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Rossel S, Peters J, Charzinski N, Eichsteller A, Laakmann S, Neumann H, Martínez Arbizu P. A universal tool for marine metazoan species identification: towards best practices in proteomic fingerprinting. Sci Rep 2024; 14:1280. [PMID: 38218969 PMCID: PMC10787734 DOI: 10.1038/s41598-024-51235-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/02/2024] [Indexed: 01/15/2024] Open
Abstract
Proteomic fingerprinting using MALDI-TOF mass spectrometry is a well-established tool for identifying microorganisms and has shown promising results for identification of animal species, particularly disease vectors and marine organisms. And thus can be a vital tool for biodiversity assessments in ecological studies. However, few studies have tested species identification across different orders and classes. In this study, we collected data from 1246 specimens and 198 species to test species identification in a diverse dataset. We also evaluated different specimen preparation and data processing approaches for machine learning and developed a workflow to optimize classification using random forest. Our results showed high success rates of over 90%, but we also found that the size of the reference library affects classification error. Additionally, we demonstrated the ability of the method to differentiate marine cryptic-species complexes and to distinguish sexes within species.
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Affiliation(s)
- Sven Rossel
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), 26382, Wilhelmshaven, Germany.
| | - Janna Peters
- German Centre for Marine Biodiversity Research (DZMB), Senckenberg am Meer, 20146, Hamburg, Germany
| | - Nele Charzinski
- Marine Biodiversity Research, Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
| | - Angelina Eichsteller
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), 26382, Wilhelmshaven, Germany
- Marine Biodiversity Research, Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
| | - Silke Laakmann
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 26129, Oldenburg, Germany
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Hermann Neumann
- Institute for Sea Fisheries, Thuenen Institute, 27572, Bremerhaven, Germany
| | - Pedro Martínez Arbizu
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), 26382, Wilhelmshaven, Germany
- Marine Biodiversity Research, Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
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MALDI-TOF MS-Based Approaches for Direct Identification of Gram-Negative Bacteria and BlaKPC-Carrying Plasmid Detection from Blood Cultures: A Three-Year Single-Centre Study and Proposal of a Diagnostic Algorithm. Microorganisms 2022; 11:microorganisms11010091. [PMID: 36677383 PMCID: PMC9860562 DOI: 10.3390/microorganisms11010091] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022] Open
Abstract
The rapid identification of pathogens of bloodstream infections (BSIs) and the detection of antibiotic resistance markers are critically important for optimizing antibiotic therapy and infection control. The purpose of this study was to evaluate two approaches based on MALDI-TOF MS technology for direct identification of Gram-negative bacteria and automatic detection of Klebsiella pneumoniae carbapenemase (KPC) producers using the Bruker MBT Subtyping IVD Module in a large routine laboratory over a three-year period. MALDI-TOF MS analysis was performed directly from blood culture (BC) bottles following bacterial pellet recovery by Rapid MBT Sepsityper® Kit and on blood agar 4-h subcultures. Automated detection of blaKPC-carrying pKpQIL-plasmid by Bruker MBT Subtyping Module was evaluated in BCs tested positive to K. pneumoniae or E. coli. The results were compared with those obtained with conventional reference methods. Among the 2858 (93.4%) monomicrobial BCs, the overall species identification rates of the Rapid Sepsityper and the short-term subculture protocols were 84.5% (n = 2416) and 90.8% (n = 2595), respectively (p < 0.01). Excellent specificity for KPC-producers identification were observed for both MALDI-TOF MS protocols. The pKpQIL plasmid-related peak was detected in overall 91 of the 120 (75.8%) KPC-producing isolates. Notably, 14 out of the 17 (82.3%) K. pneumoniae isolates carrying blaKPC variants associated with ceftazidime/avibactam resistance and tested negative by the immunocromatography assay, were correctly identified as KPC-producers by MALDI-TOF MS. In conclusion, combination of both Rapid Sepsityper and short-term subculture protocols may represent an optimal solution to promptly identify more than 95% of Gram-negative bacteria causing BSIs. MALDI Biotyper® platform enabled a reliable and robust automated detection of KPC producers in parallel with species identification. However, integration of molecular or immunocromatographic assays are recommended according to local epidemiology.
