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Bonnefoy C, Vannini M, Degand N, Gaudart A, Lotte R, Buisson-Touati C, Ruimy R, Lamy B. Multiplex microarray PCR Unyvero BCU system to accelerate relevant antimicrobial treatment in polymicrobial bloodstream infection. Eur J Clin Microbiol Infect Dis 2024; 43:1545-1557. [PMID: 38834891 DOI: 10.1007/s10096-024-04868-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 05/28/2024] [Indexed: 06/06/2024]
Abstract
PURPOSE To evaluate the performance of a rapid multiplex microarray-based method (Unyvero BCU system, BCU) to identify microorganisms and detect antimicrobial resistance directly from positive blood culture (BC) bottles with polymicrobial growth, and to assess relevance of information provided for timely guidance of polymicrobial bloodstream infection treatment. METHODS Accuracy, time-to-actionable results and potential impact of BCU on antimicrobial treatment were compared with those of standard of care during a prospective study for the sample analysis (November 2017-November 2018) and a retrospective study for the clinical data analysis and the time-to-result analysis. The study was complemented with an experimental study, based on spiked blood cultures to assess the ability of the method to detect antimicrobial resistance genes. RESULTS Sixty-five clinical polymicrobial BC samples (163 total microorganisms) and 30 simulated polymicrobial BC samples (60 strains) were included. BCU reported 84.6% samples as polymicrobial, correctly identified all the bacteria of the mix for 72.3% samples (47/65) and detected bacteria that were missed by the conventional culture for 13.8% samples. All identifications and antimicrobial resistances were accurately detected for 61.5% (40/65) samples. Limitations concerned the detection of anaerobes, enterococci and enterobacterial susceptibility to third generation cephalosporins. BCU results would have guided antimicrobial treatment for 50.8% of the cases (33/65) in a timely and relevant manner, had no impact for 27.7% (18/65) and been misleading for 18.5% (12/65). CONCLUSIONS Despite some limitations, the Unyvero BCU system is a rapid and reliable method for polymicrobial BC sample analysis.
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Affiliation(s)
- C Bonnefoy
- Laboratoire de Bactériologie, Hôpital l'Archet, Centre Hospitalier Universitaire de Nice, Nice, France
| | - M Vannini
- Laboratoire de Bactériologie, Hôpital l'Archet, Centre Hospitalier Universitaire de Nice, Nice, France
| | - N Degand
- Laboratoire de Bactériologie, Hôpital l'Archet, Centre Hospitalier Universitaire de Nice, Nice, France
- Current affiliation: Service de Biologie, Centre Hospitalier d'Antibes Juan les Pins, Antibes, France
| | - A Gaudart
- Laboratoire de Bactériologie, Hôpital l'Archet, Centre Hospitalier Universitaire de Nice, Nice, France
| | - R Lotte
- Université Côte d'Azur, CHU, INSERM, C3M, Nice, France
| | - C Buisson-Touati
- Laboratoire de Bactériologie, Hôpital l'Archet, Centre Hospitalier Universitaire de Nice, Nice, France
| | - R Ruimy
- Université Côte d'Azur, CHU, INSERM, C3M, Nice, France
| | - B Lamy
- Université Côte d'Azur, CHU, INSERM, C3M, Nice, France.
- Current affiliation: Université Sorbonne Paris Nord, APHP, Hôpitaux universitaires Paris Seine Saint-Denis, Bobigny, France.
- Service de microbiologie clinique, Hôpital Avicenne, Hôpitaux Universitaires de Paris Seine Saint-Denis - AP-HP, 125, rue de Stalingrad, 93000, Bobigny, France.
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Thomas JK, Clark J, Arora V, Burgess DS, Burgess DR, Mynatt RP, VanHoose JD, Wallace KL, Cotner SE. Performance of ePlex® blood culture identification panels in clinical isolates and characterization of antimicrobial stewardship opportunities. Diagn Microbiol Infect Dis 2024; 109:116269. [PMID: 38692201 DOI: 10.1016/j.diagmicrobio.2024.116269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 05/03/2024]
Abstract
We assessed the performance of GenMark's ePlex® Blood Culture Identification (BCID) Panels for overall agreement of organism identification and resistance mechanism detection with standard microbiologic methods. This study included patients with a positive blood culture from May 2020 to January 2021. The primary outcomes were to assess concordance of ePlex® organism identification with standard identification methods and concordance of ePlex® genotypic resistance mechanism detection with standard phenotypic susceptibility testing. Secondary outcomes included panel specific performance and characterization of antimicrobial stewardship opportunities. The overall identification concordance rate in 1276 positive blood cultures was 98.1%. The overall concordance for the presence of resistance markers was 98.2% and concordance for the absence of resistance markers was 100%. A majority of ePlex® results (69.5%) represented opportunities for potential antimicrobial stewardship intervention. High concordance rates between the ePlex® BCID panels and standard identification and susceptibility methods enable utilization of results to guide rapid antimicrobial optimization.
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Affiliation(s)
- Jenni K Thomas
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA
| | - Justin Clark
- University of Kentucky College of Pharmacy, Lexington, KY, USA
| | - Vaneet Arora
- University of Kentucky College of Medicine, Lexington, KY, USA; Department of Pathology and Laboratory Medicine, University of Kentucky HealthCare, Lexington, KY, USA
| | - David S Burgess
- University of Kentucky College of Pharmacy, Lexington, KY, USA
| | - Donna R Burgess
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA; University of Kentucky College of Pharmacy, Lexington, KY, USA
| | - Ryan P Mynatt
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA
| | - Jeremy D VanHoose
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA
| | - Katie L Wallace
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA; University of Kentucky College of Pharmacy, Lexington, KY, USA
| | - Sarah E Cotner
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA; University of Kentucky College of Pharmacy, Lexington, KY, USA.
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McIver CJ, Pratama R, Jose G, Caagbay D, Montgomery L, Bhardwaj N, Mukerjee C, Taylor PC, Stevens R. A novel molecular assay conducted on the BD Max system to facilitate reflex testing for vanA and vanB in clinical isolates of enterococci. Pathology 2024:S0031-3025(24)00144-2. [PMID: 38981818 DOI: 10.1016/j.pathol.2024.04.005] [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: 09/20/2023] [Revised: 03/18/2024] [Accepted: 04/03/2024] [Indexed: 07/11/2024]
Abstract
Infections caused by vancomycin-resistant enterococci (VRE) are common. Real-time PCR assays targeting vanA and vanB facilitate screening of patients in healthcare settings to limit the risk of dissemination, especially amongst those at high-risk of infection or with limited treatment options. Such assays are commonly performed as reflex testing procedures where they augment phenotypic techniques and shorten turnaround time to benefit timely clinical management. 'Random access' and 'sample-to-result' real-time PCR platforms are suited for this application as they are of low complexity and less technically demanding. Modelled on these attributes, we configured a real-time PCR assay (VRE BD) for detection of vanA/B in clinical isolates of enterococci, adapted for the BD Max System (Becton Dickinson). We applied an unconventional approach by testing suspensions of microorganisms in water to circumvent the traditional pre-analytical genomic extraction process. Our objective of this study was to assess the performance of this assay for detection of VRE in cultures by validating against a traditional real-time PCR assay based on the LightCycler 2.0 platform (Roche, VRE RO). A high level of analytical sensitivity and specificity (≥99.0%) for both genes was obtained when testing suspensions derived from blood agar. Results for suspensions obtained from chromID VRE (Edwards Group) showed a similar level of performance for vanA detection (100%), but not for the vanB target (≥90.9%) where a lesser number of isolates were available for testing. However, our results for VRE detection in isolates from these media were repeatable and reproducible, and equated to positive and negative predictive values of ≥95.2% and ≥97.8%, respectively. Furthermore, the VRE BD assay was also able to accurately detect VRE in clinical and spiked BacT/ALERT (bioMérieux) blood cultures. Thus, the technical simplicity, short turnaround time and robustness of this high performing assay for VRE is suitable for reflex testing. In addition, the format developed for the BD Max platform has potential application for reflex testing other molecular targets of clinical importance.
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Affiliation(s)
- Christopher J McIver
- Microbiology Department, New South Wales Health Pathology, St George Hospital, Kogarah, NSW, Australia; School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia.
| | - Ryanbi Pratama
- Microbiology Department, New South Wales Health Pathology, St George Hospital, Kogarah, NSW, Australia
| | - Gismin Jose
- Microbiology Department, New South Wales Health Pathology, St George Hospital, Kogarah, NSW, Australia
| | - Dale Caagbay
- Microbiology Department, New South Wales Health Pathology, St George Hospital, Kogarah, NSW, Australia
| | - Leanne Montgomery
- Microbiology Department, New South Wales Health Pathology, St George Hospital, Kogarah, NSW, Australia
| | - Narinder Bhardwaj
- Microbiology Department, New South Wales Health Pathology, St George Hospital, Kogarah, NSW, Australia
| | - Chinmoy Mukerjee
- Microbiology Department, New South Wales Health Pathology, St George Hospital, Kogarah, NSW, Australia; School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Peter C Taylor
- Microbiology Department, New South Wales Health Pathology, St George Hospital, Kogarah, NSW, Australia; School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Robert Stevens
- Microbiology Department, New South Wales Health Pathology, St George Hospital, Kogarah, NSW, Australia
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Chen HY, Tseng HY, Chen CL, Lin YC, Liang SJ, Tu CY, Chen WC, Hsueh PR. The real-world impact of the BioFire FilmArray blood culture identification 2 panel on antimicrobial stewardship among patients with bloodstream infections in intensive care units with a high burden of drug-resistant pathogens. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2024:S1684-1182(24)00111-7. [PMID: 38942661 DOI: 10.1016/j.jmii.2024.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/03/2024] [Accepted: 06/17/2024] [Indexed: 06/30/2024]
Abstract
BACKGROUND The increasing prevalence of drug-resistant pathogens leads to delays in adequate antimicrobial treatment in intensive care units (ICU). The real-world influence of the BioFire FilmArray Blood Culture Identification 2 (BCID2) panel on pathogen identification, diagnostic concordance with conventional culture methods, and antimicrobial stewardship in the ICU remains unexplored. METHODS This retrospective observational study, conducted from July 2021 to August 2023, involved adult ICU patients with positive blood cultures who underwent BCID2 testing. The concordance between BCID2 and conventional culture results was examined, and its impact on antimicrobial stewardship was assessed through a comprehensive retrospective review of patient records by intensivists. RESULTS A total of 129 blood specimens from 113 patients were analysed. Among these patients, a high proportion of drug-resistant strains were noted, including carbapenem-resistant Klebsiella pneumoniae (CRKP) (57.1%), carbapenem-resistant Acinetobacter calcoaceticus-baumannii complex (100%), methicillin-resistant Staphylococcus aureus (MRSA) (70%), and vancomycin-resistant Enterococcus faecium (VRE) (100%). The time from blood culture collection to obtaining BCID2 results was significantly shorter than conventional culture (46.2 h vs. 86.9 h, p < 0.001). BCID2 demonstrated 100% concordance in genotype-phenotype correlation in antimicrobial resistance (AMR) for CRKP, carbapenem-resistant Escherichia coli, MRSA, and VRE. A total of 40.5% of patients received inadequate empirical antimicrobial treatment. The antimicrobial regimen was adjusted or confirmed in 55.4% of patients following the BCID2 results. CONCLUSIONS In the context of a high burden of drug-resistant pathogens, BCID2 demonstrated rapid pathogen and AMR detection, with a noticeable impact on antimicrobial stewardship in BSI in the ICU.
