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Tian PP, Su SS, Zhu LS, Wang T, Yang H, Du MY, Ding CZ, Wang L, Fan W, Yi HW. Short-term culture for rapid identification by mass spectrometry and automated antimicrobial susceptibility testing from positive bottles. BMC Infect Dis 2024; 24:566. [PMID: 38844852 PMCID: PMC11157804 DOI: 10.1186/s12879-024-09475-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 06/04/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Early and appropriate antibiotic treatment improves the clinical outcome of patients with sepsis. There is an urgent need for rapid identification (ID) and antimicrobial susceptibility testing (AST) of bacteria that cause bloodstream infection (BSI). Rapid ID and AST can be achieved by short-term incubation on solid medium of positive blood cultures using MALDI-TOF mass spectrometry (MS) and the BD M50 system. The purpose of this study is to evaluate the performance of rapid method compared to traditional method. METHODS A total of 124 mono-microbial samples were collected. Positive blood culture samples were short-term incubated on blood agar plates and chocolate agar plates for 5 ∼ 7 h, and the rapid ID and AST were achieved through Zybio EXS2000 MS and BD M50 System, respectively. RESULTS Compared with the traditional 24 h culture for ID, this rapid method can shorten the cultivation time to 5 ∼ 7 h. Accurate organism ID was achieved in 90.6% of Gram-positive bacteria (GP), 98.5% of Gram-negative bacteria (GN), and 100% of fungi. The AST resulted in the 98.5% essential agreement (EA) and 97.1% category agreements (CA) in NMIC-413, 99.4% EA and 98.9% CA in PMIC-92, 100% both EA and CA in SMIC-2. Besides, this method can be used for 67.2% (264/393) of culture bottles during routine work. The mean turn-around time (TAT) for obtaining final results by conventional method is approximately 72.6 ± 10.5 h, which is nearly 24 h longer than the rapid method. CONCLUSIONS The newly described method is expected to provide faster and reliable ID and AST results, making it an important tool for rapid management of blood cultures (BCs). In addition, this rapid method can be used to process most positive blood cultures, enabling patients to receive rapid and effective treatment.
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Affiliation(s)
- Peng-Peng Tian
- Laboratory Department, The First Affiliated Hospital of Yangtze University, Jing Zhou, Hubei, China
| | - Shan-Shan Su
- Laboratory Department, The First Affiliated Hospital of Yangtze University, Jing Zhou, Hubei, China
| | - Li-Sha Zhu
- Laboratory Department, The First Affiliated Hospital of Yangtze University, Jing Zhou, Hubei, China
| | - Tian Wang
- Laboratory Department, The First Affiliated Hospital of Yangtze University, Jing Zhou, Hubei, China
| | - Hui Yang
- Laboratory Department, The First Affiliated Hospital of Yangtze University, Jing Zhou, Hubei, China
| | - Meng-Yao Du
- Laboratory Department, The First Affiliated Hospital of Yangtze University, Jing Zhou, Hubei, China
| | - Cai-Zhi Ding
- Laboratory Department, The People's Hospital of Songzi, Jingzhou, Hubei, China
| | - Li Wang
- Laboratory Department, The First Affiliated Hospital of Yangtze University, Jing Zhou, Hubei, China
| | - Wen Fan
- Laboratory Department, The First Affiliated Hospital of Yangtze University, Jing Zhou, Hubei, China.
| | - Hua-Wei Yi
- Laboratory Department, The First Affiliated Hospital of Yangtze University, Jing Zhou, Hubei, China.
- Hubei Provincial Clinical Research Center for Individualized Diagnosis and Treatment of Cancer, The First People's Hospital of Jingzhou, Jingzhou, Hubei, China.
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Singh V, Agarwal J, Nath SS, Sharma A. Evaluation of Direct Antimicrobial Susceptibility Testing from Positive Flagged Blood Cultures in Sepsis Patients. Indian J Crit Care Med 2024; 28:387-392. [PMID: 38585311 PMCID: PMC10998512 DOI: 10.5005/jp-journals-10071-24687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/05/2024] [Indexed: 04/09/2024] Open
Abstract
Background Presently, many laboratories are equipped with automated system for antimicrobial susceptibility testing (AST) for minimum inhibitory concentration-based reporting which enables the clinician to choose the right antimicrobial for timely treatment of sepsis. The study aimed to assess performance of direct AST from blood culture positive broth using automated AST system for accuracy and time taken to release the report. Materials and methods The present study conducted in a 25-bedded ICU in North India for 12 months. Single morphotype of bacteria on gram stain from positively flagged blood culture bottles were included, which was directly identified (using an in-house protocol) with MALDI-TOF-MS from positive blood culture broths. DAST was carried out from 200 such blood culture broths and results were compared with reference AST (RAST) which was also done using VITEK-2 using overnight grown bacterial colonies as per standard protocol. Results Among 60 isolates of Enterobacterales, 99% categorical agreement for both E. coli and K. pneumoniae observed by two methods were tested for AST. Among non-fermenters, Pseudomonas aeruginosa showed a categorical agreement of 99.6%, as compared with Acinetobacter spp. and exotic GNBs, which showed 95-96% agreement. A significant difference of 18-24 hours was noted in time to release the report between DAST and RAST, for GNB and GPC both. Conclusion Direct AST from positive flagged blood culture bottles can significantly reduce the time to release the bacterial susceptibility report by up to 24 hours, at the same time maintaining the accuracy. How to cite this article Singh V, Agarwal J, Nath SS, Sharma A. Evaluation of Direct Antimicrobial Susceptibility Testing from Positive Flagged Blood Cultures in Sepsis Patients. Indian J Crit Care Med 2024;28(4):387-392.