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Oviaño M, Ingebretsen A, Steffensen AK, Croxatto A, Prod’hom G, Quiroga L, Bou G, Greub G, Rodríguez-Temporal D, Rodríguez-Sánchez B. Multicenter Evaluation of Rapid BACpro ® II for the Accurate Identification of Microorganisms Directly from Blood Cultures Using MALDI-TOF MS. Diagnostics (Basel) 2021; 11:diagnostics11122251. [PMID: 34943488 PMCID: PMC8700617 DOI: 10.3390/diagnostics11122251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/23/2021] [Accepted: 11/28/2021] [Indexed: 01/14/2023] Open
Abstract
The identification of microorganisms directly from blood cultures using MALDI-TOF MS has been shown to be the most impacting application of this methodology. In this study, a novel commercial method was evaluated in four clinical microbiology laboratories. Positive blood culture samples (n = 801) were processed using a rapid BACpro® II kit and then compared with the routine gold standard. A subset of monomicrobial BCs (n = 560) were analyzed in parallel with a Sepsityper® Kit (Bruker Daltonics, Bremen, Germany) and compared with the rapid BACpro® II kit. In addition, this kit was also compared with two different in-house methods. Overall, 80.0% of the monomicrobial isolates (609/761; 95% CI 71.5-88.5) were correctly identified by the rapid BACpro® II kit at the species level (92.3% of the Gram negative and 72.4% of the Gram positive bacteria). The comparison with the Sepsityper® Kit showed that the rapid BACpro® II kit generated higher rates of correct species-level identification for all categories (p > 0.0001), except for yeasts identified with score values > 1.7. It also proved superior to the ammonium chloride method (p > 0.0001), but the differential centrifugation method allowed for higher rates of correct identification for Gram negative bacteria (p > 0.1). The percentage of accurate species-level identification of Gram positive bacteria was particularly noteworthy in comparison with other commercial and in-house methods.
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Affiliation(s)
- Marina Oviaño
- Department of Microbiology, Complejo Hospitalario Universitario A Coruña, 15006 A Coruña, Spain; (M.O.); (G.B.)
| | - André Ingebretsen
- Department of Microbiology, Oslo University Hospital, P.O. Box 4950 Nydalen, 0188 Oslo, Norway; (A.I.); (A.K.S.)
| | - Anne K. Steffensen
- Department of Microbiology, Oslo University Hospital, P.O. Box 4950 Nydalen, 0188 Oslo, Norway; (A.I.); (A.K.S.)
- Faculty of Medicine, University of Oslo, 0372 Oslo, Norway
| | - Antony Croxatto
- Institute of Microbiology, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland; (A.C.); (G.P.); (G.G.)
| | - Guy Prod’hom
- Institute of Microbiology, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland; (A.C.); (G.P.); (G.G.)
| | - Lidia Quiroga
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain;
- Instituto de Investigación Sanitaria and Hospital General Universitario Gregorio Marañón (IiSGM), 28007 Madrid, Spain
| | - Germán Bou
- Department of Microbiology, Complejo Hospitalario Universitario A Coruña, 15006 A Coruña, Spain; (M.O.); (G.B.)
| | - Gilbert Greub
- Institute of Microbiology, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland; (A.C.); (G.P.); (G.G.)
| | - David Rodríguez-Temporal
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain;
- Instituto de Investigación Sanitaria and Hospital General Universitario Gregorio Marañón (IiSGM), 28007 Madrid, Spain
- Correspondence: (D.R.-T.); (B.R.-S.)
| | - Belén Rodríguez-Sánchez
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain;
- Instituto de Investigación Sanitaria and Hospital General Universitario Gregorio Marañón (IiSGM), 28007 Madrid, Spain
- Correspondence: (D.R.-T.); (B.R.-S.)