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Affiliation(s)
- Hsu-Yuan Chen
- Division of Pulmonary and Critical Care, Department of Internal Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - How-Yang Tseng
- Division of Pulmonary and Critical Care, Department of Internal Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Chieh-Lung Chen
- Division of Pulmonary and Critical Care, Department of Internal Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Yu-Chao Lin
- Division of Pulmonary and Critical Care, Department of Internal Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan; School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan
| | - Shinn-Jye Liang
- Division of Pulmonary and Critical Care, Department of Internal Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Chih-Yen Tu
- Division of Pulmonary and Critical Care, Department of Internal Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan; School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan
| | - Wei-Cheng Chen
- Division of Pulmonary and Critical Care, Department of Internal Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan; School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan; Graduate Institute of Biomedical Sciences, College of Medicine, China Medical University, Taichung, Taiwan.
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan; PhD Program for Aging, School of Medicine, China Medical University, Taichung, Taiwan; Department of Laboratory Medicine, School of Medicine, China Medical University, Taichung, Taiwan.
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Li Y, Huang K, Yin J, Tan Z, Zhou M, Dai J, Yi B. Clinical evaluation of a multiplex droplet digital PCR for pathogen detection in critically ill COVID-19 patients with bloodstream infections. Infection 2024; 52:1027-1039. [PMID: 38127118 PMCID: PMC11143000 DOI: 10.1007/s15010-023-02157-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Nosocomial bloodstream infections (nBSI) have emerged as a clinical concern for physicians treating COVID-19 patients. In this study, we aimed to evaluate the effectiveness of a multiplex ddPCR in detecting bacterial pathogens in the blood of COVID-19 critically ill patients. METHODS This prospective diagnostic study included RT-PCR-confirmed COVID-19 patients admitted to our hospital from December 2022 to February 2023. A multiplex ddPCR assay was used to detect common bacterial pathogens and AMR genes in blood samples of the patients, along with antimicrobial susceptibility testing (AST). The diagnostic performance of the ddPCR assay was evaluated by comparing the results with those obtained through blood culture and clinical diagnosis. Additionally, the ability of ddPCR in detecting bacterial resistance was compared with the AST results. RESULTS Of the 200 blood samples collected from 184 patients, 45 (22.5%) were positive using blood culture, while 113 (56.5%) were positive for bacterial targets using the ddPCR assay. The ddPCR assay outperformed blood culture in pathogen detection rate, mixed infection detection rate, and fungal detection rate. Acinetobacter baumannii and Klebsiella pneumoniae were the most commonly detected pathogens in COVID-19 critically ill patients, followed by Enterococcus and Streptococcus. Compared to blood culture, ddPCR achieved a sensitivity of 75.5%, specificity of 51.0%, PPV of 30.9%, and NPV of 87.8%, respectively. However, there were significant differences in sensitivity among different bacterial species, where Gram-negative bacteria have the highest sensitivity of 90.3%. When evaluated on the ground of clinical diagnosis, the sensitivity, specificity, PPV and NPV of ddPCR were 78.1%, 90.5%, 94.7%, and 65.5%, respectively. In addition, the ddPCR assay detected 23 cases of blaKPC, which shown a better consistent with clinical test results than other detected AMR genes. Compared to blaKPC, there were few other AMR genes detected, indicating that the application of other AMR gene detection in the COVID-19 critically ill patients was limited. CONCLUSION The multiplex ddPCR assay had a significantly higher pathogen detection positivity than the blood culture, which could be an effective diagnostic tool for BSIs in COVID-19 patients and to improve patient outcomes and reduce the burden of sepsis on the healthcare system, though there is room for optimization of the panels used.- Adjusting the targets to include E. faecalis and E. faecium as well as Candida albicans and Candida glabrata could improve the ddPCR' s effectiveness. However, further research is needed to explore the potential of ddPCR in predicting bacterial resistance through AMR gene detection.
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Affiliation(s)
- Yanbing Li
- Department of Laboratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Kangkang Huang
- Department of Laboratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Jun Yin
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Zheren Tan
- Intensive Care Unit, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Manli Zhou
- Department of Laboratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Jiaoyang Dai
- Department of Laboratory Medicine, Xiangya Medical School, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Bin Yi
- Department of Laboratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
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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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Vineeth VK, Nambi PS, Gopalakrishnan R, Sethuraman N, Ramanathan Y, Chandran C, Ramasubramanian V. Clinical Utility of Blood Culture Identification 2 Panel in Flagged Blood Culture Samples from the Intensive Care Unit of a Tertiary Care Hospital. Indian J Crit Care Med 2024; 28:461-466. [PMID: 38738189 PMCID: PMC11080102 DOI: 10.5005/jp-journals-10071-24709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 04/11/2024] [Indexed: 05/14/2024] Open
Abstract
Background The availability of rapid diagnostic platforms for positive blood cultures has accelerated the speed at which the clinical microbiology laboratory can identify the causative organism and facilitate early appropriate antimicrobial therapy. There is a paucity of data regarding the clinical utility of the blood culture identification 2 (BCID2) panel test and its correlation with phenotypic drug susceptibility testing (DST) in flagged blood culture bottles from intensive care units (ICUs) in countries such as India, which have high rates of multidrug-resistant gram-negative bacteria (MDR-GNB). Materials and methods We conducted a retrospective observational study in a tertiary care ICU on 200 patients above 18 years of age in whom a BCID2 test was ordered when blood cultures flagged positive. Results We found 99% concordance between BCID2 and cultures in the identification of bacteria and yeasts and 96.5% concordance between phenotypic and genotypic DST. Furthermore, BCID2 was available about 1.5 days earlier than conventional ID and DST and played a key role in tailoring antimicrobials in 82.5% of the patients. Polymyxin-based therapy was discontinued earlier after an empiric dose in 138 patients (69%) based on BCID2 reports. Conclusion In critically ill patients with monomicrobial bacteremia, BCID2 rapidly identifies bacteria and antimicrobial resistance (AMR) genes and is significantly faster than conventional culture and sensitivity testing. Antibiotics were escalated in more than a third of patients and de-escalated in almost a fifth on the same day. We recommend that all ICUs routinely incorporate the test in their antibiotic decision-making process and in antimicrobial stewardship. How to cite this article Vineeth VK, Nambi PS, Gopalakrishnan R, Sethuraman N, Ramanathan Y, Chandran C, et al. Clinical Utility of Blood Culture Identification 2 Panel in Flagged Blood Culture Samples from the Intensive Care Unit of a Tertiary Care Hospital. Indian J Crit Care Med 2024;28(5):461-466.
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Affiliation(s)
- Vashemane K Vineeth
- Department of General Medicine, Infectious Diseases Division, Yenepoya Medical College, Yenepoya (Deemed to be University), Mangaluru, Karnataka, India
| | | | - Ram Gopalakrishnan
- Department of Infectious Diseases, Apollo Hospitals, Chennai, Tamil Nadu, India
| | - Nandini Sethuraman
- Department of Microbiology, Apollo Hospitals, Chennai, Tamil Nadu, India
| | - Yamunadevi Ramanathan
- Department of Infectious Diseases, Institute of Infection Control, Apollo Hospitals, Chennai, Tamil Nadu, India
| | - Chitra Chandran
- Department of Molecular Diagnostics, Apollo Hospitals, Chennai, Tamil Nadu, India
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Cox CR, Weghorn KN, Ruger K, Powers-Fletcher MV, Powell EA, Mortensen JE. Clinical utility of multiplex PCR in the detection of pathogens from sterile body fluids. J Clin Microbiol 2024; 62:e0161123. [PMID: 38470149 PMCID: PMC11005351 DOI: 10.1128/jcm.01611-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/21/2024] [Indexed: 03/13/2024] Open
Abstract
Rapid identification of pathogens in normally sterile body fluid (NSBF) is essential for appropriate patient management, specifically antimicrobial therapy. Limited sensitivity and increased time to detection of traditional culture prompted us to evaluate additional testing to contribute to the diagnosis of infection. The purpose of this study was to evaluate the GenMark Dx ePlex Blood Culture Identification (BCID) Panels on positive body fluids inoculated into blood culture bottles for the detection of microorganisms. A total of 88 positive body fluids from blood culture bottles were analyzed using a Gram-Positive, Gram-Negative, and/or Fungal pathogen BCID Panel based on the Gram stain result. Each result was compared to routine culture performed from the positive bottle. When using culture as a reference standard, we found the ePlex multiplex panel performed with a positive percent agreement of 96.5% and a negative percent agreement of 99.8%. The use of multiplex PCR may be a useful supplement to routine culture for NSBF in blood culture bottles. IMPORTANCE The identification of pathogens in normally sterile body fluid (NSBF) is performed using routine culture, the current gold standard. Limitations of this method include sensitivity and increased turnaround times which could potentially delay vital patient care, especially antimicrobial therapy. Adaptations of NSBF in blood culture bottles prompted us to consider the utility of additional methods to bridge the gap in diagnostic challenges for these life-threatening infections. Multiplex molecular panels have been manufactured for use with multiple specimen types including blood, cerebral spinal fluid, stool, and respiratory. Therefore, the purpose of this study was to evaluate the off-label use of ePlex Blood Culture Identification Panels on positive body fluids grown in blood culture bottles for the detection of microorganisms for research purposes.