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Affiliation(s)
- Vikramjeet Singh
- Department of Microbiology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Jyotsna Agarwal
- Department of Microbiology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Soumya S Nath
- Department of Anaesthesiology and Critical Care, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Avneesh Sharma
- Department of Microbiology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
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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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4
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Arana DM, Hernández-Hermida Y, Cacho-Calvo J. A simple double differential centrifugation-wash procedure to rapidly obtain bacterial identification and direct antimicrobial susceptibility testing from positive blood cultures. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2023; 41:225-229. [PMID: 36610834 DOI: 10.1016/j.eimce.2021.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/29/2021] [Indexed: 01/07/2023]
Abstract
INTRODUCTION This study proposes a simple and rapid method for both bacterial identification and direct antimicrobial susceptibility testing (AST) by using MALDI-TOF and a double differential centrifugation-wash procedure from positive blood cultures. METHODS Fifty-two positive blood cultures (37 gramnegative bacilli and 15 grampositive cocci) were studied by two methods for identification and AST: a reference method, and the rapid MALDI-TOF method obtaining a purified pellet by using a double differential centrifugation procedure. RESULTS A total of 1101 MIC values (mg/l) were interpreted according to EUCAST clinical breakpoints and compared using the two methods simultaneously. Discrepancies in 81 MIC values (7.35%) were detected. By analyzing standard parameters, we obtained 98.28% essential agreement and 92.65% categorical agreement considering all isolates tested. CONCLUSION This method provides rapid bacterial identification and AST, offering definitive results 24-48h earlier than the conventional method (p<0.001) and improving the turnaround time in blood culture diagnostics, especially in laboratories without 24-h on-call.
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Affiliation(s)
- David M Arana
- Servicio de Microbiología, Hospital Universitario de Getafe, Madrid, Spain.
| | | | - Juana Cacho-Calvo
- Servicio de Microbiología, Hospital Universitario de Getafe, Madrid, Spain
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5
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KAYIN DİNÇ M, ÖZENCİ V, AYDEMİR SŞ. Rapid diagnosis of bacteria and determination of sensitivity in blood culture. EGE TIP DERGISI 2022. [DOI: 10.19161/etd.1125186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Aim: In patients with bloodstream infection; identifying the causative agent in a short time and applying appropriate antimicrobial therapy is very important in terms of reducing morbidity and mortality. In this study, it was aimed to evaluate a new method developed for direct identification and antibiotic susceptibility testing from blood culture.
Materials and Methods: Bacterial pellet was obtained from blood culture samples that showed positive signals in the BacT/Alert 3D system by washing and centrifugation. Identification was made from this pellet using Vitek MS, followed by direct antibiotic susceptibility testing in the VITEK 2 automated system. The results were compared with the standard method.
Results: Identification was performed on 80 blood culture samples. In the direct identification process, 73 samples were identified, of which 72 (90%) resulted in agreement with the standard method. Direct antibiotic susceptibility tests were found to be compatible with a rate of 97.9%. Among the evaluated 635 antibiotic susceptibility results; it was observed that 10 of them had major errors and 3 of them had minor errors.
Conclusions: Using the procedures applied in the study from blood culture samples, without the need for costly reagents or long processing time, it has been observed that identification and antibiotic susceptibility results can be obtained within 24 hours, similar to standard results.
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Affiliation(s)
| | - Volkan ÖZENCİ
- Buca Seyfi Demirsoy Eğitim ve Araştırma Hastanesi, İzmir, Türkiye
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Wen H, Xie S, Liang Y, Liu Y, Wei H, Sun Q, Wang W, Wen B, Zhao J. Direct Identification, Antimicrobial Susceptibility Testing, and Extended-Spectrum β-Lactamase and Carbapenemase Detection in Gram-Negative Bacteria Isolated from Blood Cultures. Infect Drug Resist 2022; 15:1587-1599. [PMID: 35418761 PMCID: PMC8995151 DOI: 10.2147/idr.s350612] [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: 01/05/2022] [Accepted: 03/23/2022] [Indexed: 12/21/2022] Open
Abstract
Purpose To shorten the turnaround time for blood culture (BC) analyses, a rapid method was developed for the direct identification, antimicrobial susceptibility testing (AST), and multidrug resistance testing of bacteria-positive BCs. Materials and Methods The mixtures in BC bottles were treated with the multistep centrifugation method developed here and the conventional culture-based method. The bacterial sediment obtained after centrifugation was analyzed directly with MALDI-TOF MS and Vitek 2 Compact, and AST was performed directly with the Kirby–Bauer (K–B) disk diffusion, VITEK 2 Compact, and E-test methods. Extended spectrum lactamases (ESBLs) were detected with discs containing cefotaxime, cefotaxime/clavulanate, ceftazidime, and ceftazidime/clavulanate, and carbapenemase was detected with the modified carbapenem inactivation method (mCIM) and EDTA-mCIM (eCIM). Results All the results of direct testing were compared to those of the conventional methods, to evaluate the accuracy of the direct methods. The accuracies of the direct Vitek 2 Compact and MALDI-TOF MS methods were 95.5% (214/224) and 90.2% (202/224), respectively. Direct AST with K–B, Vitek 2, and E-test showed category agreement of 96.0% (2611/2721), 96.1% (2614/2721), and 97.4% (2650/2721), respectively, and the major errors and very major errors were < 2% for all three methods. In the direct determination of ESBLs, the results for cefotaxime combined with cefotaxime/clavulanate were completely consistent with those after the standard isolation method. The carbapenemase detection rate with direct mCIM and eCIM was exactly the same as that with the standard method. Conclusion These direct procedures based on multistep centrifugation are not only highly accurate but are appropriate for clinical laboratory use because the turnaround time is shorter.
