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Cruz S, Abreu D, Gomes R, Martins-Oliveira I, Silva-Dias A, Perez-Viso B, Cantón R, Pina-Vaz C. An improved protocol for bacteria identification by MALDI-TOF MS directly from positive blood cultures. Eur J Clin Microbiol Infect Dis 2024; 43:605-610. [PMID: 38112967 PMCID: PMC10917851 DOI: 10.1007/s10096-023-04725-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023]
Abstract
FASTinov® developed a rapid antimicrobial susceptibility test that includes the purification of a bacterial suspension directly from positive blood cultures (BC). In order to streamline laboratory workflow, the use of the bacterial suspension obtained through FASTinov® sample prep was tested for identification (ID) by matrix absorption laser deionization-time of flight mass spectrometry (MALDI-TOF MS) (Bruker) in 364 positive BC, and its accuracy assessed comparing with the MALDI-TOF MS ID of the next-day subcultured colonies. FASTinov sample prep was highly reliable for rapid ID directly from BC with proportion of agreement of 94.9% for Gram-positive and 96.3% for Gram-negative bacteria.
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Affiliation(s)
- Sara Cruz
- Division of Microbiology, Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal
| | | | | | | | - Ana Silva-Dias
- FASTinov SA, Porto, Porto, Portugal
- CINTESIS-Center for Health Technology and Services Research, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Blanca Perez-Viso
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Cidália Pina-Vaz
- Division of Microbiology, Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal.
- FASTinov SA, Porto, Porto, Portugal.
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Suleiman M, Elamin N, Nabor R, Roberts J, Tang P, Hasan MR, Pérez-López A. Evaluation of Immulex S. pneumoniae Omni test for the direct detection of S. pneumoniae from positive blood cultures. Heliyon 2023; 9:e22106. [PMID: 38027561 PMCID: PMC10658396 DOI: 10.1016/j.heliyon.2023.e22106] [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: 04/04/2023] [Revised: 09/06/2023] [Accepted: 11/04/2023] [Indexed: 12/01/2023] Open
Abstract
Rapid and early identification of Streptococcus pneumoniae from positive blood cultures is crucial for the management of patients with bloodstream infections (BSI). Many identification systems in microbiology laboratories have difficulty differentiating S. pneumoniae from other closely related species in the Streptococcus mitis group. To overcome this limitation, we developed a rapid workflow in our laboratory combining direct MALDI-TOF MS identification with the Immulex S. pneumoniae Omni test (SSI Diagnostica, Denmark) for rapid detection of S. pneumoniae directly from positive blood cultures. The workflow was evaluated using 51 Streptococcus isolates. Compared to conventional biochemical testing, our new workflow demonstrates 100 % specificity and sensitivity for the detection and differentiation of S. pneumoniae from other closely related species. Our new workflow is accurate, cost-effective, and can easily be implemented in microbiology laboratories that already perform direct MALDI-TOF identification from positive blood cultures to improve the management of patients with invasive pneumococcal disease. Importance Invasive pneumococcal disease remains a major public health problem worldwide. Reducing the time to identify Streptococcus pneumoniae in positive blood cultures allows patients to be treated sooner with more targeted and effective antibiotics. We evaluated a two-step protocol where positive blood cultures are first tested directly by MALDI-TOF MS and any samples containing Streptococcus species are tested by Immulex S. pneumoniae Omni test to both detect and differentiate S. pneumoniae from other closely related Streptococcus species. Our study results showed 100 % sensitivity and specificity, and a much faster turn-around time than conventional methods.
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Affiliation(s)
| | | | | | | | - Patrick Tang
- Sidra Medicine, PO BOX 26999, Doha, Qatar
- Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Mohammad Rubayet Hasan
- Medical Scientific Department, LifeLabs, Toronto, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
| | - Andrés Pérez-López
- Sidra Medicine, PO BOX 26999, Doha, Qatar
- Weill Cornell Medical College in Qatar, Doha, Qatar
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Kaushal S, Priyadarshi N, Garg P, Singhal NK, Lim DK. Nano-Biotechnology for Bacteria Identification and Potent Anti-bacterial Properties: A Review of Current State of the Art. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2529. [PMID: 37764558 PMCID: PMC10536455 DOI: 10.3390/nano13182529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/26/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023]
Abstract
Sepsis is a critical disease caused by the abrupt increase of bacteria in human blood, which subsequently causes a cytokine storm. Early identification of bacteria is critical to treating a patient with proper antibiotics to avoid sepsis. However, conventional culture-based identification takes a long time. Polymerase chain reaction (PCR) is not so successful because of the complexity and similarity in the genome sequence of some bacterial species, making it difficult to design primers and thus less suitable for rapid bacterial identification. To address these issues, several new technologies have been developed. Recent advances in nanotechnology have shown great potential for fast and accurate bacterial identification. The most promising strategy in nanotechnology involves the use of nanoparticles, which has led to the advancement of highly specific and sensitive biosensors capable of detecting and identifying bacteria even at low concentrations in very little time. The primary drawback of conventional antibiotics is the potential for antimicrobial resistance, which can lead to the development of superbacteria, making them difficult to treat. The incorporation of diverse nanomaterials and designs of nanomaterials has been utilized to kill bacteria efficiently. Nanomaterials with distinct physicochemical properties, such as optical and magnetic properties, including plasmonic and magnetic nanoparticles, have been extensively studied for their potential to efficiently kill bacteria. In this review, we are emphasizing the recent advances in nano-biotechnologies for bacterial identification and anti-bacterial properties. The basic principles of new technologies, as well as their future challenges, have been discussed.
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Affiliation(s)
- Shimayali Kaushal
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea;
| | - Nitesh Priyadarshi
- National Agri-Food Biotechnology Institute (NABI), Sector-81, Mohali 140306, India; (N.P.); (P.G.)
| | - Priyanka Garg
- National Agri-Food Biotechnology Institute (NABI), Sector-81, Mohali 140306, India; (N.P.); (P.G.)
| | - Nitin Kumar Singhal
- National Agri-Food Biotechnology Institute (NABI), Sector-81, Mohali 140306, India; (N.P.); (P.G.)
| | - Dong-Kwon Lim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea;
- Department of Integrative Energy Engineering, College of Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Brain Science Institute, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
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Comparing the Efficacy of MALDI-TOF MS and Sequencing-Based Identification Techniques (Sanger and NGS) to Monitor the Microbial Community of Irrigation Water. Microorganisms 2023; 11:microorganisms11020287. [PMID: 36838251 PMCID: PMC9960253 DOI: 10.3390/microorganisms11020287] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
In order to intensify and guarantee the agricultural productivity and thereby to be able to feed the world's rapidly growing population, irrigation has become very important. In parallel, the limited water resources lead to an increase in usage of poorly characterized sources of water, which is directly linked to a higher prevalence of foodborne diseases. Therefore, analyzing the microorganisms or even the complete microbiome of irrigation water used for food production can prevent the growing numbers of such cases. In this study, we compared the efficacy of MALDI-TOF Mass spectrometry (MALDI TOF MS) identification to 16S rRNA gene Sanger sequencing of waterborne microorganisms. Furthermore, we analyzed the whole microbial community of irrigation water using high-throughput 16S rRNA gene amplicon sequencing. The identification results of MALDI-TOF MS and 16S rRNA gene Sanger sequencing were almost identical at species level (66.7%; 64.3%). Based on the applied cultivation techniques, Acinetobacter spp., Enterobacter spp., Pseudomonas spp., and Brevundimonas spp. were the most abundant cultivable genera. In addition, the uncultivable part of the microbiome was dominated by Proteobacteria followed by Actinobacteria, Bacteroidota, Patescibacteria, and Verrucomicrobiota. Our findings indicate that MALDI-TOF MS offers a fast, reliable identification method and can act as an alternative to 16S rRNA gene Sanger sequencing of isolates. Moreover, the results suggest that MALDI-TOF MS paired with 16S rRNA gene amplicon sequencing have the potential to support the routine monitoring of the microbiological quality of irrigation water.