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Affiliation(s)
- Christina R. Cox
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Kristin N. Weghorn
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Katie Ruger
- Department of Pathology and Laboratory Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Margaret V. Powers-Fletcher
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Eleanor A. Powell
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Joel E. Mortensen
- Department of Pathology and Laboratory Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
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Harboe-Sjåvik H, Endresen KH, Åsheim S, Sundsfjord A. FilmArray (BCID2) provides essential and timely results in bloodstream infections in small acute care hospitals without conventional microbiology services. APMIS 2024; 132:267-276. [PMID: 38214228 DOI: 10.1111/apm.13374] [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: 07/25/2023] [Accepted: 11/29/2023] [Indexed: 01/13/2024]
Abstract
We have evaluated the performance of FilmArray BCID2 in reactive blood cultures in a small acute care hospital compared to conventional diagnostics at a regional microbiological laboratory. This is a retrospective observational study of BactAlert reactive blood cultures (n = 160) from Helgeland Hospital, July-December 2021, analysed by BCID2 locally and conventional culture at a regional laboratory. The overall clinical and analytic sensitivity with BCID2 were 87.2% and 97.8%, respectively. The false-negative BCID2 rate was low (n = 4; 2.9%). No false-positive BCID2 results were observed. The BCID2 data were available on average 1.88 days earlier than culture-based results, due to long transport time to the regional laboratory. The BCID2 provided results to support a significantly earlier optimized targeted antibiotic treatment in 27% of the cases according to national guidelines for empirical treatment of BSI. The high clinical and analytical sensitivity, and specificity support the use of BCID2 as a robust supplement to traditional cultivation of positive blood cultures. The significant time gain to microbial identification and detection of resistance determinants suggests a great clinical importance of BCID2 in small acute care hospitals with long transport time to conventional clinical microbiology services.
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Affiliation(s)
- Hege Harboe-Sjåvik
- Department of Health Care Quality and Research, Helgeland Hospital Trust, Mo i Rana, Norway
| | | | - Sandra Åsheim
- Department of Microbiology, Nordland Hospital Trust, Bodø, Norway
| | - Arnfinn Sundsfjord
- Host-Microbe-Interaction Research Group, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
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Matsuura H, Arimoto K, Takahashi Y, Kishimoto M. Combination of a multiplex pneumonia panel and Gram staining for antimicrobial selection to treat lower respiratory tract infection. Pneumonia (Nathan) 2024; 16:4. [PMID: 38438932 PMCID: PMC10913398 DOI: 10.1186/s41479-024-00125-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 01/09/2024] [Indexed: 03/06/2024] Open
Abstract
AIM This study aimed to examine the utility of simultaneously performed the Film Array pneumonia panels (pneumonia panels) and Gram staining with the same specimens and evaluate their effect on antimicrobial selection. METHODS This prospective study, conducted from April 2022 to January 2023, enrolled adult patients with pneumonia, including those with ventilator-associated pneumonia (VAP). Specimens obtained at the time of sputum culture were tested using Gram staining and the pneumonia panel. The patients' characteristics and pneumonia panel results were assessed. We also evaluated the selection of antimicrobial agents for drug-resistant bacteria detected by the pneumonia panel. RESULTS This study comprised 39 patients: 25 patients (64.1%) underwent intubation, including 7 (17.9%) patients with VAP. Most tests were performed at the time of admission, while some were performed during hospitalization. Good quality sputum was obtained from intubated patients. The pneumonia panel detected drug-resistant bacteria in 12 cases. Six patients required antimicrobial escalation, while the antimicrobial regimen remained unchanged for 2 patients in whom Pseudomonas aeruginosa was detected and had already received meropenem. The attending physician did not change the antimicrobials, considering the results of Gram staining and the patient's general condition in 4 patients. CONCLUSIONS The pneumonia panel might be useful for detecting drug-resistant organisms at an early stage. It may be important to take the Gram staining results and the patient's condition into account with pneumonia panel for appropriate antibiotic prescription.
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Affiliation(s)
- Hiroshi Matsuura
- Osaka Prefectural Nakakawachi Emergency and Critical Care Center, 3-4-13 Nishiiwata, Higashiosaka, Osaka, 578-0947, Japan.
| | - Koudai Arimoto
- Osaka Prefectural Nakakawachi Emergency and Critical Care Center, 3-4-13 Nishiiwata, Higashiosaka, Osaka, 578-0947, Japan
| | - Yoshihito Takahashi
- Osaka Prefectural Nakakawachi Emergency and Critical Care Center, 3-4-13 Nishiiwata, Higashiosaka, Osaka, 578-0947, Japan
| | - Masafumi Kishimoto
- Osaka Prefectural Nakakawachi Emergency and Critical Care Center, 3-4-13 Nishiiwata, Higashiosaka, Osaka, 578-0947, Japan
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11
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Basu S, Salvi A, Shetty A, Rodrigues C. Being positive may not be perfect. Indian J Med Microbiol 2024; 48:100519. [PMID: 38029841 DOI: 10.1016/j.ijmmb.2023.100519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/12/2023] [Accepted: 11/22/2023] [Indexed: 12/01/2023]
Affiliation(s)
- Shaoli Basu
- Department of Microbiology, P.D. Hinduja Hospital and Medical Research Centre, Mahim, Mumbai, 400016, India.
| | - Asmita Salvi
- Department of Microbiology, P.D. Hinduja Hospital and Medical Research Centre, Mahim, Mumbai, 400016, India.
| | - Anjali Shetty
- Department of Microbiology, P.D. Hinduja Hospital and Medical Research Centre, Mahim, Mumbai, 400016, India.
| | - Camilla Rodrigues
- Department of Microbiology, P.D. Hinduja Hospital and Medical Research Centre, Mahim, Mumbai, 400016, India.
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12
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Guner Ozenen G, Ayhan FY, Kacar P, Gulderen M, Yangin Ergon E, Ergun D, Ozbay T, Bayram A, Ozbakır H, Devrim I. Detection of Pathogens in Cerebrospinal Fluid With the BIOFIRE Blood Culture Identification 2 Panel in Two Neonates With Healthcare-associated Central Nervous System Infections. Pediatr Infect Dis J 2024; 43:e117-e118. [PMID: 38241646 DOI: 10.1097/inf.0000000000004200] [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] [Indexed: 01/21/2024]
Affiliation(s)
- Gizem Guner Ozenen
- Department of Pediatric Infectious Diseases, University of Health Sciences Dr. Behçet Uz Children's Hospital, Izmir, Turkey
| | - Fahri Yuce Ayhan
- Department of Medical Microbiology, University of Health Sciences Dr. Behçet Uz Children's Hospital, Izmir, Turkey
| | - Pelin Kacar
- Department of Pediatric Infectious Diseases, University of Health Sciences Dr. Behçet, Uz Children's Hospital, Izmir, Turkey
| | - Mustafa Gulderen
- Department of Pediatric Infectious Diseases, University of Health Sciences Dr. Behçet Uz Children's Hospital, Izmir, Turkey
| | - Ezgi Yangin Ergon
- Department of Neonatology, University of Health Sciences Dr. Behçet Uz Children's Hospital, Izmir, Turkey
| | - Deniz Ergun
- Department of Pediatric Infectious Diseases, University of Health Sciences Dr. Behçet Uz Children's Hospital, Izmir, Turkey
| | - Tezcan Ozbay
- Department of Neonatology, University of Health Sciences Dr. Behçet Uz Children's Hospital, Izmir, Turkey
| | - Arzu Bayram
- Department of Medical Microbiology, University of Health Sciences Dr. Behçet Uz Children's Hospital, Izmir, Turkey
| | - Hincal Ozbakır
- Department of Pediatric Infectious Diseases, University of Health Sciences Dr. Behçet Uz Children's Hospital, Izmir, Turkey
| | - Ilker Devrim
- Department of Pediatric Infectious Diseases, University of Health Sciences Dr. Behçet Uz Children's Hospital, Izmir, Turkey
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13
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Moerman A, De Waele JJ, Boelens J. An overview of point-of-care testing for infections in critically ill patients. Expert Rev Mol Diagn 2024; 24:193-200. [PMID: 38414348 DOI: 10.1080/14737159.2024.2322146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/19/2024] [Indexed: 02/29/2024]
Abstract
INTRODUCTION Molecular diagnostic systems for point-of-care (POC) testing are nowadays routinely used and are part of many labs. Although often intended for bedside use outside of the microbiology lab, there is still room for expansion. AREAS COVERED This review discusses the two techniques that are currently the most widespread, real-time polymerase-chain reaction (RT-PCR) and loop-mediated isothermal amplification (LAMP). An overview is provided of the various manufacturers and products as well as the evidence and current use in clinical practice. The article further sheds light on some newer techniques, such as CRISPR-based diagnostics and lab-on-a-chip, which are still in development. EXPERT OPINION With many new platforms and techniques still in the pipeline and their potential currently not yet fully exploited, we expect the use of molecular POC testing to increase in the years to come. However, even when used in hospital - in lab, the main advantages of the tests being fast and easy to perform already provide significant benefits in terms of patient outcome.
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Affiliation(s)
- Alena Moerman
- Department of Medical microbiology, Ghent University Hospital, Gent, Belgium
| | - Jan J De Waele
- Department of Critical Care Medicine, Ghent University Hospital, Gent, Belgium
| | - Jerina Boelens
- Department of Medical microbiology, Ghent University Hospital, Gent, Belgium
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14
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Smith RD, Zhan M, Zhang S, Leekha S, Harris A, Doi Y, Evans S, Kristie Johnson J, Ernst RK. Comparison of three rapid diagnostic tests for bloodstream infections using Benefit-risk Evaluation Framework (BED-FRAME). J Clin Microbiol 2024; 62:e0109623. [PMID: 38054730 PMCID: PMC10793330 DOI: 10.1128/jcm.01096-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/20/2023] [Indexed: 12/07/2023] Open
Abstract
Rapid diagnostic tests (RDTs) for bloodstream infections have the potential to reduce time to appropriate antimicrobial therapy and improve patient outcomes. Previously, an in-house, lipid-based, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) method, Fast Lipid Analysis Technique (FLAT MS), has shown promise as a rapid pathogen identification method. In this study, FLAT MS for direct from blood culture identification was evaluated and compared to FDA-cleared identification methods using the Benefit-risk Evaluation Framework (BED-FRAME) analysis. FLAT MS was evaluated and compared to Bruker Sepsityper and bioMérieux BioFire FilmArray BCID2 using results from a previous study. For this study, 301 positive blood cultures were collected from the University of Maryland Medical Center. The RDTs were compared by their sensitivities, time-to-results, hands-on time, and BED-FRAME analysis. The overall sensitivity of all platforms compared to culture results from monomicrobial-positive blood cultures was 88.3%. However, the three RDTs differed in their accuracy for identifying Gram-positive bacteria, Gram-negative bacteria, and yeast. Time-to-results for FLAT MS, Sepsityper, and BioFire BCID2 were all approximately one hour. Hands-on times for FLAT MS, Sepsityper, and BioFire BCID2 were 10 (±1.3), 40 (±2.8), and 5 (±0.25) minutes, respectively. BED-FRAME demonstrated that each RDT had utility at different pathogen prevalence and relative importance. BED-FRAME is a useful tool that can used to determine which RDT is best for a healthcare center.
