnosing different infectious conditions over the last decade. KEY POINTS: • Detection of VOCs enables bacterial differentiation in various medical conditions. • Spectrometric methods may function as point-of-care diagnostics in near future.
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47
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Extracellular Vesicles: New Tools for Early Diagnosis of Breast and Genitourinary Cancers. Int J Mol Sci 2021; 22:ijms22168430. [PMID: 34445131 PMCID: PMC8395117 DOI: 10.3390/ijms22168430] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/29/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022] Open
Abstract
Breast cancers and cancers of the genitourinary tract are the most common malignancies among men and women and are still characterized by high mortality rates. In order to improve the outcomes, early diagnosis is crucial, ideally by applying non-invasive and specific biomarkers. A key role in this field is played by extracellular vesicles (EVs), lipid bilayer-delimited structures shed from the surface of almost all cell types, including cancer cells. Subcellular structures contained in EVs such as nucleic acids, proteins, and lipids can be isolated and exploited as biomarkers, since they directly stem from parental cells. Furthermore, it is becoming even more evident that different body fluids can also serve as sources of EVs for diagnostic purposes. In this review, EV isolation and characterization methods are described. Moreover, the potential contribution of EV cargo for diagnostic discovery purposes is described for each tumor.
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48
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Yu KC, Yamaga C, Vankeepuram L, Tabak YP. Relationships between creatinine increase and mortality rates in patients given vancomycin in 76 hospitals: The increasing role of infectious disease pharmacists. Am J Health Syst Pharm 2021; 78:2116-2125. [PMID: 34125896 DOI: 10.1093/ajhp/zxab247] [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: 11/14/2022] Open
Abstract
PURPOSE Vancomycin is a commonly used antimicrobial with the potential for renal toxicity. We evaluated vancomycin duration, changes in renal function after vancomycin initiation ("post-vancomycin" renal function changes), and associated mortality risk among hospitalized patients. METHODS We analyzed data from 76 hospitals and excluded patients with a baseline serum creatinine concentration (SCr) of >3.35 mg/dL. We estimated mortality risk relative to vancomycin duration and the magnitude of post-vancomycin SCr change, controlling for demographics, baseline SCr, underlying diseases, clinical acuity, and comorbidities. RESULTS Among 128,993 adult inpatients treated with vancomycin, 49.0% did not experience SCr elevation. Among the remaining patients, 26.0%, 11.4%, 8.8% and 4.8% experienced increases in post-vancomycin SCr of 1% to 20%, 21% to 40%, 41% to 100%, and greater than 100%, respectively. Compared to mortality risk among patients with a vancomycin therapy duration between 4 and 5 days (the lowest-mortality group), longer vancomycin therapy duration was not independently associated with higher mortality risk after adjusting for confounders. In contrast, there was a graded relationship between post-vancomycin SCr elevation and mortality. Multivariable adjusted mortality odds ratios ranged from 1.60 to 13.66, corresponding to SCr increases of 10% and greater than 200%, respectively. CONCLUSION Half of patients given vancomycin did not experience SCr elevation and had the lowest mortality, suggesting that vancomycin can be used safely if renal function is stabilized. In the large study cohort, vancomycin duration itself was not an independent predictor of mortality. Post-vancomycin SCr elevation appeared to be a driver of in-hospital mortality. Even a 10% SCr increase from baseline prior to vancomycin infusion was associated with increased mortality risk. This finding stresses the importance of closely monitoring renal function and may support the value of pharmacokinetic dosing.
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Affiliation(s)
- Kalvin C Yu
- Becton, Dickinson and Company, Franklin Lakes, NJ, USA
| | | | | | - Ying P Tabak
- Becton, Dickinson and Company, Franklin Lakes, NJ, USA
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Drevinek P, Hurych J, Antuskova M, Tkadlec J, Berousek J, Prikrylova Z, Bures J, Vajter J, Soucek M, Masopust J, Martinkova V, Adamkova J, Hysperska V, Bebrova E. Direct detection of ESKAPEc pathogens from whole blood using the T2Bacteria Panel allows early antimicrobial stewardship intervention in patients with sepsis. Microbiologyopen 2021; 10:e1210. [PMID: 34180598 PMCID: PMC8209282 DOI: 10.1002/mbo3.1210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 05/10/2021] [Accepted: 05/17/2021] [Indexed: 12/15/2022] Open
Abstract
In the microbiological diagnosis of bloodstream infections (BSI), blood culture (BC) is considered the gold standard test despite its limitations such as low sensitivity and slow turnaround time. A new FDA-cleared and CE-marked platform utilizing magnetic resonance to detect amplified DNA of the six most common and/or problematic BSI pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli; referred to as ESKAPEc) is available and may shorten the time to diagnosis and potentially improve antimicrobial utilization. Whole blood samples from hospitalized patients with clinical signs of sepsis were analyzed using the T2Bacteria Panel (T2Biosystems) and compared to simultaneously collected BC. Discrepant results were evaluated based on clinical infection criteria, combining supporting culture results and the opinion of treating physicians. A total of 55 samples from 53 patients were evaluated. The sensitivity and specificity of the T2Bacteria panel was 94% (16 out of 17 detections of T2Bacteria-targeted organisms) and 100%, respectively, with 36.4% (8 of 22) causes of BSI detected only by this method. The T2Bacteria Panel detected pathogens on average 55 hours faster than standard BC. In our study, 9 of 15 patients with positive T2Bacteria Panel results received early-targeted antibiotic therapy and/or modification of antimicrobial treatment based on T2Bacteria Panel findings. Given the high reliability, faster time to detection, and easy workflow, the technique qualifies as a point-of-care testing approach.