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Cherkaoui A, Riat A, Renzi G, Fischer A, Schrenzel J. Diagnostic test accuracy of an automated device for the MALDI target preparation for microbial identification. Eur J Clin Microbiol Infect Dis 2023; 42:153-159. [PMID: 36469165 PMCID: PMC9836989 DOI: 10.1007/s10096-022-04531-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022]
Abstract
The objective of this study was to evaluate the performance of the Copan Colibrí™ against the manual preparation of the MALDI targets. We analyzed 416 (31 different species) non-duplicate strains covering the most important species identified in clinical routine. We also assessed the intra-strain repeatability between the comparable methods. We then analyzed the performance of this new method after implementation in routine on 12,253 aerobic bacterial isolates and yeasts, encompassing a total of 42 different species. Among the 416 strains analyzed, 6.3% (26/416) and 10.8% (45/416) had a score value < 2 when processed by the Colibri™ and manual method, respectively. Only 5.9% (9/152) of the Gram positive rods and cocci had a score values < 2 by the Colibri™ versus 20.4% (31/152) by the manual method. We confirmed that this relative superiority observed for the Colibri™ was due primarily in the use of the formic acid protocol. For the Gram-negative bacteria, the results of both methods were comparable; 6.6% (17/256) and 4.7% (12/256) had a score value < 2 by the Colibri™ and the manual method, respectively. After implementation in routine, the results according to the Biotyper score cut-off values were distributed as follows: < 1.70: 2.5% (304/12,253), 1.70-1.79: 1.9% (227/12,253), 1.80-1.89: 3.1% (377/12,253), 1.90-1.99: 6.7% (825/12,253), and ≥ 2: 85.9% (10,520/12,253). The Colibrí™ coupled to MALDI-TOF/MS revealed good performances and higher intra-strain repeatability as compared to the manual preparation of the MALDI targets.
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Affiliation(s)
- Abdessalam Cherkaoui
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, 4 Rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland ,Faculty of Medicine, Geneva, Switzerland
| | - Arnaud Riat
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, 4 Rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland
| | - Gesuele Renzi
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, 4 Rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland
| | - Adrien Fischer
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, 4 Rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland
| | - Jacques Schrenzel
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, 4 Rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland ,Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
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Sharaf PH, El Backly RM, Sherif RA, Zaazou AM, Hafez SF. Microbial identification from traumatized immature permanent teeth with periapical lesions using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. BMC Oral Health 2022; 22:661. [PMID: 36587207 PMCID: PMC9805193 DOI: 10.1186/s12903-022-02562-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/03/2022] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND This study aims at identifying the microbiota in traumatized immature permanent teeth with periapical lesions using Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). METHODS The study included 16 immature maxillary central incisors with periapical lesions in 13 patients. Field decontamination and negative control samples were performed before and after access cavity preparation. Root canal samples were taken using sterile stainless-steel hand files following field decontamination. In-office inoculation and pure sub-cultures were performed. Bacterial isolates were prepared for MALDI-TOF MS (Bruker, Billerica, MA USA) analysis using the formic acid extraction method. A comparison of the prevalence of isolated microorganisms was done using a one-sample chi-square test. Comparisons between identified microbial species with the, cone beam computed tomography periapical index (CBCT PAI) scores and lesion volume were also conducted. The Chi-square test was applied to investigate the association between the categorical variables . RESULTS Out of the forty isolates recovered from the 16 traumatized teeth included in the present study with the mean patients' age of 10.93 ± 1.77, 37 isolates were reliably identified by MALDI-TOF MS. Twelve teeth (62.5%) were polymicrobial. The recovered bacteria belonged to five phyla, 15 genera and 25 species. Firmicutes were the predominant phylum (P < 0.001) over Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria. Gram positive bacteria were significantly more prevalent than Gram negative (p = 0.03). Facultative anaerobes were the most prevalent (P < 0.001) compared to the obligate anaerobes and the obligate aerobes. The latter were the least prevalent. Statistically, significant differences existed in the comparison between CBCT PAI scores according to bacterial gram staining. CONCLUSION Traumatized immature permanent teeth with periapical lesions showed a significant predominance of Gram-positive facultative anaerobes. MALDI-TOF MS provided accurate identification of numerous viable endodontic microbes.
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Affiliation(s)
- Pervine H. Sharaf
- grid.7155.60000 0001 2260 6941Conservative Dentistry Department, Faculty of Dentistry, Alexandria University, Alexandria, Egypt, Endodontic Specialist, Ministry of Health, Alexandria, Egypt
| | - Rania M. El Backly
- grid.7155.60000 0001 2260 6941Endodontics, Conservative Dentistry Department, Faculty of Dentistry, Alexandria University, Alexandria, Egypt
| | - Raef A. Sherif
- grid.7155.60000 0001 2260 6941Endodontics, Conservative Dentistry Department, Faculty of Dentistry, Alexandria University, Alexandria, Egypt
| | - Ashraf M. Zaazou
- grid.7155.60000 0001 2260 6941Endodontics, Conservative Dentistry Department, Faculty of Dentistry, Alexandria University, Alexandria, Egypt ,Faculty of Dentistry, King Abdel Aziz University, Jeddah, Saudi Arabia
| | - Soad F. Hafez
- grid.7155.60000 0001 2260 6941Medical Microbiology and Immunology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
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Sun H, Lai P, Wu W, Heng H, Si S, Ye Y, Li J, Lyu H, Zou C, Guo M, Wang Y, Geng H, Liang J. MALDI-TOF MS Based Bacterial Antibiotics Resistance Finger Print for Diabetic Pedopathy. Front Chem 2022; 9:785848. [PMID: 35096767 PMCID: PMC8795630 DOI: 10.3389/fchem.2021.785848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/27/2021] [Indexed: 11/13/2022] Open
Abstract
Diabetes mellitus has become a major global health issue. Currently, the use of antibiotics remains the best foundational strategy in the control of diabetic foot infections. However, the lack of accurate identification of pathogens and the empirical use of antibiotics at early stages of infection represents a non-targeted treatment approach with a poor curative effect that may increase the of bacterial drug resistance. Therefore, the timely identification of drug resistant bacteria is the key to increasing the efficacy of treatments for diabetic foot infections. The traditional identification method is based on bacterial morphology, cell physiology, and biochemistry. Despite the simplicity and low costs associated with this method, it is time-consuming and has limited clinical value, which delays early diagnosis and treatment. In the recent years, MALDI-TOF MS has emerged as a promising new technology in the field of clinical microbial identification. In this study, we developed a strategy for the identification of drug resistance in the diagnosis of diabetic foot infections using a combination of macro-proteomics and MALDI MS analysis. The macro-proteomics result was utilized to determine the differential proteins in the resistance group and the corresponding peptide fragments were used as the finger print in a MALDI MS analysis. This strategy was successfully used in the research of drug resistance in patients with diabetic foot infections and achieved several biomarkers that could be used as a finger print for 4 different drugs, including ceftazidime, piperacillin, levofloxacin, and tetracycline. This method can quickly confirm the drug resistance of clinical diabetic foot infections, which can help aid in the early treatment of patients.