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Affiliation(s)
- Richard D. Smith
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, Maryland, USA
| | - Min Zhan
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Shanshan Zhang
- Biostatistics Center and the Department of Biostatistics and Bioinformatics, The George Washington University, Washington, D.C., USA
| | - Surbhi Leekha
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Anthony Harris
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Scott Evans
- Biostatistics Center and the Department of Biostatistics and Bioinformatics, The George Washington University, Washington, D.C., USA
| | - J. Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Robert K. Ernst
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, Maryland, USA
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15
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Ku TSN, Al Mohajer M, Newton JA, Wilson MH, Monsees E, Hayden MK, Messacar K, Kisgen JJ, Diekema DJ, Morgan DJ, Sifri CD, Vaughn VM. Improving antimicrobial use through better diagnosis: The relationship between diagnostic stewardship and antimicrobial stewardship. Infect Control Hosp Epidemiol 2023; 44:1901-1908. [PMID: 37665212 DOI: 10.1017/ice.2023.156] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Antimicrobial stewardship programs (ASPs) exist to optimize antibiotic use, reduce selection for antimicrobial-resistant microorganisms, and improve patient outcomes. Rapid and accurate diagnosis is essential to optimal antibiotic use. Because diagnostic testing plays a significant role in diagnosing patients, it has one of the strongest influences on clinician antibiotic prescribing behaviors. Diagnostic stewardship, consequently, has emerged to improve clinician diagnostic testing and test result interpretation. Antimicrobial stewardship and diagnostic stewardship share common goals and are synergistic when used together. Although ASP requires a relationship with clinicians and focuses on person-to-person communication, diagnostic stewardship centers on a relationship with the laboratory and hardwiring testing changes into laboratory processes and the electronic health record. Here, we discuss how diagnostic stewardship can optimize the "Four Moments of Antibiotic Decision Making" created by the Agency for Healthcare Research and Quality and work synergistically with ASPs.
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Affiliation(s)
- Tsun Sheng N Ku
- Billings Clinic, Billings, Montana
- Rocky Vista University Montana College of Osteopathic Medicine, Billings, Montana
| | - Mayar Al Mohajer
- Section of Infectious Diseases, Department of Medicine, Baylor College of Medicine, Houston, Texas
- Infectious Diseases Section, Baylor St. Luke's Medical Center, Houston, Texas
- Infection Prevention, Diagnostic Stewardship and Antibiotic Stewardship, CommonSpirit Health Texas Division, Houston, Texas
| | - James A Newton
- Department of Antibiotic Stewardship, Washington Regional Medical Center, Fayetteville, Arkansas
| | - Marie H Wilson
- Infection Prevention & Control, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Elizabeth Monsees
- Performance Excellence, Children's Mercy Hospital, Kansas City, Missouri
- University of Missouri School of Medicine, Kansas City, Missouri
| | - Mary K Hayden
- Division of Infectious Diseases, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois
| | - Kevin Messacar
- Department of Pediatrics, Section of Infectious Diseases, University of Colorado/Children's Hospital Colorado, Aurora, Colorado
| | | | - Daniel J Diekema
- Division of Infectious Diseases, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, Iowa
- Maine Medical Center, Portland, Maine
| | - Daniel J Morgan
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland
- VA Maryland Healthcare System, Baltimore, Maryland
| | - Costi D Sifri
- University of Virginia School of Medicine, Charlottesville, Virginia
| | - Valerie M Vaughn
- Division of General Internal Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah
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16
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Smith RD, Johnson JK, Ernst RK. Comparison of 3 diagnostic platforms for identification of bacteria and yeast from positive blood culture bottles. Diagn Microbiol Infect Dis 2023; 107:116018. [PMID: 37478505 DOI: 10.1016/j.diagmicrobio.2023.116018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/26/2023] [Accepted: 07/03/2023] [Indexed: 07/23/2023]
Abstract
Managing bloodstream infections requires fast and accurate diagnostics. Culture-based diagnostic methods for identification from positive blood culture require 24-hour subculture, potentially delaying time to appropriate therapy. Positive blood cultures were collected (n = 301) from September 2021 to August 2022 at the University of Maryland Medical Center. Platforms compared were BioFire® BCID2, Sepsityper®, and short-term culture. For monomicrobial cultures, FilmArray® BCID2 identified 88.3% (241/273) of pathogens. Rapid Sepsityper® identified 76.9% (210/273) of pathogens. Sepsityper® extraction identified 82.4% (225/273) of pathogens. Short-term culture identified 83.5% (228/273) of pathogens. For polymicrobial cultures, Sepsityper®, short-term culture, and BioFire® BCID2 had complete identifications at 10.7% (3/28), 0%, and 92.9% (26/28), respectively. Time-to-results for Rapid Sepsityper®, Sepsityper® extraction, BioFire® BCID2, and Short-term culture were 35, 52, 65, and 306 minutes, respectively. Performance of these platforms can reduce time-to-results and may help effectively treat bloodstream infections faster. Accuracy, time-to-result, and hands-on time are important factors when evaluation diagnostic platforms.
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Affiliation(s)
- Richard D Smith
- Department of Pathology, School of Medicine, University of Maryland, Baltimore, MD, USA; Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, USA.
| | - J Kristie Johnson
- Department of Pathology, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Robert K Ernst
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, USA
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17
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Ikhimiukor OO, Souza SSR, Akintayo IJ, Marcovici MM, Workman A, Martin IW, Andam CP. Phylogenetic lineages and antimicrobial resistance determinants of clinical Klebsiella oxytoca spanning local to global scales. Microbiol Spectr 2023; 11:e0054923. [PMID: 37676032 PMCID: PMC10581156 DOI: 10.1128/spectrum.00549-23] [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: 02/04/2023] [Accepted: 07/19/2023] [Indexed: 09/08/2023] Open
Abstract
Klebsiella oxytoca is an opportunistic pathogen causing serious nosocomial infections. Knowledge about the population structure and diversity of healthcare-associated K. oxytoca from a genomic standpoint remains limited. Here, we characterized the phylogenetic relationships and genomic characteristics of 20 K. oxytoca sensu stricto isolates recovered from bloodstream infections at the Dartmouth-Hitchcock Medical Center, New Hampshire, USA from 2017 to 2021. Results revealed a diverse population consisting of 15 sequence types (STs) that together harbored 10 variants of the intrinsic beta-lactamase gene bla OXY-2, conferring resistance to penicillins. Similar sets of antimicrobial resistance (AMR) determinants reside in multiple distinct lineages, with no one lineage dominating the local population. To place the New Hampshire K. oxytoca in a broader context, we compared them to 304 publicly available genomes of clinical isolates from 18 countries. This global clinical K. oxytoca sensu stricto population is represented by over 65 STs that together harbored resistance genes against 14 antimicrobial classes, including eight bla OXY-2 variants. Three dominant STs in the global population (ST2, ST176, ST199) circulate across multiple countries and were also present in the New Hampshire population. The global K. oxytoca population is genetically diverse, but there is evidence for broad dissemination of a few lineages carrying distinct set of AMR determinants. Our findings reveal the clinical diversity of K. oxytoca sensu stricto and its importance in surveillance efforts aimed at monitoring the evolution of this drug-resistant nosocomial pathogen. IMPORTANCE The opportunistic pathogen Klebsiella oxytoca has been increasingly implicated in patient morbidity and mortality worldwide, including several outbreaks in healthcare settings. The emergence and spread of antimicrobial resistant strains exacerbate the disease burden caused by this species. Our study showed that clinical K. oxytoca sensu stricto is phylogenetically diverse, harboring various antimicrobial resistance determinants and bla OXY-2 variants. Understanding the genomic and population structure of K. oxytoca is important for international initiatives and local epidemiological efforts for surveillance and control of drug-resistant K. oxytoca.
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Affiliation(s)
- Odion O. Ikhimiukor
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Stephanie S. R. Souza
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Ifeoluwa J. Akintayo
- Institute for Infection Prevention and Hospital Epidemiology, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Michael M. Marcovici
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Adrienne Workman
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Isabella W. Martin
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Cheryl P. Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
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18
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Giannella M, Rinaldi M, Viale P. Antimicrobial Resistance in Organ Transplant Recipients. Infect Dis Clin North Am 2023; 37:515-537. [PMID: 37244806 DOI: 10.1016/j.idc.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The overall burden of the main clinically relevant bacterial multidrug-resistant organisms (MDROs) (eg, methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, extended-spectrum β-lactamase producing or extended-spectrum cephalosporin-resistant Enterobacterales, carbapenem-resistant or carbapenemase-producing Enterobacterales, MDR Pseudomonas aeruginosa, and carbapenem-resistant Acinetobacter baumannii) in solid organ transplant (SOT) populations is summarized showing prevalence/incidence, risk factors, and impact on graft/patient outcome according to the type of SOT. The role of such bacteria in donor-derived infections is also reviewed. As for the management, the main prevention strategies and treatment options are discussed. Finally, nonantibiotic-based strategies are considered as future directions for the management of MDRO in SOT setting.
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Affiliation(s)
- Maddalena Giannella
- Infectious Diseases, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy; Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Via Massarenti 11, Bologna 40137, Italy.
| | - Matteo Rinaldi
- Infectious Diseases, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy; Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Via Massarenti 11, Bologna 40137, Italy
| | - Pierluigi Viale
- Infectious Diseases, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy; Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Via Massarenti 11, Bologna 40137, Italy
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19
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Berinson B, Spenke L, Krivec L, Tanida K, Both A, Keller J, Rolvien T, Christner M, Lütgehetmann M, Aepfelbacher M, Klatte TO, Rohde H. Performance and Hypothetical Impact on Joint Infection Management of the BioFire Joint Infection Panel: a Retrospective Analysis. J Clin Microbiol 2023; 61:e0059223. [PMID: 37439678 PMCID: PMC10446873 DOI: 10.1128/jcm.00592-23] [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: 05/08/2023] [Accepted: 06/28/2023] [Indexed: 07/14/2023] Open
Abstract
Pathogen identification is key in septic arthritis. Culture-based techniques are challenging, especially when patients have been pretreated with antibiotics or when difficult-to-culture bacteria are encountered. The BioFire joint infection assay (BJA) is a multiplex PCR panel which detects 31 of the most prevalent bacterial and fungal pathogens causing septic arthritis. Here, 123 cryoconserved contemporary synovial fluid samples from 120 patients underwent BJA analysis. Results were compared to those of culture-based diagnostics (standard of care [SOC]). Clinical data were collected, and the possible impact of the molecular diagnostic application on patient management was evaluated. Fifteen of 123 synovial fluid cultures grew bacterial pathogens. All on-panel pathogens (9/15) were correctly identified by the BJA. The BJA identified four additional bacterial pathogens in four SOC-negative cases. BJA sensitivity and specificity were 100% (95% confidence interval [CI], 69.2% to 100%) and 100% (95% CI, 96.8% to 100%), respectively. Compared to the SOC, the BJA would have resulted in faster provision of species identification and molecular susceptibility data by 49 h and 99 h, respectively. Clinical data analysis indicates that in BJA-positive cases, faster species ID could have led to timelier optimization of antibiotic therapy. This retrospective study demonstrates high sensitivity and specificity of the BJA to detect on-panel organisms in bacterial arthritis. The usefulness of the BJA in prosthetic-joint infections is limited, as important pathogens (i.e., coagulase negative staphylococci and Cutibacterium acnes) are not covered. Evidence from patient data analysis suggests that the assay might prove valuable for optimizing patient management in acute arthritis related to fastidious organisms or for patients who received antibiotics prior to specimen collection.
