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Karadağ D, Ergon MC. Investigation of different methods in rapid microbial identification directly from positive blood culture bottles by MALDI-TOF MS. Microbiol Spectr 2024; 12:e0063824. [PMID: 38940589 PMCID: PMC11302275 DOI: 10.1128/spectrum.00638-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 05/21/2024] [Indexed: 06/29/2024] Open
Abstract
Many methods are being tried for rapid and accurate identification of sepsis-causing microorganisms. We analyzed the performance of three different preparation methods [MBT Sepsityper IVD Kit (Bruker Daltonics GmbH, Germany), sodium dodecyl sulfate (SDS) lysis, and differential centrifugation with protein extraction (Centrifugation +PE)] and compared in standard and Sepsityper modules of the Bruker Biotyper MALDI-TOF MS for direct identification of bacteria from 240 positive blood culture bottles of BACTEC FX (Becton Dickinson, USA). By using the standard module, correct identification at species level (score ≥2) was done in 46.7% of the samples with SDS lysis, 44.2% with centrifugation +PE, and 25.4% with the Sepsityper kit. These ratios at the genus level (score range 1.70-1.99) were 34.6%, 31.3%, and 32.5%, respectively. With SDS lysis (195), more bacteria were identified correctly than centrifugation +PE (181) and the Sepsityper kit (139). A statistically significant difference was found between SDS and the Sepsityper kit and Centrifugation +PE and the Sepsityper kit (P < 0.001, both). By using the Sepsityper module, correct identification at species level (score ≥1.8) was determined in 74.2% of the samples with SDS lysis and centrifugation +PE each and 55% with the Sepsityper kit. These ratios at the genus level (score range 1.60-1.79) were 16.3%, 10%, and 19.2%, respectively. SDS lysis (217) had significantly higher identification rates than centrifugation +PE (202) and the Sepsityper kit (178) (P = 0.028 and P < 0.001). A statistically significant difference was also observed between centrifugation +PE and the Sepsityper kit (P < 0.001). Best performance was obtained with SDS lysis among the methods. Although better performance was achieved by using Sepsityper software module, risk of misidentification should not be ignored. IMPORTANCE Sepsis is a life-threatening condition, and rapid and accurate identification of the causative microorganisms from blood cultures is crucial for timely and effective treatment. Although there are many studies on direct identification from blood cultures with MALDI-TOF MS, further standardization is still needed. In our study, we analyzed the performance of three different preparation methods and compared by using two analysis modules of the Bruker Biotyper MALDI-TOF MS for direct identification of bacteria from numerous positive blood culture bottles. The literature reports a limited number of studies that compare different preparation methods for direct blood culture identification, processing a large number of blood samples concurrently and evaluating the same samples as in our study. Moreover, although SDS is used very frequently in medical laboratories, there are few studies on direct identification from blood culture bottles. In our study, the highest correct identification rate was observed with the SDS method.
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Affiliation(s)
- Dilan Karadağ
- Department of Medical Microbiology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
- IMD Labor Oderland, Frankfurt (Oder), Germany
| | - Mahmut Cem Ergon
- Department of Medical Microbiology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
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Bai Y, Ding X, Zhao Q, Sun H, Li T, Li Z, Wang H, Zhang L, Zhang C, Xu S. Development of an organic acid compound disinfectant to control food-borne pathogens and its application in chicken slaughterhouses. Poult Sci 2022; 101:101842. [PMID: 35395532 PMCID: PMC8987602 DOI: 10.1016/j.psj.2022.101842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 12/24/2022] Open
Abstract
During poultry slaughter, cross-contamination of chicken carcasses with microorganisms (including drug-resistant bacteria) can occur because of incomplete disinfection during the pre-cooling process, and surface contact with contaminated tools and equipment. The use of disinfectants is the most common way to reduce the risk of cross-contamination and bacterial spread, as they can effectively reduce the number of bacteria. We developed a disinfectant consisting of organic acids and sodium dodecyl sulfate (SDS) and tested its bactericidal effects at different concentrations against Salmonella and Campylobacter. The main effective components in the disinfectant were citric acid, lactic acid, and SDS, and together they exerted a synergistic bactericidal effect. The bactericidal efficacy of the disinfectant increased with increasing concentrations of the 3 active ingredients. To reach a 100% reduction rate during a 15-s treatment in vitro, for Salmonella, the lowest concentrations of citric acid, lactic acid, and SDS were 0.06, 0.08, and 0.02%, respectively; and for Campylobacter, the lowest concentrations were 0.02, 0.025, and 0.0125%, respectively. The disinfectant remained effective in presence of interfering substances (e.g., 15% fetal bovine serum). Further experiments showed that the disinfectant inactivated sensitive bacteria as well as 23 drug-resistant strains of Salmonella and Campylobacter. Treatment with the disinfectant for 15 s decreased the concentrations of all tested strains by more than 4.7 log colony forming units per mL, and the reduction rate was as high as 100%. In on-site disinfection tests in chicken slaughterhouses, the disinfectant significantly reduced the number of pathogenic bacteria on carcasses during the pre-cooling process, and on tools (such as knives and gloves) during the segmentation process. Thus, this disinfectant has potential uses in preventing cross-contamination of food-borne pathogens (including resistant bacteria) in slaughterhouses.