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Direct Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Testing from Positive Blood Cultures for Rapid Identification of Bloodstream Infection-Causing Anaerobic Bacteria. J Clin Microbiol 2021; 59:e0052121. [PMID: 33883181 DOI: 10.1128/jcm.00521-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Alcalá L, Marín M, Ruiz A, Quiroga L, Zamora-Cintas M, Fernández-Chico MA, Muñoz P, Rodríguez-Sánchez B. Identifying Anaerobic Bacteria Using MALDI-TOF Mass Spectrometry: A Four-Year Experience. Front Cell Infect Microbiol 2021; 11:521014. [PMID: 33968791 PMCID: PMC8101409 DOI: 10.3389/fcimb.2021.521014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/26/2021] [Indexed: 12/23/2022] Open
Abstract
Because of the special culture requirements of anaerobic bacteria, their low growth-rate and the difficulties to isolate them, MALDI-TOF MS has become a reliable identification tool for these microorganisms due to the little amount of bacteria required and the accuracy of MALDI-TOF MS identifications. In this study, the performance of MALDI-TOF MS for the identification of anaerobic isolates during a 4-year period is described. Biomass from colonies grown on Brucella agar was directly smeared onto the MALDI-TOF target plate and submitted to on-plate protein extraction with 1μl of 100% formic acid. Sequencing analysis of the 16S rRNA gene was used as a reference method for the identification of isolates unreliably or not identified by MALDI-TOF MS. Overall, 95.7% of the isolates were identified to the species level using the updated V6 database vs 93.8% with previous databases lacking some anaerobic species; 68.5% of the total were reliably identified with high-confidence score values (≥2.0) and 95.0% with low-confidence values (score value ≥1.7). Besides, no differences between Gram-positive and Gram-negative isolates were detected beyond a slight decrease of correct species assignment for gram positive cocci (94.1% vs 95.7% globally). MALDI-TOF MS has demonstrated its usefulness for the identification of anaerobes, with high correlation with phenotypic and conventional methods. Over the study period, only 2.1% of the isolates could not be reliably identified and required molecular methods for a final identification. Therefore, MALDI-TOF MS provided reliable identification of anaerobic isolates, allowing clinicians to streamline the most appropriate antibiotic therapy and manage patients accordingly.
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Affiliation(s)
- Luis Alcalá
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Mercedes Marín
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058), Madrid, Spain
| | - Adrián Ruiz
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Lidia Quiroga
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Maribel Zamora-Cintas
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - María Antonia Fernández-Chico
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Patricia Muñoz
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058), Madrid, Spain
- Medicine Department, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Belén Rodríguez-Sánchez
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
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Wang J, Wang H, Cai K, Yu P, Liu Y, Zhao G, Chen R, Xu R, Yu M. Evaluation of three sample preparation methods for the identification of clinical strains by using two MALDI-TOF MS systems. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4696. [PMID: 33421261 PMCID: PMC7900945 DOI: 10.1002/jms.4696] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/16/2020] [Accepted: 12/09/2020] [Indexed: 05/07/2023]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized the microbial identification, especially in the clinical microbiology laboratories. However, although numerous studies on the identification of microorganisms by MALDI-TOF MS have been reported previously, few studies focused on the effect of pretreatment on identification. Due to the sensitivity of MALDI-TOF MS, different preparation methods will lead to changes in microbial protein fingerprints. In this study, for evaluating a more appropriate preparation method for the clinical microbiology identification, we analyzed the performance of three sample preparation methods on two different MALDI-TOF MS systems. A total of 321 clinical isolates, 127 species, were employed in the comparative study of three different sample preparation methods including the direct colony transfer method (DCTM), the on-target extraction method (OTEM), and the in-tube extraction method (ITEM) compatible with MALDI-TOF MS. All isolates were tested on the Microflex LT and Autof ms1000 devices. The spectra were analyzed using the Bruker biotyper and the Autof ms1000 systems. The results were confirmed by 16/18S rRNA sequencing. Results reveal that the accuracies of isolates identification by Bruker biotyper successfully identified 83.8%, 96.0%, and 95.3% after performing the DCTM, OTEM, and ITEM, respectively, while the Autof ms1000 identified 97.5%, 100%, and 99.7%. These data suggested that the identification rates are comparable among the three preparation methods using the Autof ms1000 and Bruker microflex LT systems but the OTEM is more suitable and necessary for clinical application, owing to its key advantages of simplicity and accuracy.
