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Cooper L, Yu K, Van Benten K, Patkar A, Ye G, Gregory S, Ai C, Gupta V. Hospital mortality and length of stay associated with Enterobacterales positive blood cultures: a multicenter analysis. Microbiol Spectr 2024:e0040224. [PMID: 38953323 DOI: 10.1128/spectrum.00402-24] [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: 02/26/2024] [Accepted: 06/12/2024] [Indexed: 07/04/2024] Open
Abstract
Delayed time to antimicrobial susceptibility results can impact patients' outcomes. Our study evaluated the impact of susceptibility turnaround time (TAT) and inadequate empiric antibacterial therapy (IET) in patients with bloodstream infections (BSI) caused by Enterobacterales (ENT) species on in-hospital mortality and length of stay (LOS). This retrospective, multicenter investigation which included 29,570 blood ENT-positive admissions across 161 US healthcare facilities evaluated the association between antimicrobial susceptibility testing (AST) TAT, carbapenem susceptibility, and empiric therapy on post-BSI in-hospital mortality and LOS following an ENT BSI event in adult patients. After adjusting for outcomes covariates, post-BSI in-hospital mortality was significantly higher for patients in the IET vs adequate empiric therapy (AET) group [odds ratio (OR): 1.61 (95% CI: 1.32, 1.98); P < 0.0001], and when AST TAT was >63 h [OR:1.48 (95% CI: 1.16, 1.90); P = 0.0017]. Patients with carbapenem non-susceptible (carb-NS) ENT BSI had significantly higher LOS (16.6 days, 95% CI: 15.6, 17.8) compared to carbapenem susceptible (carb-S, 12.2 days, 95% CI: 11.8, 12.6), (P < 0.0001). Extended AST TAT was significantly associated with longer LOS for TAT of 57-65 h and >65 h (P = 0.005 and P< 0.0001, respectively) compared to TAT ≤42 h (reference). Inadequate empiric therapy (IET), carb-NS, and delayed AST TAT are significantly associated with adverse hospital outcomes in ENT BSI. Workflows that accelerate AST TAT for ENT BSIs and facilitate timely and adequate therapy may reduce post-BSI in-hospital mortality rate and LOS.IMPORTANCEFor patients diagnosed with bloodstream infections (BSI) caused by Enterobacterales (ENT), delayed time to antimicrobial susceptibility (AST) results can significantly impact in-hospital mortality and hospital length of stay. However, this relationship between time elapsed from blood culture collection to AST results has only been assessed, to date, in a limited number of publications. Our study focuses on this important gap using retrospective data from 29,570 blood ENT-positive admissions across 161 healthcare facilities in the US as we believe that a thorough understanding of the dynamic between AST turnaround time, adequacy of empiric therapy, post-BSI event mortality, and hospital length of stay will help guide effective clinical management and optimize outcomes of patients with ENT infections.
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Affiliation(s)
- Lauren Cooper
- Becton, Dickinson and Company, Diagnostic Solutions, Sparks, Maryland, USA
| | - Kalvin Yu
- Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
| | - Kayla Van Benten
- Becton, Dickinson and Company, Diagnostic Solutions, Sparks, Maryland, USA
| | - Anuprita Patkar
- Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
| | - Gang Ye
- Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
| | - Sara Gregory
- Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
| | - ChinEn Ai
- Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
| | - Vikas Gupta
- Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
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Karadağ D, Ergon MC. Investigation of different methods in rapid microbial identification directly from positive blood culture bottles by MALDI-TOF MS. Microbiol Spectr 2024:e0063824. [PMID: 38940589 DOI: 10.1128/spectrum.00638-24] [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: 04/09/2024] [Accepted: 05/21/2024] [Indexed: 06/29/2024] Open
Abstract