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Affiliation(s)
- Haojie Sun
- Medical College, Soochow University, Suzhou, China
- Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, China
| | - Peng Lai
- Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, China
| | - Wei Wu
- Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Hao Heng
- Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, China
| | - Shanwen Si
- Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, China
| | - Yan Ye
- Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, China
| | - Jiayi Li
- Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, China
| | - Hehe Lyu
- Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, China
| | - Caiyan Zou
- Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, China
| | - Mengzhe Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Yu Wang
- Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, China
- *Correspondence: Jun Liang, ; Houfa Geng, ; Yu Wang,
| | - Houfa Geng
- Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, China
- *Correspondence: Jun Liang, ; Houfa Geng, ; Yu Wang,
| | - Jun Liang
- Medical College, Soochow University, Suzhou, China
- Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, China
- *Correspondence: Jun Liang, ; Houfa Geng, ; Yu Wang,
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Abstract
Sepsis remains a significant cause of neonatal mortality and morbidity, especially in low- and middle-income countries. Neonatal sepsis presents with nonspecific signs and symptoms that necessitate tests to confirm the diagnosis. Early and accurate diagnosis of infection will improve clinical outcomes and decrease the overuse of antibiotics. Current diagnostic methods rely on conventional culture methods, which is time-consuming, and may delay critical therapeutic decisions. Nonculture-based techniques including molecular methods and mass spectrometry may overcome some of the limitations seen with culture-based techniques. Biomarkers including hematological indices, cell adhesion molecules, interleukins, and acute-phase reactants have been used for the diagnosis of neonatal sepsis. In this review, we examine past and current microbiological techniques, hematological indices, and inflammatory biomarkers that may aid sepsis diagnosis. The search for an ideal biomarker that has adequate diagnostic accuracy early in sepsis is still ongoing. We discuss promising strategies for the future that are being developed and tested that may help us diagnose sepsis early and improve clinical outcomes. IMPACT: Reviews the clinical relevance of currently available diagnostic tests for sepsis. Summarizes the diagnostic accuracy of novel biomarkers for neonatal sepsis. Outlines future strategies including the use of omics technology, personalized medicine, and point of care tests.
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Evaluation of Rapid Immunochromatographic Tests for the Direct Detection of Extended Spectrum Beta-Lactamases and Carbapenemases in Enterobacterales Isolated from Positive Blood Cultures. Microbiol Spectr 2021; 9:e0078521. [PMID: 34878297 PMCID: PMC8653814 DOI: 10.1128/spectrum.00785-21] [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] [Indexed: 11/20/2022] Open
Abstract
NG-Test CTX-M MULTI and NG-Test Carba 5 (NG Biotech) are two rapid in vitro immunochromatographic assays that are widely used for the detection of the most common extended spectrum beta-lactamases (ESBL) and carbapenemases in Enterobacterales. ESBL and carbapenemases are leading causes of morbidity and mortality worldwide and their rapid detection from positive blood cultures is crucial for early initiation of effective antimicrobial therapy in bloodstream infections (BSI) involving antibiotic-resistant organisms. In this study, we developed a rapid workflow for positive blood cultures for direct identification of Enterobacterales by MALDI-TOF mass-spectrometry, followed by detection of ESBL and carbapenemases using NG-Test CTX-M MULTI and NG-Test Carba 5 (NG Biotech). The workflow was evaluated using Enterobacterales isolates (n = 114), primarily Klebsiella species (n = 50) and Escherichia coli (n = 40). Compared to the standard testing approach in our institution using BD Phoenix, our new testing approach demonstrates 100% sensitivity and specificity for organism identification and detection of ESBL and carbapenemases. Implementation of a rapid workflow in diagnostic microbiology laboratories will enable more effective antimicrobial management of patients with BSI due to ESBL- and carbapenemase-producing Enterobacterales. IMPORTANCE The incidence of bloodstream infections (BSI) with extended spectrum beta-lactamase (ESBL) producing and carbapenemase producing Enterobacterales (CPE) is increasing at an alarming rate, for which only limited therapeutic options remain available. Rapid identification of these bacteria along with their antibiotic resistance mechanisms in positive blood cultures with Gram-negative bacteria will allow for early initiation of effective therapy and limit the overuse of broad-spectrum antibiotics in BSI (1). In this study we evaluated a combined approach of testing positive blood cultures directly, using MALDI-TOF MS followed by rapid immunochromatographic tests, for the detection of ESBLs and CPEs. Our approach demonstrates 100% sensitivity and specificity for the identification of Enterobacterales and detection of ESBLs and CPEs in positive blood culture with a turnaround time (TAT) of ≤60 min compared to a TAT of 48 h required by conventional culture and susceptibility testing methods.
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A Rare Case of Ralstonia pickettii Infection in a Patient Undergoing Thyroid Surgery. Jundishapur J Microbiol 2021. [DOI: 10.5812/jjm.119418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Introduction: The incidence of infection by Ralstonia is increasing. Several reports describing infection by these bacteria in immunocompromised patients have been published. In this study, we reported a case of Ralstonia pickettii infection in a patient with normal immunity. Case Presentation: A woman presented with fever after thyroid surgery. We identified R. pickettii in her blood culture using 16S rRNA gene sequencing. The patient’s condition improved clinically upon treatment with levofloxacin. Conclusions: Our report highlights the potential of Ralstonia to cause sepsis in patients with normal immunity and emphasizes the importance of blood culture testing when a hospitalized patient has an unexplained high fever.
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Rapid direct detection of pathogens for diagnosis of joint infections by MALDI-TOF MS after liquid enrichment in the BacT/Alert blood culture system. PLoS One 2020; 15:e0243790. [PMID: 33306699 PMCID: PMC7732097 DOI: 10.1371/journal.pone.0243790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/25/2020] [Indexed: 11/19/2022] Open
Abstract
Pathogen identification is a critical step during diagnosis of infectious diseases. Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight mass spectrometry (MALDI-TOF-MS) has become the gold standard for identification of microorganisms cultured on solid media in microbiology laboratories. Direct identification of microbes from liquid specimen, circumventing the need for the additional overnight cultivation step, has been successfully established for blood culture, urine and liquor. Here, we evaluate the ability of MALDI-TOF MS for direct identification of pathogens in synovial fluid after liquid enrichment in BacT/Alert blood culture bottles. Influence of synovial specimen quality on direct species identification with the MALDI BioTyper/Sepsityper was tested with samples inoculated from pretested native synovia with concomitant inoculation of blood or pus, or highly viscous fluid. Here, we achieved >90% concordance with culture on solid medium, and only mixed-species samples posed significant problems. Performance in routine diagnostics was tested prospectively on bottles inoculated by treating physicians on ward. There, we achieved >70% concordance with culture on solid media. The major contributors to test failure were the absence of a measurable mass signal and mixed-specimen samples. The Sepsityper workflow worked well on samples derived from BacT/Alert blood culture bottles inoculated with synovial fluid, giving concordant results to identification from solid media. Host remnant material in the inoculum, such as blood or pus, had no detrimental effect on identification score values of the BioTyper system after processing with the Sepsityper workflow, and neither had the initial viscosity of the synovial sample.
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Tsuchida S, Umemura H, Nakayama T. Current Status of Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) in Clinical Diagnostic Microbiology. Molecules 2020; 25:molecules25204775. [PMID: 33080897 PMCID: PMC7587594 DOI: 10.3390/molecules25204775] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/15/2020] [Accepted: 10/15/2020] [Indexed: 12/28/2022] Open
Abstract
Mass spectrometry (MS), a core technology for proteomics and metabolomics, is currently being developed for clinical applications. The identification of microorganisms in clinical samples using matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry (MALDI-TOF MS) is a representative MS-based proteomics application that is relevant to daily clinical practice. This technology has the advantages of convenience, speed, and accuracy when compared with conventional biochemical methods. MALDI-TOF MS can shorten the time used for microbial identification by about 1 day in routine workflows. Sample preparation from microbial colonies has been improved, increasing the accuracy and speed of identification. MALDI-TOF MS is also used for testing blood, cerebrospinal fluid, and urine, because it can directly identify the microorganisms in these liquid samples without prior culture or subculture. Thus, MALDI-TOF MS has the potential to improve patient prognosis and decrease the length of hospitalization and is therefore currently considered an essential tool in clinical microbiology. Furthermore, MALDI-TOF MS is currently being combined with other technologies, such as flow cytometry, to expand the scope of clinical applications.