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Affiliation(s)
- Jinghua Wang
- Department of Clinical Microbiology LaboratoryShanghai Center for Clinical LaboratoryShanghaiChina
| | - Hualiang Wang
- Department of Clinical Microbiology LaboratoryShanghai Center for Clinical LaboratoryShanghaiChina
| | - Keya Cai
- Diagnostics DepartmentAutobio Diagnostics Co., Ltd.ZhengzhouChina
| | - Peijuan Yu
- Department of Clinical LaboratorySecond Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Yajuan Liu
- Diagnostics DepartmentAutobio Diagnostics Co., Ltd.ZhengzhouChina
| | - Gaoling Zhao
- Diagnostics DepartmentAutobio Diagnostics Co., Ltd.ZhengzhouChina
| | - Rong Chen
- Department of Clinical Microbiology LaboratoryShanghai Center for Clinical LaboratoryShanghaiChina
| | - Rong Xu
- Department of Clinical Microbiology LaboratoryShanghai Center for Clinical LaboratoryShanghaiChina
| | - Maowen Yu
- Department of Clinical LaboratoryJintang First People's HospitalChengduChina
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7
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Islam MA, Hassen WM, Tayabali AF, Dubowski JJ. Short Ligand, Cysteine-Modified Warnericin RK Antimicrobial Peptides Favor Highly Sensitive Detection of Legionella pneumophila. ACS OMEGA 2021; 6:1299-1308. [PMID: 33490789 PMCID: PMC7818584 DOI: 10.1021/acsomega.0c04753] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
Culture-based methods for the detection of Legionella pneumophila are prohibitively slow and frequently inadequate. The problem has been addressed with biosensing technology that employs a variety of ligands for the specific capture of bacteria. However, the limited success of the application of mammalian antibodies, aptamers, and nucleic acid-based probes for sensitive biosensing has generated growing interest in exploring alternative biosensing architectures, such as those based on antimicrobial peptides (AMP) that are known for their attractive therapeutic applications. We report on the successful employment of cysteine-modified warnericin RK AMP for the operation of a highly sensitive biosensor of L. pneumophila based on digital photocorrosion of GaAs/AlGaAs nanoheterostructures. The replacement of the relatively cumbersome procedure commonly applied for the attachment of antibodies to COOH-terminated mercaptohexadecanoic acid self-assembled monolayers has allowed for a significant reduction in the distance at which bacteria are immobilized above the biosensor surface. An important consequence of this approach is the attractive limit of detection of L. pneumophila estimated at 2 × 102 CFU/mL. The target bacteria were captured four times more efficiently than P. fluorescens, B. subtilis, and E. coli, which is highly promising for environmental monitoring.