Many methods are being tried for rapid and accurate identification of sepsis-causing microorganisms. We analyzed the performance of three different preparation methods [MBT Sepsityper IVD Kit (Bruker Daltonics GmbH, Germany), sodium dodecyl sulfate (SDS) lysis, and differential centrifugation with protein extraction (Centrifugation +PE)] and compared in standard and Sepsityper modules of the Bruker Biotyper MALDI-TOF MS for direct identification of bacteria from 240 positive blood culture bottles of BACTEC FX (Becton Dickinson, USA). By using the standard module, correct identification at species level (score ≥2) was done in 46.7% of the samples with SDS lysis, 44.2% with centrifugation +PE, and 25.4% with the Sepsityper kit. These ratios at the genus level (score range 1.70-1.99) were 34.6%, 31.3%, and 32.5%, respectively. With SDS lysis (195), more bacteria were identified correctly than centrifugation +PE (181) and the Sepsityper kit (139). A statistically significant difference was found between SDS and the Sepsityper kit and Centrifugation +PE and the Sepsityper kit (P < 0.001, both). By using the Sepsityper module, correct identification at species level (score ≥1.8) was determined in 74.2% of the samples with SDS lysis and centrifugation +PE each and 55% with the Sepsityper kit. These ratios at the genus level (score range 1.60-1.79) were 16.3%, 10%, and 19.2%, respectively. SDS lysis (217) had significantly higher identification rates than centrifugation +PE (202) and the Sepsityper kit (178) (P = 0.028 and P < 0.001). A statistically significant difference was also observed between centrifugation +PE and the Sepsityper kit (P < 0.001). Best performance was obtained with SDS lysis among the methods. Although better performance was achieved by using Sepsityper software module, risk of misidentification should not be ignored. IMPORTANCE Sepsis is a life-threatening condition, and rapid and accurate identification of the causative microorganisms from blood cultures is crucial for timely and effective treatment. Although there are many studies on direct identification from blood cultures with MALDI-TOF MS, further standardization is still needed. In our study, we analyzed the performance of three different preparation methods and compared by using two analysis modules of the Bruker Biotyper MALDI-TOF MS for direct identification of bacteria from numerous positive blood culture bottles. The literature reports a limited number of studies that compare different preparation methods for direct blood culture identification, processing a large number of blood samples concurrently and evaluating the same samples as in our study. Moreover, although SDS is used very frequently in medical laboratories, there are few studies on direct identification from blood culture bottles. In our study, the highest correct identification rate was observed with the SDS method.
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Affiliation(s)
- Dilan Karadağ
- Department of Medical Microbiology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
- IMD Labor Oderland, Frankfurt (Oder), Germany
| | - Mahmut Cem Ergon
- Department of Medical Microbiology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
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Iglesies-Torrent J, Garrido M, Morales J, Pitart C, Vergara A, Fernández-Pittol M. Enhancing pneumococcal bacteraemia diagnosis: A comparative assessment of culture-independent assays (MALDI-TOF-MS Sepsityper® module and a lateral flow inmunochromatography test). ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2024:S2529-993X(24)00114-X. [PMID: 38705749 DOI: 10.1016/j.eimce.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/12/2024] [Indexed: 05/07/2024]
Abstract
INTRODUCTION Pneumococcal bacteraemia is a major contributor to global morbidity and mortality. Traditional culture-based methods lack sensitivity and are time-consuming. This study aimed to assess the effectiveness of two culture-independent assays, the MALDI-TOF-MS Sepsityper® module and the lateral flow inmunochromatography test (LFICT) with the Standard F® Streptococcus pneumoniae, directly from positive blood culture (BC) bottles. METHODS A prospective study was conducted from December 2021 to July 2022. For all BC positives for S. pneumoniae a double centrifugation protocol was implemented. The resulting pellet was subsequently processed using both techniques. RESULTS The LFICT showed exceptional performance with 100% sensitivity and specificity, outperforming the MALDI-TOF-MS Sepsityper® module, which achieved 85.2% sensitivity and 100% specificity. Nevertheless, the combination of these assays offers a robust and comprehensive approach to diagnosis. CONCLUSIONS The simultaneous use of both techniques offers a promising alternative that can be integrated into routine practices directly from BC samples.