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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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Zhou M, Wu Y, Kudinha T, Jia P, Wang L, Xu Y, Yang Q. Comprehensive Pathogen Identification, Antibiotic Resistance, and Virulence Genes Prediction Directly From Simulated Blood Samples and Positive Blood Cultures by Nanopore Metagenomic Sequencing. Front Genet 2021; 12:620009. [PMID: 33841495 PMCID: PMC8024499 DOI: 10.3389/fgene.2021.620009] [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] [Received: 10/26/2020] [Accepted: 02/08/2021] [Indexed: 12/11/2022] Open
Abstract
Bloodstream infection is a major cause of morbidity and mortality worldwide. We explored whether MinION nanopore sequencing could accelerate diagnosis, resistance, and virulence profiling prediction in simulated blood samples and blood cultures. One milliliter of healthy blood samples each from direct spike (sample 1), anaerobic (sample 2), and aerobic (sample 3) blood cultures with initial inoculation of ∼30 CFU/ml of a clinically isolated Klebsiella pneumoniae strain was subjected to DNA extraction and nanopore sequencing. Hybrid assembly of Illumina and nanopore reads from pure colonies of the isolate (sample 4) was used as a reference for comparison. Hybrid assembly of the reference genome identified a total of 39 antibiotic resistance genes and 77 virulence genes through alignment with the CARD and VFDB databases. Nanopore correctly detected K. pneumoniae in all three blood samples. The fastest identification was achieved within 8 h from specimen to result in sample 1 without blood culture. However, direct sequencing in sample 1 only identified seven resistance genes (20.6%) but 28 genes in samples 2–4 (82.4%) compared to the reference within 2 h of sequencing time. Similarly, 11 (14.3%) and 74 (96.1%) of the virulence genes were detected in samples 1 and 2–4 within 2 h of sequencing time, respectively. Direct nanopore sequencing from positive blood cultures allowed comprehensive pathogen identification, resistance, and virulence genes prediction within 2 h, which shows its promising use in point-of-care clinical settings.
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Affiliation(s)
- Menglan Zhou
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yarong Wu
- Beijing Applied Biological Technologies Co., Ltd., Beijing, China
| | - Timothy Kudinha
- School of Biomedical Sciences, Charles Sturt University, Orange, NSW, Australia.,Pathology West, NSW Health Pathology, Orange, NSW, Australia
| | - Peiyao Jia
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Lei Wang
- Beijing Applied Biological Technologies Co., Ltd., Beijing, China
| | - Yingchun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Qiwen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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Dai Y, Xu X, Yan X, Li D, Cao W, Tang L, Hu M, Jiang C. Evaluation of a Rapid and Simplified Protocol for Direct Identification of Microorganisms From Positive Blood Cultures by Using Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). Front Cell Infect Microbiol 2021; 11:632679. [PMID: 33777845 PMCID: PMC7990877 DOI: 10.3389/fcimb.2021.632679] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/16/2021] [Indexed: 12/17/2022] Open
Abstract
Early and rapid identification of microorganisms is critical for reducing the mortality rate caused by bloodstream infections (BSIs). The accuracy and feasibility of directly identifying pathogens in positive blood cultures by matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been intensely confirmed. In this study, we combined density centrifugation and extra chemical lysis-extraction to develop an optimized method in the blood culture process, which significantly improved the effectiveness of direct identification by MALDI-TOF MS. The accuracy was evaluated by 2,032 positive blood culture samples (115 species of microorganism). The overall MALDI-TOF MS based identification rate with scores ≥ 1.700 was 87.60%. 94.06% of gram-negative bacteria were identified consistently to the genus level, followed by anaerobes (93.33%), gram-positive bacteria (84.46%), and fungi (60.87%). This protocol could obtain results within 10–20 min at a cost of less than $0.1 per sample, which saved up to 24 h in identifying 87.60% of the microorganism from positive blood cultures. This rapid and simplified protocol facilitates the direct identification of microorganism in positive blood cultures, and exhibits the advantages of cost-effective, time-saving, and easy-to-use. It could provide the causative organism of the patient to clinicians in time for targeted treatment and reduce mortality.