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Affiliation(s)
- M. Amirul Islam
- Interdisciplinary
Institute for Technological Innovation (3IT), CNRS UMI-3463, Laboratory
for Quantum Semiconductors and Photon-based BioNanotechnology, Department
of Electrical and Computer Engineering, Université de Sherbrooke, 3000, boul. de l’Université, Sherbrooke, Québec J1K 0A5, Canada
| | - Walid M. Hassen
- Interdisciplinary
Institute for Technological Innovation (3IT), CNRS UMI-3463, Laboratory
for Quantum Semiconductors and Photon-based BioNanotechnology, Department
of Electrical and Computer Engineering, Université de Sherbrooke, 3000, boul. de l’Université, Sherbrooke, Québec J1K 0A5, Canada
| | - Azam F. Tayabali
- Environmental
Health Science Research Bureau, Healthy
Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9, Canada
| | - Jan J. Dubowski
- Interdisciplinary
Institute for Technological Innovation (3IT), CNRS UMI-3463, Laboratory
for Quantum Semiconductors and Photon-based BioNanotechnology, Department
of Electrical and Computer Engineering, Université de Sherbrooke, 3000, boul. de l’Université, Sherbrooke, Québec J1K 0A5, Canada
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Review on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the rapid screening of microbial species: A promising bioanalytical tool. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105387] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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9
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Liu YC, Lu JJ, Lin LC, Lin HC, Chen CJ. Protein Biomarker Discovery for Methicillin-Sensitive, Heterogeneous Vancomycin-Intermediate and Vancomycin-Intermediate Staphylococcus aureus Strains Using Label-Free Data-Independent Acquisition Proteomics. J Proteome Res 2020; 20:164-171. [PMID: 33058664 DOI: 10.1021/acs.jproteome.0c00134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rapid identification of methicillin-sensitive Staphylococcus aureus (MSSA), heterogeneous vancomycin-intermediate S. aureus (hVISA), and vancomycin-intermediate S. aureus (VISA) is important for accurate treatment, timely intervention, and prevention of outbreaks. Here, 90 S. aureus isolates were analyzed for protein biomarker discovery, including MSSA, vancomycin-susceptible S. aureus (VSSA), hVISA, and VISA strains. Label-free data-independent acquisition proteomics was used to identify protein biomarkers that allow for discrimination among MSSA, hVISA, and VISA strains. There were 8786 nonredundant peptides identified, corresponding to 418 different annotated nonredundant proteins. Two VISA protein biomarkers, two hVISA protein biomarkers, and one MSSA protein biomarker with high sensitivities and specificities were discovered and verified. Data are available via MassIVE with identifier MSV000085776.
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Affiliation(s)
- Yu-Ching Liu
- Graduate Institute of Integrated Medicine, China Medical University, 91, Hsueh-Shih Rd, Taichung 40402, Taiwan
| | - Jang-Jih Lu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan 33305, Taiwan.,Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Lee-Chung Lin
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan 33305, Taiwan
| | - Hsiao-Chuan Lin
- School of Medicine, China Medical University, 91, Hsueh-Shih Rd, Taichung 40402, Taiwan.,Department of Pediatric Infectious Diseases, China Medical University Children's Hospital, Taichung 40447, Taiwan
| | - Chao-Jung Chen
- Graduate Institute of Integrated Medicine, China Medical University, 91, Hsueh-Shih Rd, Taichung 40402, Taiwan.,Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung 404, Taiwan
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Ko YJ, Kook JK, Lee CK. In-house method for direct bacterial identification in positive blood culture broths using microfiltration, bead beating, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Microbiol Methods 2020; 180:106065. [PMID: 32961240 DOI: 10.1016/j.mimet.2020.106065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 10/23/2022]
Abstract
Rapid identification of bacterial pathogens facilitates earlier optimization of antibiotic treatment and reduces morbidity and mortality in sepsis patients. The aim of this research was to design an in-house chemical-free method for direct bacterial identification in positive blood culture (BC) broths and to compare the performance of this method with that of the commercial Sepsityper® kit. The overall species identification rates for the in-house and Sepsityper methods were 88.4% and 85.8%, respectively (n = 190). Among 146 facultative anaerobes, 92.5% and 95.9% were identified to the species level using the in-house and Sepsityper methods, respectively. For 32 anaerobic bacteria, the in-house method showed a higher species identification rate (75.0%) than the Sepsityper method (53.1%). The in-house method correctly identified more Bacteroides species (100.0%) than the Sepsityper method (18.2%). Our novel in-house method and the Sepsityper method showed a high accuracy for direct bacterial identification in positive BC broths using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
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Affiliation(s)
- Young Jin Ko
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Republic of Korea; Department of Laboratory Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, College of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Chang Kyu Lee
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Republic of Korea.