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Affiliation(s)
- Hainan Wen
- The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, People’s Republic of China
| | - Shoujun Xie
- Clinical Laboratory, the Affiliated Hospital of Chengde Medical University, Chengde, Hebei, People’s Republic of China
| | - Yueyi Liang
- Clinical Laboratory, the Affiliated Hospital of Chengde Medical University, Chengde, Hebei, People’s Republic of China
| | - Yanchao Liu
- Clinical Laboratory, the Affiliated Hospital of Chengde Medical University, Chengde, Hebei, People’s Republic of China
| | - Honglian Wei
- The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, People’s Republic of China
| | - Qian Sun
- The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, People’s Republic of China
| | - Weigang Wang
- The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, People’s Republic of China
- Hebei Provincial Center for Clinical Laboratories, Shijiazhuang, Hebei, People’s Republic of China
| | - Baojiang Wen
- The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, People’s Republic of China
- Hebei Provincial Center for Clinical Laboratories, Shijiazhuang, Hebei, People’s Republic of China
| | - Jianhong Zhao
- The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, People’s Republic of China
- Hebei Provincial Center for Clinical Laboratories, Shijiazhuang, Hebei, People’s Republic of China
- Correspondence: Jianhong Zhao, The Second Hospital of Hebei Medical University, 215 West Heping Road, Shijiazhuang, Hebei Province, 050051, People’s Republic of China, Tel +86 158 03210790, Fax +86 311 66002851, Email
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Kavipriya D, Prakash SS, Dhandapani S, Rajshekar D, Sastry AS. Evaluation of the Performance of Direct Susceptibility Test by VITEK-2 from Positively Flagged Blood Culture Broth for Gram-Negative Bacilli. J Lab Physicians 2022; 13:374-379. [PMID: 34975259 PMCID: PMC8714412 DOI: 10.1055/s-0041-1732489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Background
Timely initiation of antimicrobial therapy in patients with blood stream infection is absolutely necessary to reduce mortality and morbidity. Most clinical microbiology laboratories use conventional methods for identification and antimicrobial susceptibility testing (AST) that involve biochemical methods for identification followed by AST by disk diffusion. The aim of the current study is to assess the various errors associated with direct susceptibility testing done from blood culture broth using automated AST system-Vitek-2 compact compared with the reference method of AST done from bacterial colonies.
Materials and Methods
The study was conducted in a tertiary care public sector 2,200-bedded hospital in South India for a period of 6 months. The study involved positively flagged blood culture bottles that yielded single morphotype of Gram-negative organism by Gram stain. A total of 120 bacterial isolates were collected that consisted of consecutively obtained first 60 isolates of Enterobacteriaceae family (30
Escherichia coli
and 30
Klebsiella pneumoniae
) and consecutively obtained first 60 nonfermenters (30
Pseudomonas aeruginosa
and 30
Acinetobacter baumannii).
Vitek-2 AST was done from these 120 blood culture broth, following the protocol by Biomerieux, and results were obtained. Then, Vitek-2 was done from colonies (reference method) using appropriate panel for Enterobacteriaceae and nonfermenters, and results were obtained. Both the results were compared.
Results
Nonfermenters showed a better categorical agreement of 97.6%, as compared to Enterobacteriaceae, which showed 97%. Among Enterobacteriaceae, both
E. coli
and
K. pneumoniae
showed categorical agreement of 97% each.
Conclusion
The procedure of AST directly from blood culture broth represents a simple and effective technique that can reduce the turnaround time by 24 hours, which in turn benefits the clinician in appropriate utilization of antimicrobials for better patient care.