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Affiliation(s)
- Benjamin Berinson
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Laura Spenke
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lukas Krivec
- Department of Trauma and Orthopaedic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Konstantin Tanida
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Both
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Johannes Keller
- Department of Trauma and Orthopaedic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tim Rolvien
- Department of Trauma and Orthopaedic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Christner
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marc Lütgehetmann
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Aepfelbacher
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Till Orla Klatte
- Department of Trauma and Orthopaedic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Holger Rohde
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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20
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Lapin JS, Smith RD, Hornback KM, Johnson JK, Claeys KC. From bottle to bedside: Implementation considerations and antimicrobial stewardship considerations for bloodstream infection rapid diagnostic testing. Pharmacotherapy 2023; 43:847-863. [PMID: 37158053 DOI: 10.1002/phar.2813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 05/10/2023]
Abstract
Antimicrobial stewardship (AMS) programs have been quick to adopt novel molecular rapid diagnostic technologies (mRDTs) for bloodstream infections (BSIs) to improve antimicrobial management. As such, most of the literature demonstrating the clinical and economic benefits of mRDTs for BSI is in the presence of active AMS intervention. Leveraging mRDTs to improve antimicrobial therapy for BSI is increasingly integral to AMS program activities. This narrative review discusses available and future mRDTs, the relationship between the clinical microbiology laboratory and AMS programs, and practical considerations for optimizing the use of these tools within a health system. Antimicrobial stewardship programs must work closely with their clinical microbiology laboratories to ensure that mRDTs are used to their fullest benefit while remaining cognizant of their limitations. As more mRDT instruments and panels become available and AMS programs continue to expand, future efforts must consider the expansion beyond traditional settings of large academic medical centers and how combinations of tools can further improve patient care.
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Affiliation(s)
- Jonathan S Lapin
- Department of Pharmacy Practice, University of Maryland Medical Center, Baltimore, Maryland, USA
| | - Richard D Smith
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Krutika M Hornback
- Department of Pharmacy Practice, Medical University of South Carolina (MUSC) Health, Charleston, South Carolina, USA
| | - J Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kimberly C Claeys
- Department of Pharmacy Science and Health Outcomes Research, University of Maryland School of Pharmacy, Baltimore, Maryland, USA
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21
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Mauri C, Consonni A, Briozzo E, Giubbi C, Meroni E, Tonolo S, Luzzaro F. Microbiological Assessment of the FilmArray Blood Culture Identification 2 Panel: Potential Impact in Critically Ill Patients. Antibiotics (Basel) 2023; 12:1247. [PMID: 37627667 PMCID: PMC10451250 DOI: 10.3390/antibiotics12081247] [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: 06/30/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Rapid pathogen detection and characterization from positive blood cultures are crucial in the management of patients with bloodstream infections (BSI) and in achieving their improved outcomes. In this context, the FilmArray Blood Culture Identification (BCID2) panel is an FDA approved molecular test, which can quickly identify different species and resistance determinants, thus making an impact in antimicrobial practice. In this study, we analyzed 136 positive blood cultures collected from septic critically ill patients from April 2021 to March 2023 by using the FilmArray BCID2 panel, and results obtained by fast molecular analysis were compared to those obtained by routine protocols. Overall, the BCID2 panel showed a strong concordance with conventional methods, particularly in the case of monomicrobial samples, whereas some discrepancies were found in 10/32 polymicrobial samples. Of note, this technique allowed us to identify a significant number of yeasts (37/94 samples) and to unravel the presence of several resistance markers, including both Gram-positive and Gram-negative organisms. These findings strongly support the potential use of the BCID2 panel as an adjunct to the conventional microbiology methods for the management of critically ill septic patients, thus accelerating blood pathogen and resistance genes identification, focusing antibiotic therapy, and avoiding inappropriate and excessive use of drugs.
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Affiliation(s)
- Carola Mauri
- Clinical Microbiology and Virology Unit, “A. Manzoni” Hospital, 23900 Lecco, Italy
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22
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Senok A, Dabal LA, Alfaresi M, Habous M, Celiloglu H, Bashiri S, Almaazmi N, Ahmed H, Mohmed AA, Bahaaldin O, Elimam MAE, Rizvi IH, Olowoyeye V, Powell M, Salama B. Clinical Impact of the BIOFIRE Blood Culture Identification 2 Panel in Adult Patients with Bloodstream Infection: A Multicentre Observational Study in the United Arab Emirates. Diagnostics (Basel) 2023; 13:2433. [PMID: 37510177 PMCID: PMC10378530 DOI: 10.3390/diagnostics13142433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/10/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Rapid pathogen identification is key to the proper management of patients with bloodstream infections (BSIs), especially in the intensive care setting. This multicentre study compared the time to pathogen identification results in 185 patients admitted to intensive care with a confirmed BSI, using conventional methods (n = 99 patients) and upon implementation of the BIOFIRE® Blood Culture Identification 2 (BCID2) Panel, a rapid molecular test allowing for the simultaneous identification of 43 BSI-related nucleic acids targets (n = 86 patients). The median time to result informing optimal antibiotic therapy was significantly shorter following the implementation of the BCID2 Panel (92 vs. 28 h pre vs. post BCID2 implementation; p < 0.0001). BCID2 usage in addition to conventional methods led to the identification of at least one pathogen in 98.8% patients vs. 87.9% using conventional methods alone (p = 0.003) and was associated with a lower 30-day mortality (17.3% vs. 31.6%, respectively; p = 0.019). This study at three intensive care units in the United Arab Emirates therefore demonstrates that, in addition to conventional microbiological methods and an effective antimicrobial stewardship program, the BCID2 Panel could improve the clinical outcome of patients admitted to the intensive care unit with a confirmed BSI.
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Affiliation(s)
- Abiola Senok
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai P.O. Box 505055, United Arab Emirates
| | - Laila Al Dabal
- Infectious Diseases Unit, Rashid Hospital, Dubai P.O. Box 4545, United Arab Emirates
| | - Mubarak Alfaresi
- Pathology and Laboratory Medicine, Zayed Military Hospital, Abu Dhabi P.O. Box 72763, United Arab Emirates
| | - Maya Habous
- Microbiology and Infection Control Unit, Pathology Department, Rashid Hospital, Dubai P.O. Box 4545, United Arab Emirates
| | - Handan Celiloglu
- Microbiology Department, Mediclinic City Hospital, Dubai Healthcare City, Dubai P.O. Box 505004, United Arab Emirates
| | - Safia Bashiri
- Infectious Diseases Unit, Rashid Hospital, Dubai P.O. Box 4545, United Arab Emirates
| | - Naama Almaazmi
- Infectious Diseases Unit, Rashid Hospital, Dubai P.O. Box 4545, United Arab Emirates
| | - Hassan Ahmed
- Infectious Diseases Unit, Rashid Hospital, Dubai P.O. Box 4545, United Arab Emirates
| | - Ayman A Mohmed
- Intensive Care Unit, Sheikh Khalifa General Hospital, Umm Al Quwain P.O. Box 499, United Arab Emirates
| | - Omar Bahaaldin
- Microbiology and Infection Control Unit, Pathology Department, Rashid Hospital, Dubai P.O. Box 4545, United Arab Emirates
| | - Maimona Ahmed Elsiddig Elimam
- Microbiology and Infection Control Unit, Pathology Department, Rashid Hospital, Dubai P.O. Box 4545, United Arab Emirates
| | - Irfan Hussain Rizvi
- Microbiology Department, Mediclinic City Hospital, Dubai Healthcare City, Dubai P.O. Box 505004, United Arab Emirates
| | - Victory Olowoyeye
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai P.O. Box 505055, United Arab Emirates
| | - Michaela Powell
- Data Science Department, bioMérieux Inc., Salt Lake City, UT 84108, USA
| | - Basel Salama
- Medical Affairs, bioMérieux, Dubai P.O. Box 505201, United Arab Emirates
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23
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Andrei AI, Tălăpan D, Rafila A, Popescu GA. Influence of Multiplex PCR in the Management of Antibiotic Treatment in Patients with Bacteremia. Antibiotics (Basel) 2023; 12:1038. [PMID: 37370357 PMCID: PMC10295051 DOI: 10.3390/antibiotics12061038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
The multiplex PCR assay can be a helpful diagnostic tool for patients with bacteremia. Herein, we assessed the impact of a Blood Culture Identification Panel (BCID) on both the diagnosis and treatment of patients with bacteremia. We performed a retrospective study using laboratory and clinical data to evaluate the impact of syndromic testing using a multiplex PCR testing system (BioFire® FilmArray) for the management of patients with bloodstream infections. BCID detected the pathogen in 102 (87.9%) samples out of the 116 positive blood cultures tested. The average time from the blood culture collection to the communication of the molecular test result was 23.93 h (range: 10.67-69.27 h). The main pathogen detected was Klebsiella pneumoniae (17.6%). The antimicrobial therapy was changed in accordance with the BCID results in 28 (40.6%) out of the 69 cases, wherein the treatment could have been theoretically adjusted. This allowed the adjustment of the therapy to be performed 1305.1 h faster than it would have been possible if conventional diagnostic methods had been used; this was the case for only 35.1% of the time gained if treatment was adjusted for all patients with positive BCID. Thus, although molecular tests can make a difference in the management of bloodstream infections, there is room for improvement in the clinical application of BCID results.