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Propionibacterium/Cutibacterium species-related positive samples, identification, clinical and resistance features: a 10-year survey in a French hospital. Eur J Clin Microbiol Infect Dis 2020; 39:1357-1364. [PMID: 32125556 DOI: 10.1007/s10096-020-03852-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/16/2020] [Indexed: 02/07/2023]
Abstract
A 10-year retrospective study of Propionibacterium/Cutibacterium-positive samples gathered from hospitalized patients was conducted at Nantes University hospital. A total of 2728 Propionibacterium/Cutibacterium-positive samples analyzed between 2007 and 2016 were included. Due to the implementation of MALDI-TOF identification in 2013, most non-Cutibacterium acnes isolates were identified a second time using this technology. Over that period, Cutibacterium acnes remained the most predominant species accounting for 91.5% (2497/2728) of the isolates, followed by Cutibacterium avidum (4.2%, 115/2728) and Cutibacterium granulosum (2.4%, 64/2728). Regarding the origin of samples, the orthopaedic department was the main Cutibacterium sample provider representing 51.9% (1415/2728) of all samples followed by the dermatology department (11.5%, 315/2728). Samples were recovered from various tissue locations: 31.5% (858/2728) from surgery-related samples such as shoulder, spine or hip replacement devices and 19.1% (520/2728) from skin samples. MALDI-TOF method revealed misidentification before 2013. Cutibacterium avidum was falsely identified as C. granulosum (n = 33). Consequently, MALDI-TOF technology using up-to-date databases should be preferred to biochemical identification in order to avoid biased species identification. Regarding antibiotic resistance, 14.7% (20/136) of C. acnes was resistant to erythromycin. 4.1% (41/1005) of C. acnes strains, 17.9% (12/67) of C. avidum strains and 3.6% (1/28) of C. granulosum strains were found resistant to clindamycin.
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Identification and Antimicrobial Susceptibility of Clinically Isolated Anaerobic Bacteria: A Retrospectively Study in a Jiangxi Tertiary-Care Hospital. Jundishapur J Microbiol 2019. [DOI: 10.5812/jjm.95800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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13
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Roux-Dalvai F, Gotti C, Leclercq M, Hélie MC, Boissinot M, Arrey TN, Dauly C, Fournier F, Kelly I, Marcoux J, Bestman-Smith J, Bergeron MG, Droit A. Fast and Accurate Bacterial Species Identification in Urine Specimens Using LC-MS/MS Mass Spectrometry and Machine Learning. Mol Cell Proteomics 2019; 18:2492-2505. [PMID: 31585987 PMCID: PMC6885708 DOI: 10.1074/mcp.tir119.001559] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/27/2019] [Indexed: 12/11/2022] Open
Abstract
Fast identification of microbial species in clinical samples is essential to provide an appropriate antibiotherapy to the patient and reduce the prescription of broad-spectrum antimicrobials leading to antibioresistances. MALDI-TOF-MS technology has become a tool of choice for microbial identification but has several drawbacks: it requires a long step of bacterial culture before analysis (≥24 h), has a low specificity and is not quantitative. We developed a new strategy for identifying bacterial species in urine using specific LC-MS/MS peptidic signatures. In the first training step, libraries of peptides are obtained on pure bacterial colonies in DDA mode, their detection in urine is then verified in DIA mode, followed by the use of machine learning classifiers (NaiveBayes, BayesNet and Hoeffding tree) to define a peptidic signature to distinguish each bacterial species from the others. Then, in the second step, this signature is monitored in unknown urine samples using targeted proteomics. This method, allowing bacterial identification in less than 4 h, has been applied to fifteen species representing 84% of all Urinary Tract Infections. More than 31,000 peptides in 190 samples were quantified by DIA and classified by machine learning to determine an 82 peptides signature and build a prediction model. This signature was validated for its use in routine using Parallel Reaction Monitoring on two different instruments. Linearity and reproducibility of the method were demonstrated as well as its accuracy on donor specimens. Within 4h and without bacterial culture, our method was able to predict the predominant bacteria infecting a sample in 97% of cases and 100% above the standard threshold. This work demonstrates the efficiency of our method for the rapid and specific identification of the bacterial species causing UTI and could be extended in the future to other biological specimens and to bacteria having specific virulence or resistance factors.