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Affiliation(s)
- D Kavipriya
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Suman Susan Prakash
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Sarumathi Dhandapani
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Deepashree Rajshekar
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Apurba Sankar Sastry
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
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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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Sun B, Kang X, Yue S, Lan L, Li R, Chen C, Zhang W, He S, Zhang C, Fan Y, Wang P, Zheng G, Hong W. A rapid procedure for bacterial identification and antimicrobial susceptibility testing directly from positive blood cultures. Analyst 2021; 147:147-154. [PMID: 34860216 DOI: 10.1039/d1an01210j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
There is an urgent need to develop a rapid procedure that can rapidly identify and obtain antimicrobial susceptibility testing (AST) results directly from positive blood cultures. Here, we report a semi-automatic bacterial diagnosis procedure, which includes (1) a bacterial concentration process to isolate bacteria from a positive blood culture bottle (PBCB), (2) an identification process using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), and (3) a rapid AST process based on stimulated Raman scattering imaging of deuterium oxide (D2O) incorporation in bacteria. A total of 105 samples were tested for bacterial identification, and a bacterial identification accuracy of 92.3% was achieved. AST takes about 2.5 h after identification. This semi-automatic procedure only takes 3.5 h, which is demonstrated to be the fastest process to obtain identification and AST results starting from PBCBs.
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Affiliation(s)
- Bo Sun
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China. .,Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
| | - Xixiong Kang
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
| | - Shuhua Yue
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.
| | - Lu Lan
- Vibronix Inc., West Lafayette, IN, USA
| | - Rui Li
- Vibronix Inc., West Lafayette, IN, USA
| | - Chen Chen
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.
| | - Weifeng Zhang
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.
| | - Shipei He
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.
| | - Chenxi Zhang
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
| | - Yubo Fan
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China. .,School of Medical Science and Engineering, Beihang University, Beijing, China
| | - Pu Wang
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.
| | - Guanghui Zheng
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
| | - Weili Hong
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.
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Sze DTT, Lau CCY, Chan TM, Ma ESK, Tang BSF. Comparison of novel rapid diagnostic of blood culture identification and antimicrobial susceptibility testing by Accelerate Pheno system and BioFire FilmArray Blood Culture Identification and BioFire FilmArray Blood Culture Identification 2 panels. BMC Microbiol 2021; 21:350. [PMID: 34922463 PMCID: PMC8684256 DOI: 10.1186/s12866-021-02403-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 11/25/2021] [Indexed: 12/25/2022] Open
Abstract
Background
Conventional turnaround time (TAT) for positive blood culture (PBC) identification (ID) and antimicrobial susceptibility testing (AST) is 2–3 days. We evaluated the TAT and ID/AST performance using clinical and seeded samples directly from PBC bottles with different commercial approaches: (1) Accelerate Pheno® system (Pheno) for ID/AST; (2) BioFire® FilmArray® Blood Culture Identification (BCID) Panel and/ or BCID2 for ID; (3) direct AST by VITEK® 2 (direct AST); and (4) overnight culture using VITEK® 2 colony AST. Results
A total of 141 PBC samples were included in this evaluation. Using MALDI-TOF (Bruker MALDI Biotyper) as the reference method for ID, the overall monomicrobial ID sensitivity/specificity are as follows: Pheno 97.9/99.9%; BCID 100/100%; and BCID2 100/100%, respectively. For AST performance, broth microdilution (BMD) was used as the reference method. For gram-negatives, overall categorical and essential agreements (CA/EA) for each method were: Pheno 90.3/93.2%; direct AST 92.6/88.5%; colony AST 94.4/89.5%, respectively. For gram-positives, the overall CA/EAs were as follows: Pheno 97.2/98.89%; direct AST 97.2/100%; colony AST 97.2/100%, respectively. The BCID/BCID2 and direct AST TATs were around 9–20 h (1/9-19 h for ID with resistance markers/AST), with 15 min/sample hands-on time. In comparison, Pheno TATs were around 8–10 h (1.5/7 h for ID/AST) with 2 min/sample hands-on time, maintains a clinically relevant fast report of antibiotic minimal inhibitory concentration (MIC) and allows for less TAT and hands-on time. Conclusion In conclusion, to the best of our knowledge, this is the first study conducted as such in Asia; all studied approaches achieved satisfactory performance, factors such as TAT, panel of antibiotics choices and hands-on time should be considered for the selection of appropriate rapid ID and AST of PBC methods in different laboratory settings. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02403-y.