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Affiliation(s)
| | - Míriam Garrido
- Department of Microbiology, Hospital Clínic, Barcelona, Spain
| | - Javier Morales
- Department of Microbiology, Hospital Clínic, Barcelona, Spain
| | - Cristina Pitart
- Department of Microbiology, Hospital Clínic, Barcelona, Spain; Institute for Global Health (ISGlobal), University of Barcelona, Barcelona, Spain; University of Barcelona, Barcelona, Spain
| | - Andrea Vergara
- Department of Microbiology, Hospital Clínic, Barcelona, Spain; Institute for Global Health (ISGlobal), University of Barcelona, Barcelona, Spain; University of Barcelona, Barcelona, Spain
| | - Mariana Fernández-Pittol
- Department of Microbiology, Hospital Clínic, Barcelona, Spain; Institute for Global Health (ISGlobal), University of Barcelona, Barcelona, Spain
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Watanabe N, Koyama S, Maeda T, Karaushi H, Taji Y, Kawasaki Y, Takahashi N, Mitsutake K, Ebihara Y. Direct Species Identification in Positive Blood Culture Bottles From Patients With Hematologic Malignancies. Cureus 2024; 16:e59043. [PMID: 38800333 PMCID: PMC11128060 DOI: 10.7759/cureus.59043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2024] [Indexed: 05/29/2024] Open
Abstract
Background In patients with hematologic malignancies, faster species identification is particularly important in the management of bloodstream infection because of their immunocompromised and neutropenic status. In the present study, we analyzed direct species identification in patients with hematologic malignancies, and the factors that might influence the results of species identification. Methods We performed direct species identification using a Sepsityper® kit (Bruker Corporation, Billerica, Massachusetts, United States) and compared the results with a conventional method in patients with hematologic malignancies. Forty-five positive blood culture bottles containing single microorganisms from 37 patients were analyzed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). And patients' clinical data were compared between the groups with spectral scores at acceptable and unacceptable levels. Results Direct species identification correctly identified 42 of 45 isolates and three were misidentified. While 35 of 45 isolates showed a spectral score ≥1.7 (acceptable identification), 10 isolates had a spectral score <1.7 (unacceptable identification) including three misidentified isolates. The group with a spectral score ≥1.7 had significantly lower white blood cell (p<0.01), neutrophil (p<0.01), and platelet (p<0.01) counts in addition to more frequent central venous (CV) line insertion (p=0.01). Multivariate analysis revealed that pathogen type (gram-positive or negative) and CV line insertion were associated with spectral scores. Conclusion Direct species identification using the Sepsityper kit is an upcoming approach for blood culture bottles, which were flagged as positive even in patients with hematologic malignancies when the spectral score was ≥ 1.7. Our study also indicates that direct identification is more accurate in patients with CV lines, and may be less accurate when gram-positive bacteria are detected.
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Affiliation(s)
- Noriyuki Watanabe
- Clinical Laboratory, Saitama Medical University International Medical Center, Saitama, JPN
| | - Sachie Koyama
- Clinical Laboratory, Saitama Medical University International Medical Center, Saitama, JPN
| | - Tomoya Maeda
- Department of Hemato-Oncology, Saitama Medical University International Medical Center, Saitama, JPN
| | - Haruka Karaushi
- Department of Infectious Diseases and Infection Control, Saitama Medical University International Medical Center, Saitama, JPN
| | - Yoshitada Taji
- Clinical Laboratory, Saitama Medical University International Medical Center, Saitama, JPN
| | - Yohei Kawasaki
- Department of Biostatistics, Graduate School of Medicine, Saitama Medical University, Saitama, JPN
| | - Naoki Takahashi
- Department of Hemato-Oncology, Saitama Medical University International Medical Center, Saitama, JPN
| | - Kotaro Mitsutake
- Department of Infectious Diseases and Infection Control, Saitama Medical University International Medical Center, Saitama, JPN
| | - Yasuhiro Ebihara
- Department of Laboratory Medicine, Saitama Medical University International Medical Center, Saitama, JPN
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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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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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Kim KJ, Yun SG, Cho Y, Nam MH, Ko YJ, Lee CK. Evaluation of a sterile, filter-based, in-house method for rapid direct bacterial identification and antimicrobial susceptibility testing using positive blood culture. Eur J Clin Microbiol Infect Dis 2023; 42:691-700. [PMID: 37012540 DOI: 10.1007/s10096-023-04592-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023]
Abstract
This study aimed to assess the performance of our in-house method for rapid direct bacterial identification (ID) and antimicrobial susceptibility testing (AST) using a positive blood culture (BC) broth. For Gram-negative bacteria, 4 mL of BC broth was aspirated and passed through a Sartorius Minisart syringe filter with a pore size of 5 µm. The filtrate was then centrifuged and washed. A small volume of the pellet was used for ID, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and for AST, using automated broth microdilution. For Gram-positive cocci, 4 mL of BC broth was passed through the Minisart syringe filter. Then, 4 mL of sterile distilled water was injected in the direction opposite to that of the filtration to collect the bacterial residue trapped in the filter. Compared with the conventional method performed with pure colonies on agar plates, 94.0% (234/249) were correctly identified using the in-house method, with rates of 91.4% (127/139) and 97.3% (107/110) for Gram-positive and Gram-negative isolates, respectively. Of 234 correctly identified isolates, 230 were assessed by AST. Categorical agreement and essential agreement were 93.3% and 94.5%, respectively, with a minor error rate of 3.8%, a major error rate of 3.4%, and a very major error rate of 1.6%. Our in-house preparation method showed good performance in rapid direct ID and AST using positive BC broths compared to the conventional method. This simple method can shorten the conventional turnaround time for ID and AST by at least 1 day, potentially contributing to better patient management.