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Affiliation(s)
- Yufeng Dai
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xinyi Xu
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xue Yan
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Daming Li
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wei Cao
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Lingli Tang
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China.,Clinical Molecular Diagnostic Center of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Min Hu
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China.,Clinical Molecular Diagnostic Center of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Chuanhao Jiang
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China.,Clinical Molecular Diagnostic Center of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha, China
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Ponderand L, Pavese P, Maubon D, Giraudon E, Girard T, Landelle C, Maurin M, Caspar Y. Evaluation of Rapid Sepsityper® protocol and specific MBT-Sepsityper module (Bruker Daltonics) for the rapid diagnosis of bacteremia and fungemia by MALDI-TOF-MS. Ann Clin Microbiol Antimicrob 2020; 19:60. [PMID: 33298064 PMCID: PMC7727196 DOI: 10.1186/s12941-020-00403-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/28/2020] [Indexed: 12/11/2022] Open
Abstract
During bloodstream infections, rapid adaptation of empirical treatment according to the microorganism identified is essential to decrease mortality. The aim of the present study was to assess the microbiological performances of a new rapid version of the Sepsityper® kit (Bruker Daltonics) allowing identification of bacteria and yeast by MALDI-TOF mass spectrometry directly from positive blood cultures in 10 min and of the specific MBT-Sepsityper module for spectra analysis, designed to increase identification performance. Identification rates were determined prospectively on 350 bacterial and 29 fungal positive blood cultures, and compared to conventional diagnostic method. Our rapid diagnosis strategy (Rapid Sepsityper® protocol: one spot with and one without formic acid extraction step) combined to MBT-Sepsityper module provided 65.4%, 78.9% and 62% reliable identification to the species level of monomicrobial positive blood cultures growing respectively Gram-positive, Gram-negative bacteria or yeast. Importantly, identification rates of Gram-positive bacteria were higher in anaerobic than in aerobic bottles (77.8% vs 22.2%; p = 0.004), if formic acid extraction step was performed (60.8% vs 39.2%; p = 1.8e−6) and if specific MBT-Sepsityper module was used (76.2% vs 61.9%, p = 0.041) while no significant differences were observed for Gram-negative bacteria. For yeasts identification, formic acid extraction step improved rapid identification rate by 37.9% while the specific MBT-Sepsityper module increased overall performances by 38%, providing up to 89.7% reliable identification if associated with the standard Sepsityper® protocol. These performances, associated with a reduce turnaround time, may help to implement a rapid identification strategy of bloodstream infections in the routine workflow of microbiology laboratories.
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Affiliation(s)
- Léa Ponderand
- Laboratoire de Bactériologie-Hygiène Hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France.,Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000, Grenoble, France
| | - Patricia Pavese
- Service de Médecine Infectieuse et Tropicale, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France
| | - Danièle Maubon
- Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000, Grenoble, France.,Laboratoire de Parasitologie Mycologie, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France
| | - Emmanuelle Giraudon
- Laboratoire de Parasitologie Mycologie, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France
| | - Thomas Girard
- Laboratoire de Bactériologie-Hygiène Hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France
| | - Caroline Landelle
- Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000, Grenoble, France.,Service d'Hygiène Hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France
| | - Max Maurin
- Laboratoire de Bactériologie-Hygiène Hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France.,Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000, Grenoble, France
| | - Yvan Caspar
- Laboratoire de Bactériologie-Hygiène Hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, 38000, Grenoble, France. .,Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000, Grenoble, France. .,Laboratoire de Bactériologie-Hygiène Hospitalière, Institut de Biologie et Pathologie, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043, Grenoble Cedex 9, France.