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11
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Kilic A, Palavecino EL. Performance of MicroScan Overnight Panels for antibiotic susceptibility testing of staphylococci strains directly from positive blood culture bottles. Infect Dis Now 2021; 52:179-181. [DOI: 10.1016/j.idnow.2021.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/12/2021] [Accepted: 12/10/2021] [Indexed: 11/26/2022]
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12
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Arana DM, Hernández-Hermida Y, Cacho-Calvo J. A simple double differential centrifugation-wash procedure to rapidly obtain bacterial identification and direct antimicrobial susceptibility testing from positive blood cultures. Enferm Infecc Microbiol Clin 2021. [DOI: 10.1016/j.eimc.2021.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Yoo IY, Han J, Ha SI, Cha YJ, Pil SD, Park YJ. Clinical performance of ASTA SepsiPrep kit in direct bacterial identification and antimicrobial susceptibility test using MicroIDSys Elite and VITEK-2 system. J Clin Lab Anal 2021; 35:e23744. [PMID: 33939213 PMCID: PMC8183931 DOI: 10.1002/jcla.23744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/21/2021] [Accepted: 02/09/2021] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Rapid and accurate microbial identification and antimicrobial susceptibility testing (AST) are essential for timely use of appropriate antimicrobial agents for bloodstream infection. To shorten the time for isolating colonies from the positive blood culture, various preparation methods for direct identification using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) system were developed. Here, we evaluated the SepsiPrep kit (ASTA Corp.) for direct identification of microorganisms and AST from positive blood cultures using MicroIDSys Elite MALDI-TOF MS system (ASTA Corp.) and VITEK-2 system (bioMérieux). METHODS For direct identification, a total of 124 prospective monomicrobial positive blood culture bottles were included. For direct identification, the pellet was prepared by centrifugation and washing twice. For direct AST, the pellet was suspended in 0.45% saline and adjusted to McFarland 0.5. The results from the direct identification and AST using MicroIDSys Elite and VITEK-2 system were compared to those from the conventional method performed with pure colony subcultured on agar plate. RESULTS Compared to the conventional method using pure colony, correct direct identification rate was 96.5% and 98.5% for 57 gram-positive isolates and 67 gram-negative isolates, respectively. For direct AST, among the 55 gram-positive isolates, the categorical agreement (CA) for staphylococci, streptococci, and enterococci was 96.7%, 98.4%, and 94.1%, respectively. For 66 gram-negative isolates, the CA for Enterobacterales and non-fermentative gram-negative rods was 99.0% and 96.6%, respectively. CONCLUSIONS The SepsiPrep kit was easy to use combined with MicroIDSys Elite and VITEK-2 system and also, the correct identification and AST rate were very high.
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Affiliation(s)
- In Young Yoo
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Jayho Han
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Sung Il Ha
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Young Jong Cha
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Shin Dong Pil
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Yeon-Joon Park
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea
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14
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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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15
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Kuo FC, Chien CC, Lee MS, Wang JW, Lin PC, Lee CH. Rapid diagnosis of periprosthetic joint infection from synovial fluid in blood culture bottles by direct matrix-assisted laser desorption ionization time-of-flight mass spectrometry. PLoS One 2020; 15:e0239290. [PMID: 32970712 PMCID: PMC7515592 DOI: 10.1371/journal.pone.0239290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/03/2020] [Indexed: 11/18/2022] Open
Abstract
Background The aim of this prospective study was to use direct matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) to rapidly diagnose periprosthetic joint infections (PJIs). Method Synovial fluid was taken from 77 patients (80 joints, 41 hips and 39 knees) who met the International Consensus Meeting criteria for PJI, and inoculated into blood culture bottles (BCBs) and onto conventional swabs. Positive blood cultures were analyzed using either direct or routine MALDI-TOF MS. Pathogen identification and the time to identification was recorded. Differences between groups were analyzed using the Kruskal-Wallis test and Bonferroni's post-hoc test. Results Direct and routine MALDI-TOF MS both detected 64 positive results (80%), compared to 47 (59%) by conventional swabs (p = 0.002). Direct MALDI-TOF MS identified 85.3% of the gram-positive organisms and 92.3% of the gram-negative organisms. No fungi were identified by direct MALDI-TOF MS. In 17 BCBs that were flagged positive, identification by direct MALDI-TOF MS failed. Among the positive results in the direct MALDI-TOF MS group, Staphylococcus aureus accounted for 47%, followed by Staphylococcus epidermidis (17%), Escherichia coli (9%) and Klebsiella pneumoniae (9%). The median time to microorganism identification was significantly shorter with direct MALDI-TOF MS (12.7 h, IQR: 8.9–19.6 h) than with routine MALDI-TOF MS (39.5 h, IQR: 22.8–46.0 h) or swabs (44.4 h, IQR: 27.2–72.6 h) (p < 0.0001). In pairwise comparisons, there were significant differences in the time of microorganism identification between direct MALDI-TOF MS and routine MALDI-TOF MS (p < 0.0001) or swab culture (p < 0.0001). There was no significant difference between routine MALDI-TOF MS and swab culture (p = 0.0268). Conclusion Compared with current laboratory practice, direct MALDI-TOF MS shortened the time to microorganism identification and had superior results compared to conventional swabs, except for fungi. Further studies should investigate whether the earlier administration of appropriate antimicrobial agents can improve the treatment outcomes of PJIs.
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Affiliation(s)
- Feng-Chih Kuo
- Department of Orthopaedic Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
- College of Medicine, Chang Gung University, Kaohsiung, Taiwan
| | - Chun-Chih Chien
- Laboratory Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Mel S. Lee
- Department of Orthopaedic Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
- College of Medicine, Chang Gung University, Kaohsiung, Taiwan
| | - Jun-Wen Wang
- Department of Orthopaedic Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
- College of Medicine, Chang Gung University, Kaohsiung, Taiwan
| | - Po-Chun Lin
- Department of Orthopaedic Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
- College of Medicine, Chang Gung University, Kaohsiung, Taiwan
| | - Chen-Hsiang Lee
- College of Medicine, Chang Gung University, Kaohsiung, Taiwan
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
- * E-mail:
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16
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Mancini S, Bodendoerfer E, Kolensnik-Goldmann N, Herren S, Röthlin K, Courvalin P, Böttger EC. Evaluation of standardized automated rapid antimicrobial susceptibility testing of Enterobacterales-containing blood cultures: a proof-of-principle study. J Antimicrob Chemother 2020; 75:3218-3229. [DOI: 10.1093/jac/dkaa336] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/01/2020] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Rapid antimicrobial susceptibility testing (RAST) of bacteria causing bloodstream infections is critical for implementation of appropriate antibiotic regimens.