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Li YS, Tseng WL, Lu CY. Sensitive detection of quinoline-derivatized sitagliptin in small volumes of human plasma by MALDI-TOF mass spectrometry. Talanta 2020; 218:121143. [PMID: 32797900 DOI: 10.1016/j.talanta.2020.121143] [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: 03/08/2020] [Revised: 05/04/2020] [Accepted: 05/07/2020] [Indexed: 02/08/2023]
Abstract
Dipeptidyl peptidase 4 (DPP-4) inhibitors are incretin-based medications used as oral antidiabetic agents for the treatment of type 2 diabetes. However, DPP-4 inhibitors produce side effects like acute pancreatitis, upper respiratory tract infection, nasopharyngitis, urinary tract infection, serious allergies, cardiovascular diseases, hemolysis, and retinopathy. Hence, the development of a fast and simple method to detect DPP-4 inhibitors in body fluids is important. In this study, we developed a derivatization-assisted microextraction method to enhance the detection sensitivity for trace levels of a DPP-4 inhibitor, sitagliptin, from a small volume (10 μL) of human plasma by using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Subjecting the analyte to 100 W microwave irradiation after derivatization using a quinoline alkylating reagent (8-bromomethyl quinilone, BrMQ) shortened the reaction time to ~120 s and allowed the target analyte to be easily extracted to a small volume of the organic layer (20 μL). The analyte was then detected by MALDI-TOF MS using α-cyano-4-hydroxycinnamic acid as the matrix. The relative standard deviation and relative error were below 10% in intra- and inter-day assays. Using sitagliptin-d4 as an internal standard, the limits of quantitation and detection were found to be 0.03 μg/mL and 0.01 μg/mL, respectively. All the derivatization and extraction procedures described herein were of microliter grade. This method could effectively reduce the use of organic chemicals and solvents, thereby proving to be an eco-friendly strategy that will cause no harm to the environment.
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Affiliation(s)
- Yi-Shan Li
- Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
| | - Wei-Lung Tseng
- Department of Chemistry, College of Science, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan
| | - Chi-Yu Lu
- Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan; Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, 80708, Taiwan.
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14
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Stokes W, Campbell L, Pitout J, Conly J, Church D, Gregson D. Comparison of Accelerate PhenoTest BC Kit and MALDI-TOF MS/VITEK 2 System for the rapid identification and antimicrobial susceptibility testing of gram-negative bacilli causing bloodstream infections. JOURNAL OF THE ASSOCIATION OF MEDICAL MICROBIOLOGY AND INFECTIOUS DISEASE CANADA = JOURNAL OFFICIEL DE L'ASSOCIATION POUR LA MICROBIOLOGIE MEDICALE ET L'INFECTIOLOGIE CANADA 2020; 5:145-157. [PMID: 36341310 PMCID: PMC9608732 DOI: 10.3138/jammi-2020-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/23/2020] [Indexed: 06/16/2023]
Abstract
BACKGROUND Our laboratory uses matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI) and the VITEK 2 system (DV2) directly from positive blood cultures (BC) for organism identification (ID) and antimicrobial susceptibility testing (AST). Our objective was to compare direct MALDI-DV2 with a commercial BC ID-AST platform, the Accelerate Pheno system (AXDX), in the ID-AST of clinical and seeded BC positive for gram-negative bacilli (GNB). METHODS BC positive for GNB were collected over a 3-mo period and tested using AXDX and direct MALDI-DV2 and compared with conventional methods. A subset of sterile BC were seeded with multi-drug-resistant GNB. RESULTS Twenty-nine clinical samples and 35 seeded samples were analyzed. Direct MALDI had a higher ID failure rate (31.0%) than AXDX (3.4%; p < 0.001). Time to ID-AST was 1.5-6.9 h, 5.8-16.5 h, and 21.6-33.0 h for AXDX, direct MALDI-DV2, and conventional methods, respectively (p < 0.001). For clinical samples, AXDX and DV2 had essential agreement (EA) or categorical agreement (CA) of more than 96%. For seeded samples, AXDX had EA, CA, VME, ME, and minor error (mE) of 93.2%, 89.0%, 2.2%, 0%, and 9.2%, respectively. AXDX had a large number of non-reports (6.1%) stemming from meropenem testing. DV2 had EA, CA, VME, ME, and mE of 97.5%, 94.7%, 1.3%, 0%, and 4.1%, respectively. CONCLUSIONS Direct MALDI-DV2 and AXDX both had high agreement for clinical samples, but direct MALDI-DV2 had higher agreement when challenged with MDR GNB.
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Affiliation(s)
- William Stokes
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | - Johann Pitout
- Calgary Laboratory Services, Calgary, Alberta, Canada
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Medical Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
| | - John Conly
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Disease, University of Calgary, Calgary, Alberta, Canada
| | - Deirdre Church
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
- Calgary Laboratory Services, Calgary, Alberta, Canada
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Dan Gregson
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
- Calgary Laboratory Services, Calgary, Alberta, Canada
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
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15
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Proteome Analysis of Molecular Events in Oral Pathogenesis and Virus: A Review with a Particular Focus on Periodontitis. Int J Mol Sci 2020; 21:ijms21155184. [PMID: 32707841 PMCID: PMC7432693 DOI: 10.3390/ijms21155184] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 07/11/2020] [Accepted: 07/16/2020] [Indexed: 02/07/2023] Open
Abstract
Some systemic diseases are unquestionably related to periodontal health, as periodontal disease can be an extension or manifestation of the primary disease process. One example is spontaneous gingival bleeding, resulting from anticoagulant treatment for cardiac diseases. One important aspect of periodontal therapy is the care of patients with poorly controlled disease who require surgery, such as patients with uncontrolled diabetes. We reviewed research on biomarkers and molecular events for various diseases, as well as candidate markers of periodontal disease. Content of this review: (1) Introduction, (2) Periodontal disease, (3) Bacterial and viral pathogens associated with periodontal disease, (4) Stem cells in periodontal tissue, (5) Clinical applications of mass spectrometry using MALDI-TOF-MS and LC-MS/MS-based proteomic analyses, (6) Proteome analysis of molecular events in oral pathogenesis of virus in GCF, saliva, and other oral Components in periodontal disease, (7) Outlook for the future and (8) Conclusions. This review discusses proteome analysis of molecular events in the pathogenesis of oral diseases and viruses, and has a particular focus on periodontitis.
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16
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Özenci V, Rossolini GM. Rapid microbial identification and antimicrobial susceptibility testing to drive better patient care: an evolving scenario. J Antimicrob Chemother 2020; 74:i2-i5. [PMID: 30690543 PMCID: PMC6382029 DOI: 10.1093/jac/dky529] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Antimicrobial chemotherapy for septic patients begins with empirical therapy and can be subsequently revised when the results of microbiological testing become available. In recent years, a number of novel technologies for the microbiological diagnosis of sepsis have been developed that return results in a shorter timeframe compared with conventional diagnostic approaches. These novel technologies aid antimicrobial stewardship when treating septic patients by reducing the time to appropriate antimicrobial chemotherapy. Advantages and limitations of these technologies should be well understood upon their introduction in the diagnostic workflow. Increasingly popular DNA-based technologies primarily focus on the rapid identification of pathogens, but information on antimicrobial susceptibility is lacking or limited to a few clinically relevant resistance markers. Thus, DNA-based molecular techniques can complement conventional technologies but cannot replace them. On the other hand, a novel technology that provides both rapid identification of bacterial pathogens and a rapid phenotypic antibiogram with MIC values, and which starts from positive blood cultures, is a very promising approach for fast diagnosis of sepsis. To fully leverage the advantages offered by novel diagnostic technologies for sepsis requires a careful introduction into the laboratory workflow, following an evaluation by a health technology assessment approach. It may also require some reshaping of the workflow (e.g. to process the positive blood cultures on a 24/7 schedule) and of the laboratory organization (e.g. by creating a laboratory subsection for fast diagnosis of sepsis).