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Affiliation(s)
- Keun Ju Kim
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Seung Gyu Yun
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Yunjung Cho
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Myung-Hyun Nam
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Korea
| | - Young Jin Ko
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwangju, Korea
| | - Chang Kyu Lee
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Korea.
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MALDI-TOF MS-Based Approaches for Direct Identification of Gram-Negative Bacteria and BlaKPC-Carrying Plasmid Detection from Blood Cultures: A Three-Year Single-Centre Study and Proposal of a Diagnostic Algorithm. Microorganisms 2022; 11:microorganisms11010091. [PMID: 36677383 PMCID: PMC9860562 DOI: 10.3390/microorganisms11010091] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022] Open
Abstract
The rapid identification of pathogens of bloodstream infections (BSIs) and the detection of antibiotic resistance markers are critically important for optimizing antibiotic therapy and infection control. The purpose of this study was to evaluate two approaches based on MALDI-TOF MS technology for direct identification of Gram-negative bacteria and automatic detection of Klebsiella pneumoniae carbapenemase (KPC) producers using the Bruker MBT Subtyping IVD Module in a large routine laboratory over a three-year period. MALDI-TOF MS analysis was performed directly from blood culture (BC) bottles following bacterial pellet recovery by Rapid MBT Sepsityper® Kit and on blood agar 4-h subcultures. Automated detection of blaKPC-carrying pKpQIL-plasmid by Bruker MBT Subtyping Module was evaluated in BCs tested positive to K. pneumoniae or E. coli. The results were compared with those obtained with conventional reference methods. Among the 2858 (93.4%) monomicrobial BCs, the overall species identification rates of the Rapid Sepsityper and the short-term subculture protocols were 84.5% (n = 2416) and 90.8% (n = 2595), respectively (p < 0.01). Excellent specificity for KPC-producers identification were observed for both MALDI-TOF MS protocols. The pKpQIL plasmid-related peak was detected in overall 91 of the 120 (75.8%) KPC-producing isolates. Notably, 14 out of the 17 (82.3%) K. pneumoniae isolates carrying blaKPC variants associated with ceftazidime/avibactam resistance and tested negative by the immunocromatography assay, were correctly identified as KPC-producers by MALDI-TOF MS. In conclusion, combination of both Rapid Sepsityper and short-term subculture protocols may represent an optimal solution to promptly identify more than 95% of Gram-negative bacteria causing BSIs. MALDI Biotyper® platform enabled a reliable and robust automated detection of KPC producers in parallel with species identification. However, integration of molecular or immunocromatographic assays are recommended according to local epidemiology.
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Yang H, Smith RD, Sumner KP, Goodlett DR, Johnson JK, Ernst RK. A Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Direct-from-Urine-Specimen Diagnostic for Gram-Negative Pathogens. Microbiol Spectr 2022; 10:e0373022. [PMID: 36255333 PMCID: PMC9769899 DOI: 10.1128/spectrum.03730-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 09/28/2022] [Indexed: 01/10/2023] Open
Abstract
Urinary tract infections (UTIs) pose a major public health burden. The vast majority of UTIs are caused by Gram-negative bacteria. Current culture-based pathogen identification methods may require up to 24 to 48 h of incubation. In this study, we developed and evaluated a method for Gram-negative pathogen identification direct from urine, without culture, via matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in approximately 1 h. Urine samples were collected (n = 137) from the University of Maryland Medical Center clinical microbiology laboratory. To identify bacteria direct from urine, two methods were evaluated. First, 1 μL of urine was directly spotted onto the MALDI target plate, and second, 1 mL of urine was centrifuged at 8,000 rpm for 5 min before processing using the fast lipid analysis technique (FLAT). Mass spectra were acquired on the Bruker MALDI Biotyper sirius system in the negative-ion mode. Results were compared to those of standard culture methods. When 1 μL of urine was directly spotted, positive agreement was 81.5% (101/124) and, after centrifugation, 94.4% (117/124) relative to that of standard culture methods. Negative agreement for both methods was 100% (13/13). The time to results for both of the specimen preparation methods using the FLAT extraction protocol was approximately 1 h, with minimal hands-on time required (<5 min). The ability to rapidly identify pathogens directly from urine, without the need for culture, allows for faster turnaround times and, potentially, improved patient outcomes. Overall, the FLAT extraction protocol, in combination with lipid A identification, provides a reproducible and accurate method to rapidly identify urinary pathogens. IMPORTANCE This study describes and evaluates a direct-from-urine extraction method that allows identification of Gram-negative bacteria via MALDI-TOF MS within 1 h. Currently, identification of urinary pathogens requires 24 h of culture prior to identification. While this method may not replace culture, we demonstrate its utility in screening for common urinary pathogens. By providing identifications in under 1 h, clinicians can potentially treat patients sooner with more-targeted antimicrobial therapy. In turn, earlier treatment can improve patient outcome and antimicrobial stewardship. Furthermore, MADLI-TOF MS is a readily available, easy-to-use diagnostic tool in clinical laboratories, making implementation of this method possible.