Objectives
We have established a procedure to prepare standardized bacterial inocula for Enterobacterales-containing clinical blood cultures and assessed antimicrobial susceptibility testing (AST) data generated with the WASPLabTM automated reading system.
Methods
A total of 258 blood cultures containing Enterobacterales were examined. Bacteria were enumerated by flow cytometry using the UF-4000 system and adjusted to an inoculum of 106 cfu/mL. Disc diffusion plates were automatically streaked, incubated for 6, 8 and 18 h and imaged using the fully automated WASPLabTM system. Growth inhibition zones were compared with those obtained with inocula prepared from primary subcultures following the EUCAST standard method. Due to time-dependent variations of the inhibition zone diameters, early AST readings were interpreted using time-adjusted tentative breakpoints and areas of technical uncertainty.
Results and conclusions
Inhibition zones obtained after 18 h incubation using an inoculum of 106 cfu/mL prepared directly from blood cultures were highly concordant with those of the EUCAST standard method based on primary subcultures, with categorical agreement (CA) of 95.8%. After 6 and 8 h incubation, 89.5% and 93.0% of the isolates produced interpretable results, respectively, with CA of >98.5% and very low numbers of clinical categorization errors for both the 6 h and 8 h readings. Overall, with the standardized and automated RAST method, consistent AST data from blood cultures containing Enterobacterales can be generated after 6–8 h of incubation and subsequently confirmed by standard reading of the same plate after 18 h.
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Affiliation(s)
- Stefano Mancini
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Schweiz
| | - Elias Bodendoerfer
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Schweiz
| | | | - Sebastian Herren
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Schweiz
| | - Kim Röthlin
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Schweiz
| | | | - Erik C Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Schweiz
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17
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Evaluation of EUCAST rapid antimicrobial susceptibility testing (RAST) directly from blood culture bottles. Eur J Clin Microbiol Infect Dis 2020; 39:993-998. [DOI: 10.1007/s10096-020-03815-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/12/2020] [Indexed: 01/09/2023]
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18
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Boland L, Streel C, De Wolf H, Rodriguez H, Verroken A. Rapid antimicrobial susceptibility testing on positive blood cultures through an innovative light scattering technology: performances and turnaround time evaluation. BMC Infect Dis 2019; 19:989. [PMID: 31752735 PMCID: PMC6873430 DOI: 10.1186/s12879-019-4623-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/07/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND A bacteremia diagnosis with speeded-up identification and antimicrobial susceptibility testing (AST) is mandatory to adjust empirical broad-spectrum antibiotherapy and avoid the emergence of multi-resistant bacteria. Alfred 60AST (Alifax, Polverara, PD, Italy) is an innovative automated system based on light scattering measurements allowing direct AST from positive blood cultures with rapid results. In this study we aimed to evaluate the system's performances and turnaround time (TAT) compared to routine AST. METHODS The study was conducted during 2 non-consecutive 3-month periods at the microbiology laboratory of the Cliniques universitaires Saint-Luc. All blood cultures detected positive in the 0 AM-10 AM time frame with a pure Gram-positive cocci or Gram-negative bacilli stain were included for Alfred 60AST testing. Two customized EUCAST antibiotic panels were set up composed of 1) a "Gram-negative" panel including cefuroxime, ceftazidime Enterobacteriaceae, piperacillin-tazobactam Enterobacteriaceae, ciprofloxacine, and ceftazidime Pseudomonas 2) a "Gram-positive" panel including cefoxitin Staphylococcus aureus, cefoxitin coagulase-negative (CNS) Staphylococci and ampicillin Enterococci. Categorical agreement (CA), very major errors (VME), major errors (ME), minor errors (mE) and TAT to Alfred 60AST results were calculated in comparison with AST results obtained from direct testing on positive blood cultures with the Phoenix system (Becton Dickinson, Franklin Lakes, NJ, USA). RESULTS Five hundred seventy and one hundred nine antibiotics were evaluated on respectively 166 Gram-negative bacilli and 109 Gram-positive cocci included in the studied population. During the first study period regarding Gram-negative strains a CA of 89.5% was obtained with a high rate of VME (19 and 15.4% respectively) for cefuroxime and piperacillin-tazobactam Enterobacteriaceae. Considering this, Alifax reviewed these antibiotics' formulations improving Gram-negative bacilli total CA to 92.2% with no VME during the second study period. For Gram-positive cocci, total CA was 88.1% with 2.3% VME, 13.8% ME (mainly cefoxitin CNS) and 12% mE rates both study periods combined. Median TAT to AST results was 5 h with Alfred versus 12 h34 with Phoenix. CONCLUSION The Alfred 60AST system shows correct yet improvable microbiological performances and a major TAT reduction compared to direct automated AST testing. Clinical studies measuring the impact of the approach on antibiotic management of patients with bacteremia are recommended.