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Affiliation(s)
- Alina-Ioana Andrei
- Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- “Prof. Dr. Matei Balș” National Institute of Infectious Diseases, 021105 Bucharest, Romania
| | - Daniela Tălăpan
- Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- “Prof. Dr. Matei Balș” National Institute of Infectious Diseases, 021105 Bucharest, Romania
| | - Alexandru Rafila
- Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- “Prof. Dr. Matei Balș” National Institute of Infectious Diseases, 021105 Bucharest, Romania
| | - Gabriel Adrian Popescu
- Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- “Prof. Dr. Matei Balș” National Institute of Infectious Diseases, 021105 Bucharest, Romania
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24
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Hirai J, Mori N, Sakanashi D, Morishita Y, Kuge Y, Kishino T, Asai N, Hagihara M, Takahashi N, Mikamo H. Usefulness of the FilmArray blood culture identification panel for identifying causative pathogens of bone and joint infections. J Infect Chemother 2023; 29:722-725. [PMID: 37088145 DOI: 10.1016/j.jiac.2023.04.011] [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] [Revised: 03/24/2023] [Accepted: 04/17/2023] [Indexed: 04/25/2023]
Abstract
As bone and joint infections (BJIs) require long-term treatment, identifying their causative pathogens is vital. However, the detection rate of conventional culturing remains inadequate. This study aimed to evaluate the usefulness of the FilmArray blood culture identification (BCID) panel for identifying causative pathogens in patients with BJIs. We tested a BCID panel using collected samples, in addition to conventional cultures. The primary outcome was to evaluate the diagnostic performance of the BCID panel, calculated using conventional culturing methods. A total of 44 patients who underwent BJI-related specimen collection were enrolled. Of the 44 patients, 22 were diagnosed with a BJI. Conventional culture identified 15 of 22 organisms (68.2%), whereas the BCID panel identified 14 of 22 organisms (63.4%). The overall sensitivity and specificity of the BCID panel were 73.3% and 57.1%, respectively, compared to those of the conventional culture. However, the sensitivity reached 100% when only pathogens included in the BCID panel were considered. In seven culture-negative cases, the BCID panel identified three organisms (42.9%). The BCID panel also indicated the appropriate therapy against a BJI caused by methicillin-resistant Staphylococcus aureus by detecting the mecA gene. This study demonstrated that the BCID panel has the potential for early and accurate diagnosis of the causative organism of BJI using specimens such as joint fluid and bone tissue. Our results suggest that BCID panels, in addition to routine culture, may improve our ability to diagnose the causative microorganisms of BJI in clinical practice, thereby contributing to the selection of appropriate antimicrobial agents.
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Affiliation(s)
- Jun Hirai
- Department of Clinical Infectious Diseases, Aichi Medical University Hospital, Aichi, Japan; Department of Infection Control and Prevention, Aichi Medical University Hospital, Aichi, Japan.
| | - Nobuaki Mori
- Department of Clinical Infectious Diseases, Aichi Medical University Hospital, Aichi, Japan; Department of Infection Control and Prevention, Aichi Medical University Hospital, Aichi, Japan
| | - Daisuke Sakanashi
- Department of Infection Control and Prevention, Aichi Medical University Hospital, Aichi, Japan
| | - Yusuke Morishita
- Department of Orthopedic Surgery, Aichi Medical University, Aichi, Japan
| | - Yuji Kuge
- Department of Emergency and Critical Care Medicine, Aichi Medical University Hospital, Nagakute, Aichi, Japan
| | - Takaaki Kishino
- Department of Emergency and Critical Care Medicine, Aichi Medical University Hospital, Nagakute, Aichi, Japan
| | - Nobuhiro Asai
- Department of Clinical Infectious Diseases, Aichi Medical University Hospital, Aichi, Japan; Department of Infection Control and Prevention, Aichi Medical University Hospital, Aichi, Japan
| | - Mao Hagihara
- Department of Molecular Epidemiology and Biomedical Sciences, Aichi Medical University Hospital, Aichi, Japan
| | - Nobunori Takahashi
- Department of Orthopedic Surgery, Aichi Medical University, Aichi, Japan
| | - Hiroshige Mikamo
- Department of Clinical Infectious Diseases, Aichi Medical University Hospital, Aichi, Japan; Department of Infection Control and Prevention, Aichi Medical University Hospital, Aichi, Japan
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25
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Prasetyo DS, Karyanti MR, Yuniar I, Saharman YR, Holiwono L. Application of a sepsis flow chip (SFC) assay for the molecular diagnosis of paediatric sepsis. Access Microbiol 2023; 5:000474.v4. [PMID: 37223064 PMCID: PMC10202402 DOI: 10.1099/acmi.0.000474.v4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 02/06/2023] [Indexed: 05/25/2023] Open
Abstract
A delay in detecting sepsis pathogens is a problematic issue for determining definitive antibiotic therapy for the causative pathogens. The gold standard method for sepsis is blood culture but this requires 3 days to detect the definitive pathogen. Molecular methods offer rapid identification of pathogens. We evaluated the use of sepsis flow chip (SFC) assay for identifying pathogens from children with sepsis. Blood samples from children with sepsis were collected and incubated in a culture device. Positive samples were subjected to amplification-hybridization using SFC assay and culture. A total of 94 samples from 47 patients were recovered, from which 25 isolates were recovered, including Klebsiella pneumoniae (11) and Staphylococcus epidermidis (6). From 25 positive blood culture bottles subjected to SFC assay, 24 genus/species and 18 resistance genes were detected. The sensitivity, specificity and conformity was 80, 94.2 and 94.68 % respectively. SFC assay offers promise to identify pathogens from positive blood culture in paediatric patients with sepsis and may support the antimicrobial stewardship programme in hospitals.
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Affiliation(s)
- Dimas Seto Prasetyo
- Clinical Microbiology Medical Staff, Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
- Department of Microbiology Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Mulya Rahma Karyanti
- Pediatric Child Health Medical Staff, Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
- Department of Child Health Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Irene Yuniar
- Pediatric Child Health Medical Staff, Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
- Department of Child Health Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Yulia Rosa Saharman
- Clinical Microbiology Medical Staff, Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
- Department of Microbiology Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Livya Holiwono
- Clinical Microbiology Medical Staff, Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
- Department of Microbiology Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
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26
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Large-Scale Clinical Evaluation of Rapid Blood Culture Identification Panels for Bloodstream Infections at a Tertiary Hospital. Diagnostics (Basel) 2023; 13:diagnostics13061177. [PMID: 36980485 PMCID: PMC10047266 DOI: 10.3390/diagnostics13061177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/22/2023] Open
Abstract
The prompt implementation of optimal antibacterial therapy through the rapid identification of the causative organisms is essential for improving outcomes for critically ill patients with bloodstream infections. We evaluated the clinical performance of the FilmArray blood culture identification (BCID) panel for rapidly identifying causative pathogens in the bloodstream using large-scale clinical samples. We analyzed the results of identification using a BCID panel performed on 2005 positive blood culture bottles from September 2019 to June 2022. Pathogen detection efficiency and interval from Gram staining to identification using the BCID panel were compared to those of conventional identification systems—VITEK MS MALDI-TOF Mass Spectrometer and Vitek2—and antibiotic susceptibility testing—Vitek2. We detected 2167 isolates from 2005 positive blood culture bottles. In these isolates, the BCID panel showed 93% full agreement—both organisms and antimicrobial resistance genes were matched, and no off-target organisms were detected. Species-level discordance was found in 0.6% of tests. Sixty-five isolates (3.0%) were only detected by BCID, whereas 22 isolates (1.0%) from the on-target panel were not detected by BCID. This large-scale study demonstrated that the BCID panel was a reliable and rapid identification method for directly identifying bloodstream pathogens in a positive blood culture.
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27
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Evaluation of the performance of GeneSoC®, a novel rapid real-time PCR system, to detect Staphylococcus aureus and methicillin resistance in blood cultures. J Infect Chemother 2023; 29:718-721. [PMID: 36921762 DOI: 10.1016/j.jiac.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/05/2023] [Accepted: 03/08/2023] [Indexed: 03/16/2023]
Abstract
Staphylococcus aureus bacteremia results in substantial mortality. Rapid identification and the determination of methicillin susceptibility are crucial for immediate treatment with appropriate antibiotics. In the present study, we aimed to evaluate the basic assay performance of GeneSoC®, a novel rapid quantitative polymerase chain reaction (qPCR) method, for the detection of methicillin-susceptible (MS) or -resistant (MR) S. aureus in blood culture (BC) bottles. qPCR pimers and probes were desinged for femA and mecA genes to diagnose S. aureus and its methicilline-resistance status. GeneSoC® system can detect target genes within 12 min per sample using microfludic thermal cycling. A total of 100 BC-positive samples, showing clusters of gram-positive cocci using microscopy, were tested. The analytical sensitivity was demonstrated for the target sequence of femA and mecA genes at 10 copies/μL, respectively. The detection limit of the MRSA bacterial burden using this system was 104 and 103 CFU/mL for femA and mecA, respectively. Compared with culture-based identification and susceptibility testing, the sensitivity and specificity for the detection of femA (+)/mecA (+) MRSA using GeneSoC® were 90.9 and 98.9%, respectively, whereas the sensitivity and specificity for detection of femA (+)/mecA (-) MSSA were 96.2% and 97.3%, respectively. In conclusion, although this was a small sample and pilot study, the GeneSoC® system is beneficial for rapid, reliable, and highly sensitive real-time testing of MRSA and MSSA in BC bottles.
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28
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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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29
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Donnars A, Mahieu R, Declerck C, Chenouard R, Lemarié C, Pailhoriès H, Requin J, Kempf M, Eveillard M. BIOFIRE® Blood Culture IDentification 2 (BCID2) panel for early adaptation of antimicrobial therapy in adult patients with bloodstream infections: a real-life experience. Diagn Microbiol Infect Dis 2023; 105:115858. [PMID: 36442386 DOI: 10.1016/j.diagmicrobio.2022.115858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/24/2022] [Accepted: 11/05/2022] [Indexed: 11/13/2022]
Abstract
Our objective was to assess the effectiveness of a multiplex PCR panel for blood culture identification (BCID2) on the implementation of appropriate antimicrobial therapy. We conducted a monocentric pre/post study comparing the time to result from direct microscopic examination (DE) to bacterial identification (BI) in positive blood cultures between 2 different periods: P1 without BCID2 and P2 with BCID2. Appropriate treatments prescribed before DE and after DE / BCID2 and after BI / BCID2 were compared using direct proportion comparison and survival analysis. For mono-microbial bloodstream infections, the proportion of appropriate antimicrobial treatment after DE was 50% in P1 vs. 87.5% after BCID2 in P2 (P < 0.001) for Gram-negative bacteria and 33.0% in P1 vs. 64.4% in P2 (P < 0.01) for Gram-positive bacteria. A significant difference (P = 0.04) was recorded with survival curves for Gram positive bacteria. BCID2 seems effective in reducing the time for prescribing appropriate antimicrobials.