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Affiliation(s)
- Hyojik Yang
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
| | - Richard D. Smith
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
- Department of Pathology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Kylie P. Sumner
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - David R. Goodlett
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - J. Kristie Johnson
- Department of Pathology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Robert K. Ernst
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
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Duan R, Wang P. Rapid and Simple Approaches for Diagnosis of Staphylococcus aureus in Bloodstream Infections. Pol J Microbiol 2022; 71:481-489. [PMID: 36476633 PMCID: PMC9944965 DOI: 10.33073/pjm-2022-050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/01/2022] [Indexed: 12/13/2022] Open
Abstract
Staphylococcus aureus is an important causative pathogen of bloodstream infections. An amplification assay such as real-time PCR is a sensitive, specific technique to detect S. aureus. However, it needs well-trained personnel, and costs are high. A literature review focusing on rapid and simple methods for diagnosing S. aureus was performed. The following methods were included: (a) Hybrisep in situ hybridization test, (b) T2Dx system, (c) BinaxNow Staphylococcus aureus and PBP2a, (d) Gram staining, (e) PNA FISH and QuickFISH, (f) Accelerate PhenoTM system, (g) MALDI-TOF MS, (h) BioFire FilmArray, (i) Xpert MRSA/SA. These rapid and simple methods can rapidly identify S. aureus in positive blood cultures or direct blood samples. Furthermore, BioFire FilmArray and Xpert MRSA/SA identify methicillin-resistant S. aureus (MRSA), and the Accelerate PhenoTM system can also provide antimicrobial susceptibility testing (AST) results. The rapidity and simplicity of results generated by these methods have the potential to improve patient outcomes and aid in the prevention of the emergence and transmission of MRSA.
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Affiliation(s)
- Rui Duan
- Department of Laboratory Medicine and Blood Transfusion, The First People’s Hospital of Jingmen, Jingmen, Hubei Province, China
| | - Pei Wang
- Department of Laboratory Medicine and Blood Transfusion, The First People’s Hospital of Jingmen, Jingmen, Hubei Province, China, E-mail:
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Azar MM, Turbett S, Gaston D, Gitman M, Razonable R, Koo S, Hanson K, Kotton C, Silveira F, Banach DB, Basu SS, Bhaskaran A, Danziger-Isakov L, Bard JD, Gandhi R, Hanisch B, John TM, Odom John AR, Letourneau AR, Luong ML, Maron G, Miller S, Prinzi A, Schwartz I, Simner P, Kumar D. A consensus conference to define the utility of advanced infectious disease diagnostics in solid organ transplant recipients. Am J Transplant 2022; 22:3150-3169. [PMID: 35822346 DOI: 10.1111/ajt.17147] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/28/2022] [Accepted: 07/07/2022] [Indexed: 01/25/2023]
Abstract
The last decade has seen an explosion of advanced assays for the diagnosis of infectious diseases, yet evidence-based recommendations to inform their optimal use in the care of transplant recipients are lacking. A consensus conference sponsored by the American Society of Transplantation (AST) was convened on December 7, 2021, to define the utility of novel infectious disease diagnostics in organ transplant recipients. The conference represented a collaborative effort by experts in transplant infectious diseases, diagnostic stewardship, and clinical microbiology from centers across North America to evaluate current uses, unmet needs, and future directions for assays in 5 categories including (1) multiplex molecular assays, (2) rapid antimicrobial resistance detection methods, (3) pathogen-specific T-cell reactivity assays, (4) next-generation sequencing assays, and (5) mass spectrometry-based assays. Participants reviewed and appraised available literature, determined assay advantages and limitations, developed best practice guidance largely based on expert opinion for clinical use, and identified areas of future investigation in the setting of transplantation. In addition, attendees emphasized the need for well-designed studies to generate high-quality evidence needed to guide care, identified regulatory and financial barriers, and discussed the role of regulatory agencies in facilitating research and implementation of these assays. Findings and consensus statements are presented.