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Affiliation(s)
- Volkan Özenci
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden.,Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
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17
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Nomura F, Tsuchida S, Murata S, Satoh M, Matsushita K. Mass spectrometry-based microbiological testing for blood stream infection. Clin Proteomics 2020; 17:14. [PMID: 32435163 PMCID: PMC7222329 DOI: 10.1186/s12014-020-09278-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 05/04/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The most successful application of mass spectrometry (MS) in laboratory medicine is identification (ID) of microorganisms using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in blood stream infection. We describe MALDI-TOF MS-based bacterial ID with particular emphasis on the methods so far developed to directly identify microorganisms from positive blood culture bottles with MALDI-TOF MS including our own protocols. We touch upon the increasing roles of Liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS) as well. MAIN BODY Because blood culture bottles contain a variety of nonbacterial proteins that may interfere with analysis and interpretation, appropriate pretreatments are prerequisites for successful ID. Pretreatments include purification of bacterial pellets and short-term subcultures to form microcolonies prior to MALDI-TOF MS analysis. Three commercial protocols are currently available: the Sepsityper® kit (Bruker Daltonics), the Vitek MS blood culture kit (bioMerieux, Inc.), and the rapid BACpro® II kit (Nittobo Medical Co., Tokyo). Because these commercially available kits are costly and bacterial ID rates using these kits are not satisfactory, particularly for Gram-positive bacteria, various home-brew protocols have been developed: 1. Stepwise differential sedimentation of blood cells and microorganisms, 2. Combination of centrifugation and lysis procedures, 3. Lysis-vacuum filtration, and 4. Centrifugation and membrane filtration technique (CMFT). We prospectively evaluated the performance of this CMFT protocol compared with that of Sepsityper® using 170 monomicrobial positive blood cultures. Although preliminary, the performance of the CMFT was significantly better than that of Sepsityper®, particularly for Gram-positive isolates. MALDI-TOF MS-based testing of polymicrobial blood specimens, however, is still challenging. Also, its contribution to assessment of susceptibility and resistance to antibiotics is still limited. For this purpose, liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS) should be more useful because this approach can identify as many as several thousand peptide sequences. CONCLUSION MALDI-TOF MS is now an essential tool for rapid bacterial ID of pathogens that cause blood stream infection. For the purpose of assessment of susceptibility and resistance to antibiotics of the pathogens, the roles of liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS) will increase in the future.
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Affiliation(s)
- Fumio Nomura
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8677 Japan
| | - Sachio Tsuchida
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8677 Japan
| | - Syota Murata
- Division of Laboratory Medicine, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8677 Japan
| | - Mamoru Satoh
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8677 Japan
| | - Kazuyuki Matsushita
- Division of Laboratory Medicine, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8677 Japan
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18
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Survival capacity of the common woodlouse Armadillidium vulgare is improved with a second infection of Salmonella enterica. J Invertebr Pathol 2019; 168:107278. [DOI: 10.1016/j.jip.2019.107278] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/07/2019] [Accepted: 11/08/2019] [Indexed: 11/30/2022]
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19
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Arafah K, Voisin SN, Masson V, Alaux C, Le Conte Y, Bocquet M, Bulet P. MALDI-MS Profiling to Address Honey Bee Health Status under Bacterial Challenge through Computational Modeling. Proteomics 2019; 19:e1900268. [PMID: 31657522 DOI: 10.1002/pmic.201900268] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/24/2019] [Indexed: 01/29/2023]
Abstract
Honey bees play a critical role in the maintenance of plant biodiversity and sustainability of food webs. In the past few decades, bees have been subjected to biotic and abiotic threats causing various colony disorders. Therefore, monitoring solutions to help beekeepers to improve bee health are necessary. Matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) profiling has emerged within this decade as a powerful tool to identify in routine micro-organisms and is currently used in real-time clinical diagnosis. MALDI BeeTyping is developed to monitor significant hemolymph molecular changes in honey bees upon infection with a series of entomopathogenic Gram-positive and -negative bacteria. A Serratia marcescens strain isolated from one naturally infected honey bee collected from the field is also considered. A series of hemolymph molecular mass fingerprints is individually recorded and to the authors' knowledge, the first computational model harboring a predictive score of 97.92% and made of nine molecular signatures that discriminate and classify the honey bees' systemic response to the bacteria is built. Hence, the model is challenged by classifying a training set of hemolymphs and an overall recognition of 91.93% is obtained. Through this work, a novel, time and cost saving high-throughput strategy that addresses honey bee health on an individual scale is introduced.
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Affiliation(s)
- Karim Arafah
- Plateforme BioPark Archamps, Forum 1, 260 Avenue Marie Curie, Archamps Technopole, 74160, Saint Julien en Genevois, France
| | - Sébastien Nicolas Voisin
- Plateforme BioPark Archamps, Forum 1, 260 Avenue Marie Curie, Archamps Technopole, 74160, Saint Julien en Genevois, France
| | - Victor Masson
- Plateforme BioPark Archamps, Forum 1, 260 Avenue Marie Curie, Archamps Technopole, 74160, Saint Julien en Genevois, France.,CR UGA, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR5309, Team Analytic Immunology of Chronic Diseases, Site Santé, Allée des Alpes, F-38000, Grenoble, France
| | - Cédric Alaux
- INRA, UR 406 Abeilles et Environnement, 228 route de l'aérodrome, Site Agroparc, Domaine Saint-Paul, 84914, Avignon Cedex 9, France
| | - Yves Le Conte
- INRA, UR 406 Abeilles et Environnement, 228 route de l'aérodrome, Site Agroparc, Domaine Saint-Paul, 84914, Avignon Cedex 9, France
| | | | - Philippe Bulet
- Plateforme BioPark Archamps, Forum 1, 260 Avenue Marie Curie, Archamps Technopole, 74160, Saint Julien en Genevois, France.,CR UGA, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR5309, Team Analytic Immunology of Chronic Diseases, Site Santé, Allée des Alpes, F-38000, Grenoble, France
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20
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Xu S, Zhou C, Zhang P, Feng C, Zhang T, Sun Z, Zhuang H, Chen H, Chang Q, Jiang R, Li H, Ni Y. Diagnostic Performance of MALDI-TOF MS Compared to Conventional Microbiological Cultures in Patients with Suspected Endophthalmitis. Ocul Immunol Inflamm 2019; 28:483-490. [PMID: 31116624 DOI: 10.1080/09273948.2019.1583346] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Purpose: To evaluate the performance and speed of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) when identifying the pathogenic microorganism of endophthalmitis compared to conventional microbiological culturing.Methods: Forty-four patients with suspected endophthalmitis who had undergone vitrectomy were enrolled. Vitreous specimen was analyzed using either conventional culturing or MALDI-TOF MS.Results: The identification rates of the conventional microbiological culture and MALDI-TOF MS were 45.5% (20/44) and 65.9% (29/44), respectively (Kappa value 0.787, P < 0.000). The mean detection times by the standard culturing method and MALDI-TOF MS were 5.39 ± 0.56d and 3.17 ± 0.40d (P < 0.001). The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of MALDI-TOF MS were 70.59%, 54.17%, 80.00%, and 86.67%, respectively. Polymicrobial endophthalmitis was identified in 6.82% of the patients (3/44) using conventional microbiological culturing. However, MALDI-TOF MS failed to identify any polymicrobial infection.Conclusions: With a higher sensitivity, acceptable specificity and a shorter detection time, MALDI-TOF MS was an efficient technique for the rapid identification of a pathogenic microorganism in endophthalmitis.