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Affiliation(s)
- Lidvine Boland
- Department of Laboratory Medicine, Microbiology Laboratory, Saint-Luc University Hospital and Catholic University of Louvain, Avenue Hippocrate 10, 1200 Brussels, Belgium
| | - Corentin Streel
- Department of Laboratory Medicine, Microbiology Laboratory, Saint-Luc University Hospital and Catholic University of Louvain, Avenue Hippocrate 10, 1200 Brussels, Belgium
| | - Hélène De Wolf
- Department of Laboratory Medicine, Microbiology Laboratory, Saint-Luc University Hospital and Catholic University of Louvain, Avenue Hippocrate 10, 1200 Brussels, Belgium
| | - Hector Rodriguez
- Department of Laboratory Medicine, Microbiology Laboratory, Saint-Luc University Hospital and Catholic University of Louvain, Avenue Hippocrate 10, 1200 Brussels, Belgium
| | - Alexia Verroken
- Department of Laboratory Medicine, Microbiology Laboratory, Saint-Luc University Hospital and Catholic University of Louvain, Avenue Hippocrate 10, 1200 Brussels, Belgium
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19
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Dong Z, Chen B, Pan H, Wang D, Liu M, Yang Y, Zou M, Yang J, Xiao K, Zhao R, Zheng X, Zhang L, Zhang Y. Detection of Microbial 16S rRNA Gene in the Serum of Patients With Gastric Cancer. Front Oncol 2019; 9:608. [PMID: 31338330 PMCID: PMC6629868 DOI: 10.3389/fonc.2019.00608] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/20/2019] [Indexed: 01/03/2023] Open
Abstract
Aberrance in the blood bacterial microbiome has been identified and validated in several non-infectious diseases, including cancer. The occurrence and progression of gastric cancer has been found to be associated with alterations in the microbiome composition. However, the composition of the blood microbiome in patients with gastric cancer is not well-characterized. To test this hypothesis, we conducted a case-control study to investigate the microbiota compositions in the serum of patients with gastric cancer. The serum microbiome was investigated in patients with gastric cancer, atypical hyperplasia, chronic gastritis, and in healthy controls using 16S rRNA gene sequencing targeting the V1-V2 region. Our results revealed that the structure of the serum microbiome in gastric cancer was significantly different from all other groups, and alpha diversity decreased from the healthy control to patients with gastric cancer. The serum microbiome correlated significantly with tumor-node-metastasis (TNM) stage, lymphatic metastasis, tumor diameter, and invasion depth in gastric cancer. Three genera or species, namely, Acinetobacter, Bacteroides, Haemophilus parainfluenzae, were enriched in patients with gastric cancer, whereas Sphingomonas, Comamonas, and Pseudomonas stutzeri were enriched in the healthy control. Furthermore, the structure of serum microbiota differed between gastric cancer lymphatic metastasis and non-lymphatic metastasis. As a pilot investigation to characterizing the serum microbiome in gastric cancer, our study provided a foundation for improving our understanding of the role of microbiota in the pathogenesis of gastric cancer.
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Affiliation(s)
- Zhaogang Dong
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China.,Shandong Province Key Laboratories of Medicine and Health (Tumor Marker Translational Medicine Laboratory), Qilu Hospital of Shandong University, Jinan, China
| | - Bin Chen
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, China
| | - Hongwei Pan
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China.,Shandong Province Key Laboratories of Medicine and Health (Tumor Marker Translational Medicine Laboratory), Qilu Hospital of Shandong University, Jinan, China
| | - Ding Wang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China.,Shandong Province Key Laboratories of Medicine and Health (Tumor Marker Translational Medicine Laboratory), Qilu Hospital of Shandong University, Jinan, China
| | - Min Liu
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China.,Shandong Province Key Laboratories of Medicine and Health (Tumor Marker Translational Medicine Laboratory), Qilu Hospital of Shandong University, Jinan, China
| | - Yongmei Yang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China.,Shandong Province Key Laboratories of Medicine and Health (Tumor Marker Translational Medicine Laboratory), Qilu Hospital of Shandong University, Jinan, China
| | - Mingjin Zou
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China.,Shandong Province Key Laboratories of Medicine and Health (Tumor Marker Translational Medicine Laboratory), Qilu Hospital of Shandong University, Jinan, China
| | - Junjie Yang
- College of Life Science, Qilu Normal University, Jinan, China
| | - Ke Xiao
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China.,Shandong Province Key Laboratories of Medicine and Health (Tumor Marker Translational Medicine Laboratory), Qilu Hospital of Shandong University, Jinan, China
| | - Rui Zhao
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China.,Shandong Province Key Laboratories of Medicine and Health (Tumor Marker Translational Medicine Laboratory), Qilu Hospital of Shandong University, Jinan, China
| | - Xin Zheng
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China.,Shandong Province Key Laboratories of Medicine and Health (Tumor Marker Translational Medicine Laboratory), Qilu Hospital of Shandong University, Jinan, China
| | - Lei Zhang
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, China.,Shandong Children's Microbiome Center, Qilu Children's Hospital of Shandong University, Jinan, China.,Qingdao Human Microbiome Center, The Affiliated Central Hospital of Qingdao University, Qingdao, China
| | - Yi Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China.,Shandong Province Key Laboratories of Medicine and Health (Tumor Marker Translational Medicine Laboratory), Qilu Hospital of Shandong University, Jinan, China