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Affiliation(s)
- Anne Donnars
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France
| | - Rafael Mahieu
- Service des Maladies Infectieuses et Tropicales, CHU Angers, Angers, France; Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, INCIT, Angers, France
| | - Charles Declerck
- Service des Maladies Infectieuses et Tropicales, CHU Angers, Angers, France
| | - Rachel Chenouard
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France
| | - Carole Lemarié
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France
| | - Hélène Pailhoriès
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France
| | - Jim Requin
- Service des Maladies Infectieuses et Tropicales, CHU Angers, Angers, France
| | - Marie Kempf
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France; Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, INCIT, Angers, France
| | - Matthieu Eveillard
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France; Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, INCIT, Angers, France.
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30
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Kilic A, Palavecino E. Evaluation of the combined use of the Sepsityper Kit with the Clearview PBP2a assay for identification of staphylococci strains and detection of their methicillin resistance directly from positive blood culture bottles. J Med Microbiol 2023; 72. [PMID: 36762528 DOI: 10.1099/jmm.0.001667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Affiliation(s)
- Abdullah Kilic
- Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC, USA
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31
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Whole-Genome Sequence of a Clinical Enterococcus gallinarum Strain in a Positive Hemoculture from Siriraj Hospital, Thailand. Microbiol Resour Announc 2022; 11:e0060522. [PMID: 36318019 PMCID: PMC9753668 DOI: 10.1128/mra.00605-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Enterococcus gallinarum is a rare causative agent of hospital-acquired bacteremia. Here, we reported the complete genome of E. gallinarum strain WKB01, which was directly isolated from a positive hemoculture in Siriraj Hospital, Thailand. Comprehensive analysis demonstrated the clinically relevant tetM gene presenting in its genome.
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32
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Lin HH, Tseng KH, Tien N, Lin YT, Yu J, Hsueh PR, Cho DY. Evaluation of the Rapid Sepsityper protocol and specific MBT-Sepsityper module for the identification of bacteremia and fungemia using Bruker Biotyper MALDI-TOF MS. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:1330-1333. [PMID: 35981943 DOI: 10.1016/j.jmii.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 12/27/2022]
Abstract
The rapid identification method, the Rapid Sepsityper protocol with a specific MBT-Sepsityper module (Bruker Daltonics), based on the MALDI Biotyper platform, accurately identified 93.5% (116/124) of microorganisms at the species level in the 124 flagged blood culture samples from patients with monomicrobial bloodstream infections. Gram-negative bacilli (95.6%, 43/45) had a higher identification rate than Gram-positive cocci (93.3%, 70/75) and yeasts (75%, 3/4). The Rapid Sepsityper protocol displayed poor identification performance for polymicrobial samples.
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Affiliation(s)
- Hsiu-Hsien Lin
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Kun-Hao Tseng
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Ni Tien
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan; Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Yu-Tzu Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Jiaxin Yu
- AI Innovation Center, China Medical University Hospital, Taichung, Taiwan
| | - Po-Ren Hsueh
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan; Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan; School of Medicine, China Medical University, Taichung, Taiwan.
| | - Der-Yang Cho
- Department of Neurosurgery, China Medical University Hospital, Taichung, Taiwan
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Sepsityper ® Kit versus In-House Method in Rapid Identification of Bacteria from Positive Blood Cultures by MALDI-TOF Mass Spectrometry. Life (Basel) 2022; 12:life12111744. [PMID: 36362899 PMCID: PMC9693840 DOI: 10.3390/life12111744] [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: 10/12/2022] [Revised: 10/24/2022] [Accepted: 10/28/2022] [Indexed: 11/16/2022] Open
Abstract
In order to further accelerate pathogen identification from positive blood cultures (BC), various sample preparation protocols to identify bacteria with MALDI-TOF MS directly from positive BCs have been developed. We evaluated an in-house method in comparison to the Sepsityper® Kit (Bruker Daltonics, Bremen, Germany) as well as the benefit of an on-plate formic acid extraction step following positive signal by the BACTECTM FX system. Confirmation of identification was achieved using subcultured growing biomass used for MALDI-TOF MS analysis. A total of 113 monomicrobial positive BCs were analyzed. The rates of Gram-positive bacteria correctly identified to the genus level using in-house method and Sepsityper® Kit were 63.3% (38/60) and 81.7% (49/60), respectively (p = 0.025). Identification rates at species level for Gram-positive bacteria with in-house method and Sepsityper® kit were 30.0% (18/60) and 66.7% (40/60), respectively (p < 0.001). Identification rates of Gram-negative bacteria were similar with the in-house method and Sepsityper® Kit. Additional on-plate formic acid extraction demonstrated significant improvement in the identification rate of Gram-positive bacteria at both genus and species level for both in-house (p = 0.001, p < 0.001) and Sepsityper® Kit methods (p = 0.007, p < 0.001). Our in-house method is a candidate for laboratory routines with Sepsityper® Kit as a back-up solution when identification of Gram-positive bacteria is unsuccessful.
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Peri AM, Ling W, Furuya-Kanamori L, Harris PNA, Paterson DL. Performance of BioFire Blood Culture Identification 2 Panel (BCID2) for the detection of bloodstream pathogens and their associated resistance markers: a systematic review and meta-analysis of diagnostic test accuracy studies. BMC Infect Dis 2022; 22:794. [PMID: 36266641 PMCID: PMC9585790 DOI: 10.1186/s12879-022-07772-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 10/09/2022] [Indexed: 11/10/2022] Open
Abstract
Background Early identification of bloodstream pathogens and their associated antimicrobial resistance may shorten time to optimal therapy in patients with sepsis. The BioFire Blood Culture Identification 2 Panel (BCID2) is a novel multiplex PCR detecting 43 targets directly from positive blood cultures, reducing turnaround times.
Methods We have performed a systematic review and meta-analysis of diagnostic test accuracy studies to assess the BCID2 performance for pathogen identification and resistance markers detection compared to gold standard culture-based methods (including phenotypic and/or genotypic characterization). Results Nine studies were identified reporting data to build 2 × 2 tables for each BCID2 target, including 2005 blood cultures. The pooled specificity of the assay was excellent (> 97%) across most subgroups of targets investigated, with a slightly broader confidence interval for S. epidermidis (98.1%, 95% CI 93.1 to 99.5). Pooled sensitivity was also high for the major determinants of bloodstream infection, including Enterobacterales (98.2%, 95% CI 96.3 to 99.1), S. aureus (96.0%, 95% CI 90.4 to 98.4), Streptococcus spp. (96.7%, 95% CI 92.8 to 98.5), P. aeruginosa (92.7%, 95% CI 83.1 to 97.0), E. faecalis (92.3%, 95% CI 83.5 to 96.6), as well as blaCTX-M (94.9, 95% CI 85.7 to 98.3), carbapenemases (94.9%, 95% CI 83.4 to 98.6) and mecA/C & MREJ (93.9%, 95% CI 83.0 to 98.0). Sensitivity for less common targets was slightly lower, possibly due to their under-representation in the included studies. Conclusions BCID2 showed good performance for detecting major determinants of bloodstream infection and could support early antimicrobial treatment, especially for ESBL or carbapenemase-producing Gram-negative bacilli and methicillin-resistant S. aureus. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07772-x.
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Affiliation(s)
- Anna Maria Peri
- University of Queensland Centre for Clinical Research, Herston, QLD, 4029, Australia.
| | - Weiping Ling
- University of Queensland Centre for Clinical Research, Herston, QLD, 4029, Australia
| | - Luis Furuya-Kanamori
- University of Queensland Centre for Clinical Research, Herston, QLD, 4029, Australia
| | - Patrick N A Harris
- University of Queensland Centre for Clinical Research, Herston, QLD, 4029, Australia.,Central Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, 4029, Australia
| | - David L Paterson
- University of Queensland Centre for Clinical Research, Herston, QLD, 4029, Australia.,Infectious Diseases Unit, Royal Brisbane and Women's Hospital, Herston, QLD, 4029, Australia
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35
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False Negative Escherichia coli Result from the BioFire FilmArray Blood Culture Identification 2 Panel. J Clin Microbiol 2022; 60:e0233921. [PMID: 36214564 PMCID: PMC9667767 DOI: 10.1128/jcm.02339-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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36
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García-Rivera C, Parra-Grande M, Merino E, Boix V, Rodríguez JC. Concordance of the Filmarray Blood Culture Identification Panel 2 and classical microbiological methods in a bacteriemia diagnostic unit. Diagn Microbiol Infect Dis 2022; 104:115787. [DOI: 10.1016/j.diagmicrobio.2022.115787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/20/2022] [Accepted: 08/06/2022] [Indexed: 11/24/2022]
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Peri AM, Bauer MJ, Bergh H, Butkiewicz D, Paterson DL, Harris PN. Performance of the BioFire Blood Culture Identification 2 panel for the diagnosis of bloodstream infections. Heliyon 2022; 8:e09983. [PMID: 35874050 PMCID: PMC9304729 DOI: 10.1016/j.heliyon.2022.e09983] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 03/01/2022] [Accepted: 07/13/2022] [Indexed: 01/09/2023] Open
Abstract
Background Conventional blood cultures methods are associated with long turnaround times, preventing early treatment optimization in bloodstream infections. The BioFire Blood Culture Identification 2 (BCID2) Panel is a new multiplex PCR applied on positive blood cultures, reducing time to pathogen identification and resistant markers detection. Methods We conducted a prospective observational study including positive blood cultures from Intensive Care Units and Emergency Departments and performed BCID2 in addition to conventional testing. Concordance between the two methods was assessed and BCID2 performance characteristics were evaluated. Resistance markers detected by BCID2 were confirmed by in-house PCR. Whole genome sequencing was performed in discordant cases. Results Among 60 monomicrobial blood cultures, BCID2 correctly identified 55/56 (91.7%) on-panel pathogens, showing an overall concordance of 98%. In 4/60 cases BCID2 did not detect any target and these all grew BCID2 off-panel bacteria. Only one discordant case was found. Sensitivity and specificity for Gram-positive bacteria on monomicrobial samples were 100% (95% CI 85.8-100%) and 100% (95% CI 90.3-100%) respectively, while for Gram-negatives 100% (95% CI 87.7-100) and 96.9% (95% CI 83.8-99.9%), respectively. Among two polymicrobial blood cultures, full concordance was observed in one case only. BCID2 identified antimicrobial resistance genes in 6/62 samples, all confirmed by in-house PCR (3 mecA/C S. epidermidis, 3 bla CTX-M E. coli). Estimated time to results gained using BCID2 as compared to conventional testing was 9.69 h (95% CI: 7.85-11.53). Conclusions BCID2 showed good agreement with conventional methods. Studies to assess its clinical impact are warranted.