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7
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Review on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the rapid screening of microbial species: A promising bioanalytical tool. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105387] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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8
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Wang Y, Jin Y, Bai Y, Song Z, Chu W, Zhao M, Hao Y, Lu Z. Rapid method for direct identification of positive blood cultures by MALDI-TOF MS. Exp Ther Med 2020; 20:235. [PMID: 33178337 DOI: 10.3892/etm.2020.9365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 08/27/2020] [Indexed: 12/22/2022] Open
Abstract
Application of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) using positive blood cultures (BCs) is a revolution in identification of microorganisms in clinical microbiology laboratories. Although there are several commercial pretreatment protocols they are expensive. Here, we evaluated the performance of a locally produced Bioyong pre-treatment kit for the direct identification of microorganisms in positive BCs by MALDI-TOF MS method. The mocked positive BCs were performed using 200 Thermo aerobic blood culture bottles and 200 aerobic Scenker blood culture bottles. A total of 200 organisms were invovled, including 91 strains of Gram-positive bacteria, 97 strains of Gram-negative bacteria and 12 strains of Candida. The positive BCs were subcultured and identified by classical biochemical Vitek II testing as the gold standard of identification. The Bioyong pre-treatment kit could successfully identify microorganisms in 189 (94.5%) Thermo positive BCs and 189 (94.5%) Scenker positive blood cultures, respectively. In total, 94 (96.9%) Gram-negative bacteria, 86 (94.5%) Gram-positive bacteria and 9 (75.0%) candida isolated from Thermo positive BCs were correctly identified to species level and 95 (97.9%) Gram-negative bacteria, 86 (94.5%) Gram-positive bacteria and 8 (66.7%) candida isolated from Scenker positive BCs were correctly identified to species level. This method provides a rapid, accurate identification of bacteria and Candida within one hour in positive blood cultures. Routine application of this technique will improve the antimicrobial treatment within 24 h among the patients with bacteremia and candidemia.
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Affiliation(s)
- Yueling Wang
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Yan Jin
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Yuanyuan Bai
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Zhen Song
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Wenjun Chu
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Mengqi Zhao
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Yingying Hao
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China.,Department of Clinical Laboratory, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, P.R. China
| | - Zhiming Lu
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China.,Department of Clinical Laboratory, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, P.R. China
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Huang YL, Sun QL, Li JP, Hu YY, Zhou HW, Zhang R. Evaluation of an in-house MALDI-TOF MS rapid diagnostic method for direct identification of micro-organisms from blood cultures. J Med Microbiol 2018; 68:41-47. [PMID: 30418107 DOI: 10.1099/jmm.0.000866] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Bloodstream infections are major causes of morbidity and mortality among hospitalized patients worldwide. Early identification of micro-organisms from blood culture can facilitate earlier optimization of treatment. The objective of this study was to assess an in-house method based on a new matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) platform (Clin-TOF MS) for direct organism identification. METHODOLOGY We studied the performance of the in-house method for direct identification and the conventional sub-culture method in parallel. Identification from subcultures was analysed with Bruker MS as the reference method. RESULTS A total of 666 blood cultures with a single micro-organism that flagged positive after no more than a 3-day incubation period were collected. The identification accuracy of the in-house Clin-TOF MS method for direct identification and the sub-culture method was 88.6 and 100 %, respectively. The in-house method exhibited better performance for Gram-negative bacteria than for Gram-positive bacteria (93.3 vs 81.6 %). The accuracy rate for anaerobes was 100 % (3/3). The lowest accurate identification rate was for yeast; this was only 20 %. Lytic Anaerobic/F (LAF) and Plus Aerobic/F (PAF) provided the highest accurate identification rates, and it was noteworthy that the accuracy rate for FAN Aerobic (FA) was 82 %, which is higher than previously reported and showed that the method was effective. CONCLUSION Our study provides an effective sample preparation method for the direct identification of pathogens from positive blood culture vials via Clin-TOF MS at a very low cost of about $0.5 per sample and with a short turnaround time of about 20 min. This will help clinicians make precise diagnoses and provide targeted prescriptions, reducing the risk of the potential development of resistance.