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Affiliation(s)
- Sisi Xu
- Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China.,NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
| | - Chunmei Zhou
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Peijun Zhang
- Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China.,NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
| | - Chaoyi Feng
- Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China.,NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
| | - Ting Zhang
- Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China.,NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
| | - Zhongcui Sun
- Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China.,NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
| | - Hong Zhuang
- Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China.,NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
| | - Han Chen
- Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China.,NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
| | - Qing Chang
- Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China.,NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
| | - Rui Jiang
- Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China.,NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
| | - Huayin Li
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yingqin Ni
- Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China.,NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
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21
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Nadjm B, Dat VQ, Campbell JI, Dung VTV, Torre A, Tu NTC, Van NTT, Trinh DT, Lan NPH, Trung NV, Hang NTT, Hoi LT, Baker S, Wolbers M, Chau NVV, Van Kinh N, Thwaites GE, van Doorn HR, Wertheim HFL. A randomised controlled trial of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDITOF-MS) versus conventional microbiological methods for identifying pathogens: Impact on optimal antimicrobial therapy of invasive bacterial and fungal infections in Vietnam. J Infect 2019; 78:454-460. [PMID: 30914268 PMCID: PMC6529875 DOI: 10.1016/j.jinf.2019.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 03/19/2019] [Accepted: 03/19/2019] [Indexed: 11/28/2022]
Abstract
MALDITOF MS provided more rapid identification of invasive bacterial and fungal pathogens than conventional microbiology. MALDITOF MS did not increase the proportion of patients on optimal therapy at 24 or 48 hours after positive culture. MALDITOF MS did not increase the proportion of patients receiving adequate therapy at 24 hours after positive culture. The most common reason for therapy being sub-optimal was use of overly broad spectrum or unnecessary multiple antibiotics.
Objectives We assessed the impact of MALDITOF-MS on the timeliness of optimal antimicrobial therapy through a parallel-arm randomised controlled trial in two hospitals in Vietnam. Methods We recruited patients with a pathogen (bacterial or fungal) cultured from a normally sterile sample. Samples were randomly assigned (1:1) to identification by MALDITOF-MS or conventional diagnostics. The primary outcome was the proportion on optimal antimicrobial therapy within 24 h of positive culture, determined by a blinded independent review committee. Trial registered at ClinicalTrials.gov (NCT02306330). Results Among 1005 randomised patients, pathogens were isolated from 628 (326 intervention, 302 control), with 377 excluded as likely contaminants or discharged/died before positive culture. Most isolates were cultured from blood (421/628, 67.0%). The proportion receiving optimal antimicrobial therapy within 24 h (the primary outcome) or 48 h of growth was not significantly different between MALDITOF-MS and control arms (135/326, 41.4% vs 120/302, 39.7%; Adjusted Odds ration (AOR) 1.17, p = 0.40 and 151/326, 46.3% vs 141/302, 46.7%; AOR 1.05 p = 0.79, respectively). Conclusions MALDITOF-MS, in the absence of an antimicrobial stewardship programme, did not improve the proportion on optimal antimicrobial therapy at 24 or 48 h after first growth in a lower-middle income setting with high rates of antibiotic resistance.
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Affiliation(s)
- Behzad Nadjm
- Oxford University Clinical Research Unit, Hanoi & Ho Chi Minh City, Viet Nam; Centre for Tropical Medicine & Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.
| | - Vu Quoc Dat
- Oxford University Clinical Research Unit, Hanoi & Ho Chi Minh City, Viet Nam; Department of Infectious Diseases, Hanoi Medical University, Hanoi, Viet Nam
| | - James I Campbell
- Oxford University Clinical Research Unit, Hanoi & Ho Chi Minh City, Viet Nam; Centre for Tropical Medicine & Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Vu Tien Viet Dung
- Oxford University Clinical Research Unit, Hanoi & Ho Chi Minh City, Viet Nam
| | - Alessandro Torre
- Oxford University Clinical Research Unit, Hanoi & Ho Chi Minh City, Viet Nam
| | - Nguyen Thi Cam Tu
- Oxford University Clinical Research Unit, Hanoi & Ho Chi Minh City, Viet Nam
| | - Ninh Thi Thanh Van
- Oxford University Clinical Research Unit, Hanoi & Ho Chi Minh City, Viet Nam
| | | | | | | | | | - Le Thi Hoi
- National Hospital for Tropical Diseases, Hanoi, Viet Nam
| | - Stephen Baker
- Oxford University Clinical Research Unit, Hanoi & Ho Chi Minh City, Viet Nam; Centre for Tropical Medicine & Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Marcel Wolbers
- Oxford University Clinical Research Unit, Hanoi & Ho Chi Minh City, Viet Nam
| | | | | | - Guy E Thwaites
- Oxford University Clinical Research Unit, Hanoi & Ho Chi Minh City, Viet Nam; Centre for Tropical Medicine & Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Hanoi & Ho Chi Minh City, Viet Nam; Centre for Tropical Medicine & Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Heiman F L Wertheim
- Centre for Tropical Medicine & Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom; Department of Medical Microbiology, RadboudUMC, Nijmegen, The Netherlands
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22
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Chew R, Otome O, Harris O, Walton A, Hewson D, Luppino M, Cowan RU. Rapid micro-organism identification from blood and enrichment fluid cultures using MALDI-TOF mass spectrometry following abbreviated incubation on chocolate agar plates in a high-throughput regional microbiology laboratory. Infect Dis (Lond) 2019; 51:312-316. [PMID: 30730248 DOI: 10.1080/23744235.2019.1565417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Rusheng Chew
- a Department of Infectious Diseases , Barwon Health , Victoria , Australia.,b Department of Microbiology , St. John of God Pathology , Victoria , Australia.,c School of Medicine , University of Queensland , Queensland , Australia
| | - Ohide Otome
- a Department of Infectious Diseases , Barwon Health , Victoria , Australia.,b Department of Microbiology , St. John of God Pathology , Victoria , Australia
| | - Owen Harris
- b Department of Microbiology , St. John of God Pathology , Victoria , Australia
| | - Aaron Walton
- a Department of Infectious Diseases , Barwon Health , Victoria , Australia.,b Department of Microbiology , St. John of God Pathology , Victoria , Australia
| | - Darren Hewson
- b Department of Microbiology , St. John of God Pathology , Victoria , Australia
| | - Michael Luppino
- b Department of Microbiology , St. John of God Pathology , Victoria , Australia
| | - Raquel U Cowan
- a Department of Infectious Diseases , Barwon Health , Victoria , Australia.,b Department of Microbiology , St. John of God Pathology , Victoria , Australia
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Diagnosis and treatment of catheter-related bloodstream infection: Clinical guidelines of the Spanish Society of Infectious Diseases and Clinical Microbiology and (SEIMC) and the Spanish Society of Spanish Society of Intensive and Critical Care Medicine and Coronary Units (SEMICYUC). Med Intensiva 2019; 42:5-36. [PMID: 29406956 DOI: 10.1016/j.medin.2017.09.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/29/2017] [Accepted: 09/29/2017] [Indexed: 12/14/2022]
Abstract
Catheter-related bloodstream infections (CRBSI) constitute an important cause of hospital-acquired infection associated with morbidity, mortality, and cost. The aim of these guidelines is to provide updated recommendations for the diagnosis and management of CRBSI in adults. Prevention of CRBSI is excluded. Experts in the field were designated by the two participating Societies (the Spanish Society of Infectious Diseases and Clinical Microbiology and [SEIMC] and the Spanish Society of Spanish Society of Intensive and Critical Care Medicine and Coronary Units [SEMICYUC]). Short-term peripheral venous catheters, non-tunneled and long-term central venous catheters, tunneled catheters and hemodialysis catheters are covered by these guidelines. The panel identified 39 key topics that were formulated in accordance with the PICO format. The strength of the recommendations and quality of the evidence were graded in accordance with ESCMID guidelines. Recommendations are made for the diagnosis of CRBSI with and without catheter removal and of tunnel infection. The document establishes the clinical situations in which a conservative diagnosis of CRBSI (diagnosis without catheter removal) is feasible. Recommendations are also made regarding empirical therapy, pathogen-specific treatment (coagulase-negative staphylococci, Staphylococcus aureus, Enterococcus spp., Gram-negative bacilli, and Candida spp.), antibiotic lock therapy, diagnosis and management of suppurative thrombophlebitis and local complications.