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20
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Li W, Sun E, Wang Y, Pan H, Zhang Y, Li Y, Zhang X, Li C, Du L, Wang C. Rapid Identification and Antimicrobial Susceptibility Testing for Urinary Tract Pathogens by Direct Analysis of Urine Samples Using a MALDI-TOF MS-Based Combined Protocol. Front Microbiol 2019; 10:1182. [PMID: 31231323 PMCID: PMC6560049 DOI: 10.3389/fmicb.2019.01182] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 05/09/2019] [Indexed: 01/12/2023] Open
Abstract
Usually, 18–48 h are needed for the identification of microbial pathogens causing urinary tract infections (UTIs) by urine culture. Moreover, antimicrobial susceptibility testing (AST) takes an additional 18–24 h. Rapid identification and AST of the pathogens allow fast and precise treatment. The objective of this study was to shorten the time of diagnosis of UTIs by combining pathogen screening through flow cytometry, microbial identification by matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS), and AST using the VITEK 2 system for the direct analysis of urine samples. We analyzed 1,638 urine samples from patients with suspected UTIs submitted to the microbiology laboratory for culture. Each urine sample had an approximate volume of 30 mL and was divided into three aliquots. Urine processing included differential centrifugation and two washes to enrich the bacterial fraction for direct MALDI-TOF MS and direct AST. From a total of 1,638 urine samples, 307 were found to be positive through UF-1000i screening. Among them, 265 had significant growth of a single-microorganism. Direct identification was obtained in 229 (86.42%) out of these 265 samples, and no pathogens were misidentified. Moreover, species-level identification was obtained in 163 (88.59%) out of the 184 samples with Gram-negative bacteria, and 27 (38.03%) out of the 71 samples with Gram-positive bacteria. VITEK 2 AST was performed for 117 samples with a single-microorganism. Enterobacteriaceae data showed an agreement rate of antimicrobial categories of 94.83% (1,229/1,296), with minor, major, and very major error rates of 4.17% (54/1,296), 0.92% (12/1,296), and 0.08% (1/1,296), respectively. For Enterococcus spp., the overall categorical agreement was 92.94% (158/170), with a minor error rate of 2.94% (5/170) and major error rate of 4.12% (7/170). The turnaround time of this combined protocol to diagnose UTIs was 1 h for pathogen identification and 6–24 h for AST; noteworthily, only 6–8 h are needed for AST of Enterobacteriaceae using the VITEK 2 system. Overall, our findings show that the combination of flow cytometry, MALDI-TOF MS, and VITEK 2 provided a direct, rapid, and reliable identification and AST method for assessing urine samples, especially for Gram-negative bacterial infections.
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Affiliation(s)
- Wei Li
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Enhua Sun
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Ying Wang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Hongwei Pan
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Yi Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Yong Li
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Xin Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Chen Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China
| | - Chuanxin Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China
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21
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Dubourg G, Raoult D, Fenollar F. Emerging methodologies for pathogen identification in bloodstream infections: an update. Expert Rev Mol Diagn 2019; 19:161-173. [DOI: 10.1080/14737159.2019.1568241] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Didier Raoult
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
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22
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Hogan CA, Watz N, Budvytiene I, Banaei N. Rapid antimicrobial susceptibility testing by VITEK®2 directly from blood cultures in patients with Gram-negative rod bacteremia. Diagn Microbiol Infect Dis 2019; 94:116-121. [PMID: 30711413 DOI: 10.1016/j.diagmicrobio.2019.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/28/2018] [Accepted: 01/01/2019] [Indexed: 10/27/2022]
Abstract
OBJECTIVE Optimizing therapy for bacteremia is currently limited by the 1-2-day turnaround time required for antimicrobial susceptibility testing (AST). Here, we assess a rapid AST method with VITEK®2 (bioMérieux, France) directly from positive blood cultures. METHODS Patient-derived positive blood cultures with Gram-negative rods identified as Enterobacteriaceae and Pseudomonas aeruginosa were prospectively tested, and other blood culture bottles were spiked with carbapenem-resistant Enterobacteriaceae (CRE). Positive cultures were subjected to red blood cell lysis and centrifugation, and setup on VITEK®2. RESULTS A total of 109 patient blood cultures and 52 spiked blood cultures were tested. Overall, essential agreement was 97.7% [95% confidence interval (CI) 96.4-99.0], and categorical agreement was 96.8% (95% CI 95.0-98.6). Mean turnaround time from setup to susceptibility results for Enterobacteriaceae in the clinical cultures was 9.0 (±1.3) h. CONCLUSIONS Direct susceptibility testing of blood cultures by VITEK®2 for Enterobacteriaceae is an accurate, practical, and inexpensive diagnostic strategy for rapid automated AST.
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Affiliation(s)
- C A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, USA
| | - N Watz
- Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, USA
| | - I Budvytiene
- Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, USA
| | - N Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, USA; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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