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Affiliation(s)
- Yong-Lu Huang
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou 310009, PR China
| | - Qiao-Ling Sun
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou 310009, PR China
| | - Jia-Ping Li
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou 310009, PR China
| | - Yan-Yan Hu
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou 310009, PR China
| | - Hong-Wei Zhou
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou 310009, PR China
| | - Rong Zhang
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou 310009, PR China
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10
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Lee JE, Jo SJ, Park KG, Suk HS, Ha SI, Shin JS, Park YJ. Evaluation of modified saponin preparation method for the direct identification and antimicrobial susceptibility testing from positive blood culture. J Microbiol Methods 2018; 154:118-123. [PMID: 30321566 DOI: 10.1016/j.mimet.2018.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/05/2018] [Accepted: 10/05/2018] [Indexed: 11/19/2022]
Abstract
BACKGROUND We evaluated the two in-house sample preparation methods (saponin method (SAP) and [saponin + Sputazyme] method (SSPZ)) for direct identification of microorganisms using MALDI-TOF MS from positive blood culture bottles. Also, we evaluated the [saponin + Sputazyme] method for direct antimicrobial susceptibility testing (AST) using Vitek 2 system. METHODS For direct identification, 163 prospective, monomicrobial positive blood culture bottles and 25 contrived blood culture bottles spiked with 25 infrequently isolated bacterial strains were included. For direct AST, pellets obtained by SSPZ method from 102 prospective blood culture bottles were tested. The results from the direct identification and AST were compared with those from the routine diagnostic method performed with colonies sub cultured on solid media. RESULTS In 163 prospective specimens, SAP method correctly identified 132/163 (81.0%) isolates and SSPZ method correctly identified 148/163 (90.8%) isolates (P = .018). Among the 92 Gram-positive isolates, the correct identification rate was significantly higher with the SSPZ method than the SAP method (92.4% vs. 81.5%), respectively (P = .041). However, the SSPZ method failed to identify Streptococcus pneumoniae. Among the 64 Gram-negative isolates, the correct identification rate was 82.8% (53/64) and 87.5% (56/64) for the former and the latter method, respectively (P = .491). Compared with standard methods direct AST showed 98.5% (1523/1547) agreement. CONCLUSION The addition of Sputazyme improved the identification of commonly isolated bacteria, especially for Gram-positive isolates and yeasts and can be applied for direct antimicrobial susceptibility testing of bacteria. Although SAP method showed better results for Campylobacter spp. and anaerobic bacteria, considering their very low incidence, routine use of SSPZ will be more practical.
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Affiliation(s)
- Ji Eun Lee
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sung Jin Jo
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Kang Gyun Park
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hyun Soo Suk
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sung Il Ha
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jeong Seob Shin
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yeon-Joon Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
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Anson LW, Chau K, Sanderson N, Hoosdally S, Bradley P, Iqbal Z, Phan H, Foster D, Oakley S, Morgan M, Peto TEA, Modernizing Medical Microbiology Informatics Group Mmmig, Crook DW, Pankhurst LJ. DNA extraction from primary liquid blood cultures for bloodstream infection diagnosis using whole genome sequencing. J Med Microbiol 2018; 67:347-357. [PMID: 29458686 PMCID: PMC5882078 DOI: 10.1099/jmm.0.000664] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Speed of bloodstream infection diagnosis is vital to reduce morbidity and mortality. Whole genome sequencing (WGS) performed directly from liquid blood culture could provide single-assay species and antibiotic susceptibility prediction; however, high inhibitor and human cell/DNA concentrations limit pathogen recovery. We develop a method for the preparation of bacterial DNA for WGS-based diagnostics direct from liquid blood culture. METHODOLOGY We evaluate three commercial DNA extraction kits: BiOstic Bacteraemia, Amplex Hyplex and MolYsis Plus. Differential centrifugation, filtration, selective lysis and solid-phase reversible immobilization bead clean-up are tested to improve human cells/DNA and inhibitor removal. Using WGS (Illumina/MinION), we assess human DNA removal, pathogen recovery, and predict species and antibiotic susceptibility inpositive blood cultures of 44 Gram-negative and 54 Staphylococcus species.Results/Key findings. BiOstic kit extractions yield the greatest mean DNA concentration, 94-301 ng µl-1, versus 0-2.5 ng µl-1 using Amplex and MolYsis kits. However, we note higher levels of inhibition (260/280 ratio 0.9-2.1) and human DNA (0.0-4.4×106 copies) in BiOstic extracts. Differential centrifugation (2000 g, 1 min) prior to BiOstic extraction reduces human DNA by 63-89 % with selective lysis minimizing by a further 62 %. Post-extraction bead clean-up lowers inhibition. Overall, 67 % of sequenced samples (Illumina MiSeq) contain <10 % human DNA, with >93 % concordance between WGS-based species and susceptibility predictions and clinical diagnosis. If >60 % of sequencing reads are human (7/98 samples) susceptibility prediction becomes compromised. Novel MinION-based WGS (n=9) currently gives rapid species identification but not susceptibility prediction. CONCLUSION Our method for DNA preparation allows WGS-based diagnosis direct from blood culture bottles, providing species and antibiotic susceptibility prediction in a single assay.