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Affiliation(s)
- Marwan M Azar
- Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sarah Turbett
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - David Gaston
- John's Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Melissa Gitman
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Sophia Koo
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kimberly Hanson
- University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Camille Kotton
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Fernanda Silveira
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - David B Banach
- University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Sankha S Basu
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Lara Danziger-Isakov
- Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio, USA
| | - Jennifer Dien Bard
- Children's Hospital Los Angeles, University of Southern California, Los Angeles, California, USA
| | - Ronak Gandhi
- Department of Pharmacy Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Benjamin Hanisch
- Children's National Hospital, Washington, District of Columbia, USA
| | - Teny M John
- The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Audrey R Odom John
- Perelman School of Medicine, University of Pennsylvania, Children's Hospital of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Alyssa R Letourneau
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Me-Linh Luong
- Department of Microbiology, University of Montreal, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, Canada
| | - Gabriela Maron
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Steve Miller
- University of California San Francisco School of Medicine, San Francisco, California, USA
| | - Andrea Prinzi
- Infectious Disease Medical Science Liaison, Denver, Colorado, USA
| | - Ilan Schwartz
- Faculty of Medicine and Dentistry, University of Alberta, University of Alberta, Alberta, Canada
| | - Patricia Simner
- John's Hopkins University School of Medicine, Baltimore, Maryland, USA
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12
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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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13
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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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14
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Pranada AB, Cordovana M, Meyer M, Hubert H, Abdalla M, Ambretti S, Steinmann J. Identification of micro-organism from positive blood cultures: comparison of three different short culturing methods to the Rapid Sepsityper workflow. J Med Microbiol 2022; 71. [PMID: 35930326 DOI: 10.1099/jmm.0.001571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sepsis is one of the leading causes of death worldwide. The rapid identification (ID) of the causative micro-organisms is crucial for the patients' clinical outcome. MALDI-TOF MS has been widely investigated to speed up the time-to-report for ID from positive blood cultures, and many different procedures and protocols were developed, all of them attributable either to the direct separation of microbial cells from the blood cells, or to a short subculture approach. In this study, the Rapid Sepsityper workflow (MBT Sepsityper IVD Kit, Bruker Daltonics GmbH and Co. KG, Bremen, Germany) was compared to three different short subculturing methods, established into the routine practice of three different clinical microbiology laboratories. A total of N=503 routine samples were included in this study and tested in parallel with the two approaches. Results of the rapid procedures were finally compared to routine proceedings with Gram-staining and overnight subculture. Among monomicrobial samples, the Rapid Sepsityper workflow enabled overall the correct identification of 388/443 (87.6 %) micro-organisms, while the short subculturing methods of 267/435 (61.8 %). Except for the performance with Streptococcus pneumoniae, in each one of the three sites the Rapid Sepsityper workflow proved to be superior to the short subculture method, regardless of the protocol applied, and it delivered a result from 1 to 5 h earlier.
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Affiliation(s)
- Arthur B Pranada
- Department of Medical Microbiology, MVZ Dr. Eberhard & Partner Dortmund, Dortmund, Germany
| | | | | | | | | | - Simone Ambretti
- Operative Unit of Microbiology IRCSS Sant'Orsola, Bologna, Italy
| | - Joerg Steinmann
- Institute for Clinical Hygiene, Medical Microbiology and Infectiology, Klinikum Nürnberg, Paracelsus Medical University, Nürnberg, Germany
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15
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Costa SP, Carvalho CM. Burden of bacterial bloodstream infections and recent advances for diagnosis. Pathog Dis 2022; 80:6631550. [PMID: 35790126 DOI: 10.1093/femspd/ftac027] [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: 01/27/2022] [Revised: 06/07/2022] [Accepted: 07/01/2022] [Indexed: 11/13/2022] Open
Abstract
Bloodstream infections (BSIs) and subsequent organ dysfunction (sepsis and septic shock) are conditions that rank among the top reasons for human mortality and have a great impact on healthcare systems. Their treatment mainly relies on the administration of broad-spectrum antimicrobials since the standard blood culture-based diagnostic methods remain time-consuming for the pathogen's identification. Consequently, the routine use of these antibiotics may lead to downstream antimicrobial resistance and failure in treatment outcomes. Recently, significant advances have been made in improving several methodologies for the identification of pathogens directly in whole blood especially regarding specificity and time to detection. Nevertheless, for the widespread implementation of these novel methods in healthcare facilities, further improvements are still needed concerning the sensitivity and cost-effectiveness to allow a faster and more appropriate antimicrobial therapy. This review is focused on the problem of BSIs and sepsis addressing several aspects like their origin, challenges, and causative agents. Also, it highlights current and emerging diagnostics technologies, discussing their strengths and weaknesses.