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Affiliation(s)
- Pavel Drevinek
- Department of Medical Microbiology2nd Faculty of MedicineCharles UniversityMotol University HospitalPragueCzech Republic
| | - Jakub Hurych
- Department of Medical Microbiology2nd Faculty of MedicineCharles UniversityMotol University HospitalPragueCzech Republic
| | - Milena Antuskova
- Department of Medical Microbiology2nd Faculty of MedicineCharles UniversityMotol University HospitalPragueCzech Republic
| | - Jan Tkadlec
- Department of Medical Microbiology2nd Faculty of MedicineCharles UniversityMotol University HospitalPragueCzech Republic
| | - Jan Berousek
- Department of Anesthesiology and ICM2nd Faculty of MedicineCharles UniversityMotol University HospitalPragueCzech Republic
| | - Zuzana Prikrylova
- Department of Anesthesiology and ICM2nd Faculty of MedicineCharles UniversityMotol University HospitalPragueCzech Republic
| | - Jiri Bures
- Department of Anesthesiology and ICM2nd Faculty of MedicineCharles UniversityMotol University HospitalPragueCzech Republic
| | - Jaromir Vajter
- Department of Anesthesiology and ICM2nd Faculty of MedicineCharles UniversityMotol University HospitalPragueCzech Republic
| | - Martin Soucek
- Department of Internal Medicine1st Faculty of MedicineCharles University in PragueMotol University HospitalPragueCzech Republic
| | - Jan Masopust
- Department of Internal Medicine1st Faculty of MedicineCharles University in PragueMotol University HospitalPragueCzech Republic
| | - Vendula Martinkova
- Department of SurgeryFaculty of MedicineCharles UniversityMotol University HospitalPragueCzech Republic
| | - Jaroslava Adamkova
- Department of SurgeryFaculty of MedicineCharles UniversityMotol University HospitalPragueCzech Republic
| | - Veronika Hysperska
- Department of Rehabilitation and Sports Medicine2nd Faculty of MedicineCharles UniversityMotol University HospitalPragueCzech Republic
| | - Eliska Bebrova
- Department of Medical Microbiology2nd Faculty of MedicineCharles UniversityMotol University HospitalPragueCzech Republic
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Puzniak L, Bauer KA, Yu KC, Moise P, Finelli L, Ye G, De Anda C, Vankeepuram L, Gupta V. Effect of Inadequate Empiric Antibacterial Therapy on Hospital Outcomes in SARS-CoV-2-Positive and -Negative US Patients With a Positive Bacterial Culture: A Multicenter Evaluation From March to November 2020. Open Forum Infect Dis 2021; 8:ofab232. [PMID: 34141818 PMCID: PMC8204877 DOI: 10.1093/ofid/ofab232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/25/2021] [Indexed: 12/20/2022] Open
Abstract
Background Increased utilization of antimicrobial therapy has been observed during the coronavirus disease 2019 pandemic. We evaluated hospital outcomes based on the adequacy of antibacterial therapy for bacterial pathogens in US patients. Methods This multicenter retrospective study included patients with ≥24 hours of inpatient admission, ≥24 hours of antibiotic therapy, and discharge/death from March to November 2020 at 201 US hospitals in the BD Insights Research Database. Included patients had a test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and a positive bacterial culture (gram-positive or gram-negative). We used generalized linear mixed models to evaluate the impact of inadequate empiric therapy (IET), defined as therapy not active against the identified bacteria or no antimicrobial therapy in the 48 hours following culture, on in-hospital mortality and hospital and intensive care unit length of stay (LOS). Results Of 438 888 SARS-CoV-2-tested patients, 39 203 (8.9%) had positive bacterial cultures. Among patients with positive cultures, 9.4% were SARS-CoV-2 positive, 74.4% had a gram-negative pathogen, 25.6% had a gram-positive pathogen, and 44.1% received IET for the bacterial infection. The odds of mortality were 21% higher for IET (odds ratio [OR], 1.21; 95% CI, 1.10–1.33; P < .001) compared with adequate empiric therapy. IET was also associated with increased hospital LOS (LOS, 16.1 days; 95% CI, 15.5–16.7 days; vs LOS, 14.5 days; 95% CI, 13.9–15.1 days; P < .001). Both mortality and hospital LOS findings remained consistent for SARS-CoV-2-positive and -negative patients. Conclusions Bacterial pathogens continue to play an important role in hospital outcomes during the pandemic. Adequate and timely therapeutic management may help ensure better outcomes.
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Affiliation(s)
| | | | - Kalvin C Yu
- Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
| | | | - Lyn Finelli
- Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Gang Ye
- Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
| | | | | | - Vikas Gupta
- Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
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