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Affiliation(s)
- Luke W Anson
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK.,Present address: Genomic Research Laboratory, Division of Infectious Diseases, University of Geneva Hospitals, Rue Gabrielle-Perret-Gentil, 4, CH-1211 Geneva 14, Switzerland
| | - Kevin Chau
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Nicholas Sanderson
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Sarah Hoosdally
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Phelim Bradley
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Zamin Iqbal
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Hang Phan
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK.,NIHR Health Protection Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - Dona Foster
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Sarah Oakley
- Microbiology Laboratory, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, OX3 9DU, UK
| | - Marcus Morgan
- Microbiology Laboratory, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, OX3 9DU, UK
| | - Tim E A Peto
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK.,National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | | | - Derrick W Crook
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK.,National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, OX3 9DU, UK.,Public Health England, Wellington House, 133-155 Waterloo Rd, Lambeth, London SE1 8UG, UK
| | - Louise J Pankhurst
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
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Zhou M, Yang Q, Kudinha T, Sun L, Zhang R, Liu C, Yu S, Xiao M, Kong F, Zhao Y, Xu YC. An Improved In-house MALDI-TOF MS Protocol for Direct Cost-Effective Identification of Pathogens from Blood Cultures. Front Microbiol 2017; 8:1824. [PMID: 29033904 PMCID: PMC5625089 DOI: 10.3389/fmicb.2017.01824] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/06/2017] [Indexed: 11/23/2022] Open
Abstract
Background: Bloodstream infection is a major cause of morbidity and mortality in hospitalized patients worldwide. Delays in the identification of microorganisms often leads to a poor prognosis. The application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) directly to blood culture (BC) broth can potentially identify bloodstream infections earlier, and facilitate timely management. Methods: We developed an “in-house” (IH) protocol for direct MALDI-TOF MS based identification of organisms in positive BCs. The IH protocol was initially evaluated and improved with spiked BC samples, and its performance was compared with the commercial Sepsityper™ kit using both traditional and modified cut-off values. We then studied in parallel the performance of the IH protocol and the colony MS identifications in positive clinical BC samples using only modified cut-off values. All discrepancies were investigated by “gold standard” of gene sequencing. Results: In 54 spiked BC samples, the IH method showed comparable results with Sepsityper™ after applying modified cut-off values. Specifically, accurate species and genus level identification was achieved in 88.7 and 3.9% of all the clinical monomicrobial BCs (284/301, 94.4%), respectively. The IH protocol exhibited superior performance for Gram negative bacteria than for Gram positive bacteria (92.8 vs. 82.4%). For anaerobes and yeasts, accurate species identification was achieved in 80.0 and 90.0% of the cases, respectively. For polymicrobial cultures (17/301, 5.6%), MALDI-TOF MS correctly identified a single species present in all the polymicrobial BCs under the Standard mode, while using the MIXED method, two species were correctly identified in 52.9% of the samples. Comparisons based on BC bottle type, showed that the BACTEC™ Lytic/10 Anaerobic/F culture vials performed the best. Conclusion: Our study provides a novel and effective sample preparation method for MALDI-TOF MS direct identification of pathogens from positive BC vials, with a lower cost ($1.5 vs. $ 7) albeit a slightly more laborious extracting process (an extra 15 min) compared with Sepsityper™ kit.
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Affiliation(s)
- Menglan Zhou
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Qiwen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Timothy Kudinha
- Charles Sturt University, Leeds Parade, Orange, NSW, Australia
| | - Liying Sun
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| | - Rui Zhang
- Becton Dickinson Medical Devices Company, Shanghai, China
| | - Chang Liu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Shuying Yu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Meng Xiao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, Westmead Hospital, Westmead, NSW, Australia
| | - Yupei Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Ying-Chun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
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