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Affiliation(s)
- Susana P Costa
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.,International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal.,Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias (INESC MN) and IN - Institute of Nanoscience and Nanotechnology, Rua Alves Redol, 9 1000-029 Lisbon, Portugal
| | - Carla M Carvalho
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
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16
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Kuo P, LeCrone K, Chiu M, Realegeno S, Pride DT. Analysis of the FAST™ System for expedited identification and antimicrobial susceptibility testing of bloodborne pathogens. Diagn Microbiol Infect Dis 2022; 104:115783. [DOI: 10.1016/j.diagmicrobio.2022.115783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/03/2022]
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17
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Kim JM, Chung SH, Kim I, Kim JS. Comparison of peaks in the matrix-assisted laser desorption ionization time-of-flight mass spectrometry spectra of Staphylococcus aureus grown on various blood agar plates. J Microbiol Methods 2022; 196:106471. [PMID: 35460710 DOI: 10.1016/j.mimet.2022.106471] [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: 11/02/2021] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 12/27/2022]
Abstract
Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) is routinely used for bacterial identification in clinical laboratories. Bacterial protein expression may differ according to their growth conditions, especially the culture medium composition. We aimed to study the peak variations of Staphylococcus aureus grown on various blood agar plates (BAP), especially phenol-soluble modulin-mec (PSM-mec) peak (m/z 2409) associated with mecA gene conferring methicillin resistance. Methicillin-resistant S. aureus (MRSA) ATCC 43300 and eight clinical MRSA isolates were cultured on various commercial BAPs including tryptic soy agar-based BAPs, Columbia agar-based BAP and in-house BAPs with the addition of yeast extract. Analysis of the MALDI-TOF peaks of S. aureus, cultured on various BAPs, revealed the peak intensities of low-molecular weight proteins to vary depending on the composition of BAPs, especially the presence or absence of yeast extract. Especially, the PSM-mec and delta-toxin peaks showed low intensity for S. aureus ATCC 43300 and clinical isolates. No significant differences were found in the number of peaks, but some peaks had lower intensity, corresponding to the medium containing yeast extract, in low-mass region (<m/z 4000). BAPs based on tryptic soy agar rather than Columbia agar seems to be appropriate for the detection of PSM-mec, a methicillin resistance marker of S. aureus and delta-toxin, an agr function indicator.
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Affiliation(s)
- Jung-Min Kim
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea
| | - Sung Hee Chung
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea
| | - Inhee Kim
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea
| | - Jae-Seok Kim
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea.
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18
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MALDI-Based Mass Spectrometry in Clinical Testing: Focus on Bacterial Identification. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12062814] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The term “proteome” refers to the total of all proteins expressed in an organism. The term “proteomics” refers to the field of research that includes not only information on the expression levels of individual proteins, but also their higher-order structures, intermolecular interactions, and post-translational modifications. The core technology, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), is available for protein analysis thanks to the work of Koichi Tanaka and John Fenn, who were awarded the Nobel Prize in Chemistry in 2002. The most successful proteome analysis in clinical practice is rapid microbial identification. This method determines the bacterial species by comparing the proteome profile of the bacteria obtained by matrix-assisted laser desorption ionization-time of flight MS (MALDI-TOF MS) with a database. MS is superior in simplicity, speed, and accuracy to classic speciation by staining and phenotyping. In clinical microbiology, MS has had a large impact on the diagnosis and treatment of infectious disease. Early diagnosis and treatment of infectious disease are important, and rapid identification by MALDI-TOF MS has made a major contribution to this field.