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Application of MALDI Biotyper System for Rapid Identification of Bacteria Isolated from a Fresh Produce Market. Curr Microbiol 2019; 76:290-296. [PMID: 30603962 DOI: 10.1007/s00284-018-01624-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 12/21/2018] [Indexed: 12/18/2022]
Abstract
MALDI-TOF MS has revolutionized the identification of microorganisms and has become an indispensable part of routine diagnostics in the clinical microbiological laboratory. However, application of this technique in microbial surveillance outside of clinical settings is limited. In this study, we have evaluated the performance of a Bruker MALDI Biotyper System for the identification of bacteria isolated from the hand palms of fresh produce handlers and their surrounding environments in a wholesale fresh produce market in Doha, Qatar. The accuracy was verified against the results obtained by bacterial 16S rRNA gene sequencing. A total of 105 isolates were tested, of which 67 (64%) isolates were identified by MALDI-TOF MS and 101 isolates (96%) were identified by 16S rRNA gene sequencing, either at the genus level or species level. However, MALDI-TOF MS identified more isolates (41%) at the species level than 16S rRNA gene sequencing (28%). MALDI-TOF MS was particularly useful in the species level identification of Enterobacteriaceae. MALDI-TOF MS successfully identified most known human pathogens in a rapid and cost-effective manner but failed to identify a significant number of isolates that were of environmental origin, suggesting room for further expansion of the reference database.
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Nabal S, Mormeneo S, García-Lechuz JM. Highlights at the 28th Congress of the European Society of Clinical Microbiology and Infectious Diseases (ESCMID), 2018. REVISTA ESPANOLA DE QUIMIOTERAPIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE QUIMIOTERAPIA 2019; 32 Suppl 2:16-21. [PMID: 31475803 PMCID: PMC6755366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
| | | | - Juan M. García-Lechuz
- Correspondence: Juan M. García-Lechuz Servicio de Microbiología. Hospital Universitario Miguel Servet. Zaragoza E-mail:
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Tsuchida S, Murata S, Miyabe A, Satoh M, Takiwaki M, Ashizawa K, Terada T, Ito D, Matsushita K, Nomura F. Application of the biocopolymer preparation system, rapid BACpro® II kit, for mass-spectrometry-based bacterial identification from positive blood culture bottles by the MALDI Biotyper system. J Microbiol Methods 2018; 152:86-91. [PMID: 30075236 DOI: 10.1016/j.mimet.2018.07.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/25/2018] [Accepted: 07/29/2018] [Indexed: 12/20/2022]
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is increasingly used for identification of microorganisms from positive blood cultures. Pretreatments to effectively remove non-bacterial components and selectively collect microorganisms are a prerequisite for successful identification, and a variety of home-brew and commercial protocols have been reported. Although commercially available kits, mainly the Sepsityper Kit, are increasingly used, the identification rates reported often are not satisfactory, particularly for Gram-positive isolates. We recently developed a method to collect bacteria from positive blood culture bottles using a polyallylamine-polystyrene copolymer that has been used in wastewater processing. This pretreatment protocol is now commercially available as the rapid BACpro® II kit (Nittobo Medical Co., Tokyo, Japan). The operation time required for processing using this novel kit is approximately 10 min, and the entire procedure can be completed within a biosafety cabinet. Since the performance of the rapid BACpro® II kit has not been tested using the MALDI Biotyper system, we prospectively evaluated the performance of the rapid BACpro® II kit as compared with the Sepsityper® kit. Performance of the rapid BACpro® II kit was evaluated using a total of 193 monomicrobial cases of positive blood culture. Medium from blood culture bottles was pretreated by the rapid BACpro® II kit or the Sepsityper® Kit, and isolated cells were subjected to direct identification by MS fingerprinting in parallel with conventional subculturing for reference identification. The overall MALDI-TOF MS-based identification rates with >1.7 score and >2.0 score obtained using the rapid BACpro® II kit were 99.5% and 80.8%, respectively, whereas those obtained using the Sepsityper® Kit were 89.1% and 68.4%, respectively (P < 0.05 for >1.7 and P < 0.05 for >2.0 by Pearsons's chi-square). In Gram-positive cases, the rapid BACpro® II kit gave identification rate of 100% with >1.7 score and 69.4% with >2.0 score, whereas there were 84.7% and 56.8%, respectively by the Sepsityper® Kit (P < 0.05 for >1.7). These results are preliminary, but considering that this new kit is easy to perform and the identification rates are promising, the rapid BACpro® II kit deserves assessment in a larger-scale study with a variety of platforms for MS-based bacterial identification.
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Affiliation(s)
- Sachio Tsuchida
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Syota Murata
- Department of Clinical Laboratory, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Akiko Miyabe
- Department of Clinical Laboratory, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Mamoru Satoh
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Masaki Takiwaki
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | | | | | - Daisuke Ito
- R&D Department, Nittobo Medical Co., Ltd, Japan
| | - Kazuyuki Matsushita
- Department of Clinical Laboratory, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan; Division of Clinical Genetics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Fumio Nomura
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan; Division of Clinical Genetics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan.
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Mizrahi A, Amzalag J, Couzigou C, Péan De Ponfilly G, Pilmis B, Le Monnier A. Clinical impact of rapid bacterial identification by MALDI-TOF MS combined with the bêta-LACTA™ test on early antibiotic adaptation by an antimicrobial stewardship team in bloodstream infections. Infect Dis (Lond) 2018; 50:668-677. [DOI: 10.1080/23744235.2018.1458147] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- A. Mizrahi
- Laboratoire de Microbiologie clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | - J. Amzalag
- Laboratoire de Microbiologie clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | - C. Couzigou
- Equipe mobile de Microbiologie clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | - G. Péan De Ponfilly
- Laboratoire de Microbiologie clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | - B. Pilmis
- Equipe mobile de Microbiologie clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | - A. Le Monnier
- Laboratoire de Microbiologie clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France
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Tsuchida S, Murata S, Miyabe A, Satoh M, Takiwaki M, Matsushita K, Nomura F. An improved in-house lysis-filtration protocol for bacterial identification from positive blood culture bottles with high identification rates by MALDI-TOF MS. J Microbiol Methods 2018; 148:40-45. [PMID: 29608928 DOI: 10.1016/j.mimet.2018.03.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 03/26/2018] [Indexed: 01/04/2023]
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is now a well-established method for identification of microorganisms from positive blood cultures. Pretreatments to effectively remove non-bacterial proteins are a prerequisite for successful identification, and a variety of protocols have been reported. Although commercially available kits, mainly the Sepsityper Kit, are increasingly used, the identification rates reported often are not satisfactory, particularly for Gram-positive isolates. We developed a new, in-house lysis-filtration protocol and prospectively evaluated its performance compared to the Sepsityper kit. The in-house protocol consists of three simple steps: lysis by ammonium chloride, aspiration with a syringe fitted with a 0.45-μm membrane, and centrifugation to collect microbes. The novel protocol requires only 20 min. Performance of the in-house protocol was evaluated using a total of 117 monomicrobial cases of positive blood culture. Medium from blood culture bottles was pretreated by the in-house protocol or the commercial kit, and isolated cells were subjected to direct identification by mass spectrometry fingerprinting in parallel with conventional subculturing for reference identification. The overall MALDI-TOF MS-based identification rates with score > 1.7 and > 2.0 obtained using the in-house protocol were 99.2% and 85.5%, respectively, whereas those obtained using the Sepsityper Kit were 85.4% and 61.5%, respectively. For Gram-positive cases, the in-house protocol yielded scores >1.7 and > 2.0 at 98.5% and 76.1%, respectively, whereas the commercial kit yielded these scores at 76.1% and 43.3%, respectively. Although these are preliminary results, these values suggest that this easy lysis-filtration protocol deserves assessment in a larger-scale test.