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Affiliation(s)
- Florence Roux-Dalvai
- Proteomics platform, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada
| | - Clarisse Gotti
- Proteomics platform, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada
| | - Mickaël Leclercq
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada
| | - Marie-Claude Hélie
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
| | - Maurice Boissinot
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
| | | | | | - Frédéric Fournier
- Proteomics platform, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada
| | - Isabelle Kelly
- Proteomics platform, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada
| | - Judith Marcoux
- Proteomics platform, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada
| | - Julie Bestman-Smith
- Laboratoire de microbiologie-infectiologie, CHU de Québec-Université Laval, pavillon Hôpital de l'Enfant-Jésus, Québec City, Québec, Canada
| | - Michel G Bergeron
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada; Département de microbiologie-infectiologie et d'immunologie, Faculté de médecine, Université Laval, Québec City, Québec, Canada
| | - Arnaud Droit
- Proteomics platform, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada; Computational Biology Laboratory, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada; Département de Médecine Moléculaire, Faculté de médecine, Université Laval, Québec City, QC, Canada.
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14
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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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15
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Nagy E, Schuetz A. Advancing MALDI-TOF MS applications in anaerobic bacteriology. Anaerobe 2018; 54:189-190. [PMID: 30541685 DOI: 10.1016/j.anaerobe.2018.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Elisabeth Nagy
- Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary.
| | - Audrey Schuetz
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA.
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16
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Ramirez-Estrada S, Peña-Lopez Y, Kalwaje Eshwara V, Rello J. Ventilator-associated events versus ventilator-associated respiratory infections-moving into a new paradigm or merging both concepts, instead? ANNALS OF TRANSLATIONAL MEDICINE 2018; 6:425. [PMID: 30581833 PMCID: PMC6275412 DOI: 10.21037/atm.2018.10.54] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 10/21/2018] [Indexed: 01/06/2023]
Abstract
Despite ventilator-associated respiratory infections (VARI) are reported as the most common and fatal complications related to mechanical ventilation (MV), they are not the unique occurrences. The new classification of ventilator-associated events (VAE) proposed by the centers for disease control and prevention (CDC) enhance the spectra of complications due to MV including both infection-related and non-infectious events. Both VAEs and VARIs are associated with prolonged duration of MV, longer stay in hospital and in the intensive care unit (ICU) and more antibiotic consumption, nonetheless patients with VAEs have worst outcomes. The VARI and VAE algorithms are focused on different targets and the correlation between both classifications is shown to be poor. The diagnostic criteria of the traditional classification have limited accuracy and the non-infectious complications may be misinterpreted as VARI. While the VAE surveillance enhances the spectra of MV complications but excludes less severe VARIs. Noninfective events explain up to 30% of VAEs, the main causes being atelectasis, acute respiratory distress syndrome, pulmonary edema and pulmonary embolism. The bundles assessing VAE are associated with less incidence of VAP and improved outcomes but they fail to reduce the rates of VAE. Automated VAE surveillance is efficient and useful as a quality indicator in the ICU while the differences in the interpretation of VARI criteria limit its role in the design of global protocols and preventive strategies. We suggest that a more comprehensive strategy should combine both algorithms with emphasis on clinical outcomes.
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Affiliation(s)
- Sergio Ramirez-Estrada
- Critical Care Department, Clínica Corachan, Barcelona, Spain
- Medicine Department, Universitat Autónoma de Barcelona, (UAB), Barcelona, Spain
| | | | - Vandana Kalwaje Eshwara
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Jordi Rello
- Vall d'Hebron Institut of Research, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBERES), Instituto Salud Carlos III, Madrid, Spain
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