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Direct Rapid Identification from Positive Blood Cultures by MALDI-TOF MS: Specific Focus on Turnaround Times. Microbiol Spectr 2021; 9:e0110321. [PMID: 34908465 PMCID: PMC8672911 DOI: 10.1128/spectrum.01103-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Early availability of pathogen identification in bloodstream infections has critical importance in patients' management. This study investigated the accuracy and feasibility of the direct rapid identification (RID) method from positive blood cultures (BCs) by MALDI-TOF MS and its impact on the turnaround time (TAT) compared to the short-term incubation routine identification (SIRID) method. Pellets prepared from 328 BCs using a serum separator tube in the RID method and colonies on agar plates in the SIRID method were identified with MALDI Biotyper. BCs on weekdays from 6 a.m. to 4 p.m. were defined as the daytime signal group (DSG); BCs from 4 p.m. to 6 a.m. were defined as the night signal group (NSG). Comparison between the two methods was performed with 310 monomicrobial BCs. Two hundred ninety-five (95.2%) monomicrobial BCs yielded an identification result with the RID method. Of the 295 BCs, 289 (97.9%) were identified correctly at the species level, 4 (1.4%) were at the genus level, and 2 (0.7%) were misidentified. In the RID method, at score cutoff values of 1.2, 1.3, 1.4 and 1.5, the rates of correct identifications at the species level were 97.9%, 98.9%, 99.3%, and 100%, respectively. The mean TAT in the DSG was significantly lower (P < 0.001) in the RID method (mean: 2.86 h; 95% CI: 2.65 to 3.07) compared to the SIRID method (mean: 19.49 h; 95% CI: 18.08 to 20.89). Correct identification rates at the species level were 100% in Gram-negative bacteria, 88.9% in Gram-positive bacteria, and 93.2% of all BCs isolates with the RID method. The TAT was improved remarkably in DSG, which might contribute to empirical antibiotic therapies of patients. IMPORTANCE Using MALDI-TOF MS directly from BCs reduces the time required for pathogen identification, and the TATs for final identification have been compared with overnight incubation from solid media in previous studies. However, identification from a short incubation of agar plates has been increasingly accepted and successfully implemented in routine laboratories, but there is no data comparing direct MALDI-TOF MS with the short-term incubated agar plates. Our study showed that the TAT improved remarkably by applying a RID method by MALDI-TOF MS twice a day periodically when compared to the SIRID method.
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MALDI-TOF MS in a Medical Mycology Laboratory: On Stage and Backstage. Microorganisms 2021; 9:microorganisms9061283. [PMID: 34204665 PMCID: PMC8231132 DOI: 10.3390/microorganisms9061283] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/31/2021] [Accepted: 06/03/2021] [Indexed: 12/12/2022] Open
Abstract
The implementation of MALDI-TOF MS in medical microbiology laboratories has revolutionized practices and significantly reduced turnaround times of identification processes. However, although bacteriology quickly benefited from the contributions of this technique, adjustments were necessary to accommodate the specific characteristics of fungi. MALDI-TOF MS is now an indispensable tool in clinical mycology laboratories, both for the identification of yeasts and filamentous fungi, and other innovative uses are gradually emerging. Based on the practical experience of our medical mycology laboratory, this review will present the current uses of MALDI-TOF MS and the adaptations we implemented, to allow their practical execution in a daily routine. We will also introduce some less mainstream applications, like those for fungemia, or even still under development, as is the case for the determination of sensitivity to antifungal agents or typing methods.
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21
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Impact of Accelerate Pheno and BacT/Alert Virtuo on Clinical Processes and Outcomes in Patients with Sepsis and Concurrent Gram-Negative Bacteremia. Antimicrob Agents Chemother 2021; 65:AAC.02364-20. [PMID: 33753337 DOI: 10.1128/aac.02364-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/14/2021] [Indexed: 12/14/2022] Open
Abstract
The Accelerate Pheno and BacT/Alert Virtuo systems may improve bacteremia management. Here, we evaluated the impact of both devices on outcomes in patients with sepsis and concurrent Gram-negative bacteremia. This quasiexperimental study included a retrospective preimplementation and a prospective postimplementation group. Patients ≥18 years old with Gram-negative bacteremia were included. Patients with neutropenia, pregnant patients, those who were transferred from an outside hospital with active bloodstream infections, and those with polymicrobial bacteremia were excluded. Blood culture incubation in the BacT/Alert 3D device and microdilution antimicrobial susceptibility testing from culture plate growth were used prior to implementation of the BacT/Alert Virtuo and Accelerate Pheno systems. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) identification directly from blood culture was used pre- and postimplementation. Time to Gram stain results, identification, susceptibility reporting, initiation of narrow-spectrum Gram-negative therapy at 72 h, 30-day inpatient mortality, sepsis resolution, and length of hospital stay were evaluated. A total of 116 patients were included (63 preimplementation, 53 postimplementation). Median times to Gram stain and susceptibility results were significantly shorter postimplementation (P < 0.001). The postimplementation group had an improved hazard ratio for narrow-spectrum Gram-negative therapy at 72 h (hazard ratio [HR], 2.685 [95% confidence interval {CI}, 1.348 to 5.349]), a reduced hazard ratio for 30-day inpatient mortality (adjusted HR [aHR], 0.150 [95% CI, 0.026 to 0.846]), and improved sepsis resolution (92.5% versus 77.8% [P = 0.030]). The length of hospital stay was unchanged after implementation. We conclude that implementation of the BacT/Alert Virtuo and Accelerate Pheno systems improved microbiology laboratory processes, antibiotic utilization processes, and clinical outcomes. These data support the use of rapid diagnostics in sepsis with concurrent Gram-negative bacteremia.
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