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Affiliation(s)
- Sachio Tsuchida
- Division of Clinical Mass Spectrometry, Chiba University Hospital, Chiba, Japan; Department of Clinical Laboratory, Chiba University Hospital, Chiba, Japan
| | - Syota Murata
- Department of Clinical Laboratory, Chiba University Hospital, Chiba, Japan
| | - Akiko Miyabe
- Department of Clinical Laboratory, Chiba University Hospital, Chiba, Japan
| | - Mamoru Satoh
- Division of Clinical Mass Spectrometry, Chiba University Hospital, Chiba, Japan
| | - Masaki Takiwaki
- Division of Clinical Mass Spectrometry, Chiba University Hospital, Chiba, Japan
| | - Kazuyuki Matsushita
- Department of Clinical Laboratory, Chiba University Hospital, Chiba, Japan; Division of Clinical Genetics, Chiba University Hospital, Chiba, Japan
| | - Fumio Nomura
- Division of Clinical Mass Spectrometry, Chiba University Hospital, Chiba, Japan; Division of Clinical Genetics, Chiba University Hospital, Chiba, Japan.
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Rello J, van Engelen TSR, Alp E, Calandra T, Cattoir V, Kern WV, Netea MG, Nseir S, Opal SM, van de Veerdonk FL, Wilcox MH, Wiersinga WJ. Towards precision medicine in sepsis: a position paper from the European Society of Clinical Microbiology and Infectious Diseases. Clin Microbiol Infect 2018; 24:1264-1272. [PMID: 29581049 DOI: 10.1016/j.cmi.2018.03.011] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/06/2018] [Accepted: 03/10/2018] [Indexed: 12/30/2022]
Abstract
BACKGROUND Our current understanding of the pathophysiology and management of sepsis is associated with a lack of progress in clinical trials, which partly reflects insufficient appreciation of the heterogeneity of this syndrome. Consequently, more patient-specific approaches to treatment should be explored. AIMS To summarize the current evidence on precision medicine in sepsis, with an emphasis on translation from theory to clinical practice. A secondary objective is to develop a framework enclosing recommendations on management and priorities for further research. SOURCES A global search strategy was performed in the MEDLINE database through the PubMed search engine (last search December 2017). No restrictions of study design, time, or language were imposed. CONTENT The focus of this Position Paper is on the interplay between therapies, pathogens, and the host. Regarding the pathogen, microbiologic diagnostic approaches (such as blood cultures (BCs) and rapid diagnostic tests (RDTs)) are discussed, as well as targeted antibiotic treatment. Other topics include the disruption of host immune system and the use of biomarkers in sepsis management, patient stratification, and future clinical trial design. Lastly, personalized antibiotic treatment and stewardship are addressed (Fig. 1). IMPLICATIONS A road map provides recommendations and future perspectives. RDTs and identifying drug-response phenotypes are clear challenges. The next step will be the implementation of precision medicine to sepsis management, based on theranostic methodology. This highly individualized approach will be essential for the design of novel clinical trials and improvement of care pathways.
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Affiliation(s)
- J Rello
- CIBERES, Vall d'Hebron Barcelona Campus Hospital, European Study Group of Infections in Critically Ill Patients (ESGCIP), Barcelona, Spain.
| | - T S R van Engelen
- Centre for Experimental Molecular Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - E Alp
- Department of Infectious Diseases, Infection Control Committee, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - T Calandra
- Infectious Diseases Service, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - V Cattoir
- University Hospital of Rennes, Department of Clinical Microbiology, Rennes, France and National Reference Center for Antimicrobial Resistance (lab Enterococci), Rennes, France
| | - W V Kern
- Division of Infectious Diseases, Department of Medicine, University Hospital and Medical Centre, Albert-Ludwigs-University Faculty of Medicine, Freiburg, Germany; Executive Committee of ESCMID Study Group for Bloodstream Infections and Sepsis (ESGBIS), The Netherlands
| | - M G Netea
- Department of Internal Medicine and Radboud Centre for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands; Human Genomics Laboratory, Craiova University of Medicine and Pharmacy, Craiova, Romania
| | - S Nseir
- Faculté de Médecine, University of Lille and Centre de Réanimation, CHU Lille, Lille, France
| | - S M Opal
- Brown University, Infectious Diseases, Providence, RI, USA
| | - F L van de Veerdonk
- Department of Internal Medicine and Radboud Centre for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - M H Wilcox
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, University of Leeds, Leeds, UK
| | - W J Wiersinga
- Centre for Experimental Molecular Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands; Department of Medicine, Division of Infectious Diseases, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands; Executive Committee of ESCMID Study Group for Bloodstream Infections and Sepsis (ESGBIS), The Netherlands.
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30
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Osthoff M, Gürtler N, Bassetti S, Balestra G, Marsch S, Pargger H, Weisser M, Egli A. Impact of MALDI-TOF-MS-based identification directly from positive blood cultures on patient management: a controlled clinical trial. Clin Microbiol Infect 2016; 23:78-85. [PMID: 27569710 DOI: 10.1016/j.cmi.2016.08.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 08/17/2016] [Accepted: 08/18/2016] [Indexed: 01/30/2023]
Abstract
OBJECTIVES Rapid identification of pathogens directly from positive blood cultures (BC) in combination with an antimicrobial stewardship programme (ASP) is associated with improved antibiotic treatment and outcomes, but the effect of each individual intervention is less clear. The current study investigated the impact of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) versus conventional identification on antibiotic management in a setting with a well-established ASP and low resistance rates. METHODS In this single-centre open label, controlled clinical trial 425 patients with positive BCs were allocated by weekday during a 1-year period to either MALDI-TOF directly from positive BCs or conventional processing. ASP was identical throughout the study period. The primary outcome was duration of intravenous antimicrobial therapy and was analysed in an intention-to-treat approach. RESULTS In all, 368 patients were analysed (MALDI-TOF n = 168; conventional n = 200) with similar baseline characteristics. Mean duration of intravenous antimicrobial therapy (12.9 versus 13.2 days, p 0.9) and length of stay (16.1 versus 17.9 days, p 0.3) were comparable. In the clinically significant bloodstream infection subgroup (n = 242) mean time from Gram-stain to active treatment was significantly shorter (3.7 versus 6.7 h, p 0.003). Admission to the intensive care unit after bloodstream infection onset was less frequent in the MALDI-TOF group (23.1 versus 37.2%, p 0.02). CONCLUSIONS Rapid identification of contaminated BCs (n = 126) resulted in a shorter duration of intravenous antimicrobial therapy (mean 4.8 versus 7.5 days, p 0.04). Rapid identification using MALDI-TOF directly from positive BCs did not impact on duration of intravenous antimicrobial therapy, but provided fast and reliable microbiological results and may improve treatment quality in the setting of an established ASP.
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Affiliation(s)
- M Osthoff
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - N Gürtler
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - S Bassetti
- Department of Internal Medicine, University Hospital Basel, Basel, Switzerland
| | - G Balestra
- Medical Intensive Care Unit, University Hospital Basel, Basel, Switzerland
| | - S Marsch
- Medical Intensive Care Unit, University Hospital Basel, Basel, Switzerland
| | - H Pargger
- Surgical Intensive Care Unit, University Hospital Basel, Basel, Switzerland
| | - M Weisser
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - A Egli
- Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
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