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Affiliation(s)
- Anna Maria Peri
- University of Queensland Centre for Clinical Research, Herston, Brisbane City, QLD, 4029, Australia
| | - Michelle J Bauer
- University of Queensland Centre for Clinical Research, Herston, Brisbane City, QLD, 4029, Australia
| | - Haakon Bergh
- Central Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Herston, Brisbane City, QLD, 4029, Australia
| | - Dominika Butkiewicz
- University of Queensland Centre for Clinical Research, Herston, Brisbane City, QLD, 4029, Australia
| | - David L Paterson
- University of Queensland Centre for Clinical Research, Herston, Brisbane City, QLD, 4029, Australia.,Infectious Diseases Unit, Royal Brisbane and Women's Hospital, Herston, Brisbane City, QLD, 4029, Australia
| | - Patrick Na Harris
- University of Queensland Centre for Clinical Research, Herston, Brisbane City, QLD, 4029, Australia.,Central Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Herston, Brisbane City, QLD, 4029, Australia
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38
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Gerace E, Mancuso G, Midiri A, Poidomani S, Zummo S, Biondo C. Recent Advances in the Use of Molecular Methods for the Diagnosis of Bacterial Infections. Pathogens 2022; 11:pathogens11060663. [PMID: 35745518 PMCID: PMC9229729 DOI: 10.3390/pathogens11060663] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/31/2022] [Accepted: 06/05/2022] [Indexed: 12/14/2022] Open
Abstract
Infections caused by bacteria have a major impact on public health-related morbidity and mortality. Despite major advances in the prevention and treatment of bacterial infections, the latter continue to represent a significant economic and social burden worldwide. The WHO compiled a list of six highly virulent multidrug-resistant bacteria named ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) responsible for life-threatening diseases. Taken together with Clostridioides difficile, Escherichia coli, Campylobacter spp., (C. jejuni and C. coli), Legionella spp., Salmonella spp., and Neisseria gonorrhoeae, all of these microorganisms are the leading causes of nosocomial infections. The rapid and accurate detection of these pathogens is not only important for the early initiation of appropriate antibiotic therapy, but also for resolving outbreaks and minimizing subsequent antimicrobial resistance. The need for ever-improving molecular diagnostic techniques is also of fundamental importance for improving epidemiological surveillance of bacterial infections. In this review, we aim to discuss the recent advances on the use of molecular techniques based on genomic and proteomic approaches for the diagnosis of bacterial infections. The advantages and limitations of each of the techniques considered are also discussed.
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Affiliation(s)
| | - Giuseppe Mancuso
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Angelina Midiri
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Stefano Poidomani
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Sebastiana Zummo
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Carmelo Biondo
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
- Correspondence: ; Tel.: +39-090-2213322
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Kanda N, Hashimoto H, Suzuki T, Nakamura K. Performance of the new FilmArray Blood Culture Identification 2 panel and its potential impact on clinical use in patients with Gram-negative bacteremia. J Infect Chemother 2022; 28:1037-1040. [DOI: 10.1016/j.jiac.2022.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 03/29/2022] [Accepted: 04/07/2022] [Indexed: 01/02/2023]
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40
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Chung PH, Leong JY, Phillips CD, Henry GD. Microorganism Profiles of Penile Prosthesis Removed for Infection, Erosion, and Mechanical Malfunction Based on Next-Generation Sequencing. J Sex Med 2022; 19:356-363. [PMID: 34963572 DOI: 10.1016/j.jsxm.2021.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/15/2021] [Accepted: 11/29/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND Next-generation sequencing (NGS) is an emerging technology that may allow for more sensitive and sophisticated microbial testing of the microbiota of penile prostheses (PP). AIM To describe the microorganism profiles of PP explanted for infection, erosion, and mechanical malfunction using NGS. METHODS All patients who underwent PP removal by two physicians at two institutions were identified. Differences in alpha diversity (ie, number of species detected, species diversity across samples) and microbiome compositional profiles (Bray-Curtis community dissimilarities) across samples were assessed using ANOVA and PERMANOVA, respectively. OUTCOMES Number of species detected, species diversity across samples, and microbiome compositional profiles. RESULTS A total of 83 patients who underwent device removal for infection (n = 8, 10%), erosion (n = 5, 6%), and mechanical malfunction (n = 70, 84%) were included. When considering all devices, 56% (n = 48) of NGS and 29% (n = 24) of standard cultures resulted positive for presence of microorganisms. Culture only detected the most abundant NGS species in 62.5% (n = 5) of infected devices. Species richness and microbiome compositional profiles varied by surgical indication, but not by age, race, diabetes status, or implant duration. Most frequent organisms by surgical indication were Pseudomonas aeruginosa (infection), Staphylococcus epidermidis (erosion), and Escherichia coli (mechanical malfunction). The highest relative abundance organisms were P aeruginosa (infection), Corynebacterium jeikeium (erosion), and E coli (mechanical malfunction). CLINICAL IMPLICATIONS Identifying microbiome profiles of PP removed for infection, erosion, and mechanical malfunction may guide the selection of peri-operative antibiotics and PP antibiotic coatings or hydrophilic dip solutions for each individual scenario. STRENGTHS AND LIMITATIONS While this is the first study to utilize next-generation sequencing to evaluate penile prosthesis biofilm, the clinical significance of these findings has yet to be determined. A prospective, randomized trial aimed at evaluating the clinical significance of NGS in patients with PP infection is currently underway. CONCLUSION NGS testing identified distinct microbiome profiles of PP removed for infection, erosion, and mechanical malfunction. Chung PH, Leong JY, Phillips CD, Henry GD. Microorganism Profiles of Penile Prosthesis Removed for Infection, Erosion, and Mechanical Malfunction Based on Next-Generation Sequencing. J Sex Med 2022;19:356-363.
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Affiliation(s)
- Paul H Chung
- Department of Urology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA.
| | - Joon Yau Leong
- Department of Urology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA. https://twitter.com/@jyleong_md
| | - Caleb D Phillips
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
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41
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Ong SWX, Hon PY, Wee SSH, Chia JWZ, Mendis S, Izharuddin E, Lin RJ, Chia PY, Sim RCS, Chen MIC, Chow A, Yoong J, Lye DC, Teng CB, Tambyah PA, Banerjee R, Patel R, De PP, Vasoo S. Accuracy of a rapid multiplex PCR plus a chromogenic phenotypic test algorithm for detection of ESBL and carbapenemase-producing Gram-negative bacilli in positive blood culture bottles. Clin Infect Dis 2021; 74:1850-1854. [PMID: 34554228 DOI: 10.1093/cid/ciab848] [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: 07/05/2021] [Indexed: 11/12/2022] Open
Abstract
We studied the performance of an algorithm combining multiplex-PCR with phenotypic detection of ESBLs and carbapenemases directly from positive blood culture bottles in patients with Gram-negative bacteremia and found good concordance with routine cultures. Such an algorithm may be a tool to improve time-to-optimal therapy in patients with Gram-negative bacteremia.
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Affiliation(s)
- Sean Wei Xiang Ong
- National Centre for Infectious Diseases, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore
| | - Pei Yun Hon
- National Centre for Infectious Diseases, Singapore
| | - Sharon Syn Hui Wee
- Clinical Research and Innovation Office, Tan Tock Seng Hospital, Singapore
| | | | - Shehara Mendis
- Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore
| | | | - Ray Junhao Lin
- National Centre for Infectious Diseases, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore
| | - Po Ying Chia
- National Centre for Infectious Diseases, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | | | - Mark I-Cheng Chen
- National Centre for Infectious Diseases, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Angela Chow
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore.,Department of Clinical Epidemiology, Office of Clinical Epidemiology, Analytics, and Knowledge (OCEAN), Tan Tock Seng Hospital, Singapore
| | - Joanne Yoong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - David Chien Lye
- National Centre for Infectious Diseases, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.,Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Christine B Teng
- Department of Pharmacy, National University of Singapore, Singapore
| | - Paul Anantharajah Tambyah
- Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Division of Infectious Disease, National University Hospital, Singapore
| | - Ritu Banerjee
- Division of Pediatric Infectious Diseases, Vanderbilt University, Nashville, TN, USA
| | - Robin Patel
- Division of Clinical Microbiology and Infectious Diseases, Mayo Clinic, Rochester, MN, USA
| | - Partha Pratim De
- Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore
| | - Shawn Vasoo
- National Centre for Infectious Diseases, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
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A Multicenter Clinical Study To Demonstrate the Diagnostic Accuracy of the GenMark Dx ePlex Blood Culture Identification Gram-Negative Panel. J Clin Microbiol 2021; 59:e0248420. [PMID: 34232066 PMCID: PMC8373019 DOI: 10.1128/jcm.02484-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Bacteremia can progress to septic shock and death without appropriate medical intervention. Increasing evidence supports the role of molecular diagnostic panels in reducing the clinical impact of these infections through rapid identification of the infecting organism and associated antimicrobial resistance genes. We report the results of a multicenter clinical study assessing the performance of the GenMark Dx ePlex investigational-use-only blood culture identification Gram-negative panel (BCID-GN), a rapid diagnostic assay for detection of bloodstream pathogens in positive blood culture (PBC) bottles. Prospective, retrospective, and contrived samples were tested. Results from the BCID-GN were compared to standard-of-care bacterial identification methods. Antimicrobial resistance genes (ARGs) were identified using PCR and sequence analysis. The final BCID-GN analysis included 2,444 PBC samples, of which 926 were clinical samples with negative Gram stain results. Of these, 109 samples had false-negative and/or -positive results, resulting in an overall sample accuracy of 88.2% (817/926). After discordant resolution, overall sample accuracy increased to 92.9% (860/926). Pre- and postdiscordant resolution sample accuracy excludes 37 Gram-negative organisms representing 20 uncommon genera, 10 Gram-positive organisms, and 1 Candida species present in 5% of samples that are not targeted by the BCID-GN. The overall weighted positive percent agreement (PPA), which averages the individual PPAs from the 27 targets (Gram-negative and ARG), was 94.9%. The limit of detection ranged from 104 to 107 CFU/ml, except for one strain of Fusobacterium necrophorum at 108 CFU/ml.
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