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Czeszewska-Rosiak G, Złoch M, Radosińska M, Florkiewicz AB, Tretyn A, Pomastowski P. The usefulness of the MALDI-TOF MS technique in the determination of dairy samples' microbial composition: comparison of the new EXS 2600 system with MALDI Biotyper platform. Arch Microbiol 2024; 206:172. [PMID: 38492038 DOI: 10.1007/s00203-024-03885-w] [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: 11/30/2023] [Revised: 01/15/2024] [Accepted: 02/05/2024] [Indexed: 03/18/2024]
Abstract
This study compared the EXS 2600 system with the MALDI Biotyper for identifying microorganisms in dairy samples. Of the 196 bacterial isolates from milk, whey, buttermilk, cream, and dairy wastewater, the species and genus consistent identification between two systems showed 74% and 99%, respectively. However, the level of species identification rate exhibited a difference, which was higher in Zybio than in Bruker-76.0% and 66.8%, respectively. Notably, the EXS 2600 system performed better with certain yeast species and H. alvei, while the Biotyper excelled with Pseudomonas bacteria. Unique microbial compositions were found in 85% of dairy samples, with whey and buttermilk having the highest diversity. This research highlights the EXS 2600's potential as a reliable dairy microbial identification tool and underscores the need for a more diverse and comprehensive spectral database, despite the database's focus on clinical applications (as announced).
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Affiliation(s)
- Grażyna Czeszewska-Rosiak
- Chair of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Lwowska 1 Street, 87-100, Toruń, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4 Str., 87-100, Toruń, Poland
| | - Michał Złoch
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4 Str., 87-100, Toruń, Poland.
| | - Monika Radosińska
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4 Str., 87-100, Toruń, Poland
| | | | - Andrzej Tretyn
- Chair of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Lwowska 1 Street, 87-100, Toruń, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4 Str., 87-100, Toruń, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4 Str., 87-100, Toruń, Poland
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Calderaro A, Chezzi C. MALDI-TOF MS: A Reliable Tool in the Real Life of the Clinical Microbiology Laboratory. Microorganisms 2024; 12:322. [PMID: 38399726 PMCID: PMC10892259 DOI: 10.3390/microorganisms12020322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 01/28/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Matrix-Assisted Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) in the last decade has revealed itself as a valid support in the workflow in the clinical microbiology laboratory for the identification of bacteria and fungi, demonstrating high reliability and effectiveness in this application. Its use has reduced, by 24 h, the time to obtain a microbiological diagnosis compared to conventional biochemical automatic systems. MALDI-TOF MS application to the detection of pathogens directly in clinical samples was proposed but requires a deeper investigation, whereas its application to positive blood cultures for the identification of microorganisms and the detection of antimicrobial resistance are now the most useful applications. Thanks to its rapidity, accuracy, and low price in reagents and consumables, MALDI-TOF MS has also been applied to different fields of clinical microbiology, such as the detection of antibiotic susceptibility/resistance biomarkers, the identification of aminoacidic sequences and the chemical structure of protein terminal groups, and as an emerging method in microbial typing. Some of these applications are waiting for an extensive evaluation before confirming a transfer to the routine. MALDI-TOF MS has not yet been used for the routine identification of parasites; nevertheless, studies have been reported in the last few years on its use in the identification of intestinal protozoa, Plasmodium falciparum, or ectoparasites. Innovative applications of MALDI-TOF MS to viruses' identification were also reported, seeking further studies before adapting this tool to the virus's diagnostic. This mini-review is focused on the MALDI-TOF MS application in the real life of the diagnostic microbiology laboratory.
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Affiliation(s)
- Adriana Calderaro
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy;
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Sibińska E, Arendowski A, Fijałkowski P, Gabryś D, Pomastowski P. Comparison of the Bruker Microflex LT and Zybio EXS2600 MALDI TOF MS systems for the identification of clinical microorganisms. Diagn Microbiol Infect Dis 2024; 108:116150. [PMID: 38035652 DOI: 10.1016/j.diagmicrobio.2023.116150] [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: 06/20/2023] [Revised: 11/16/2023] [Accepted: 11/24/2023] [Indexed: 12/02/2023]
Abstract
The emergence of Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI TOF MS) technology has expanded the capabilities for identifying microorganisms in clinical labs, replacing traditional biochemical testing with a proteomic approach. In the present study, we compared results between the two commercial MALDI TOF MS systems, Bruker Microflex LT Biotyper and Zybio EXS2600 Ex-Accuspec, for the identification of 1979 urinary isolates by direct extraction method. Current study found that both systems identified a high percentage of isolates to at least the genus level - Bruker 95.6 % of isolates, Zybio 92.4 %. In the case of 89.5 % of all analyzed spectra, the identification results were consistent between the used devices. The highest score values and the highest percentage of spectra identified to species were obtained for gram-negative bacteria. The results show that both systems are equally good choices in terms of analytical performance for routine microbiological diagnostic procedures.
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Affiliation(s)
- Ewelina Sibińska
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., Toruń 87-100, Poland
| | - Adrian Arendowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., Toruń 87-100, Poland.
| | - Piotr Fijałkowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., Toruń 87-100, Poland
| | - Dorota Gabryś
- Radiotherapy Department, Maria Sklodowska-Curie National Research Institute of Oncology, Wybrzeże Armii Krajowej 15 Str., Gliwice 44-102, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., Toruń 87-100, Poland
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Iskender S, Heydarov S, Yalcin M, Faydaci C, Kurt O, Surme S, Kucukbasmaci O. Rapid determination of colistin resistance in Klebsiella pneumoniae by MALDI-TOF peak based machine learning algorithm with MATLAB. Diagn Microbiol Infect Dis 2023; 107:116052. [PMID: 37769565 DOI: 10.1016/j.diagmicrobio.2023.116052] [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: 03/13/2023] [Revised: 07/05/2023] [Accepted: 08/05/2023] [Indexed: 10/03/2023]
Abstract
INTRODUCTION To date, limited data exist on demonstrating the usefulness of machine learning (ML) algorithms applied to MALDI-TOF in determining colistin resistance among Klebsiella pneumoniae. We aimed to detect colistin resistance in K. pneumoniae using MATLAB on MALDI-TOF database. MATERIALS AND METHODS A total of 260 K. pneumoniae isolates were collected. Three ML models, namely, linear discriminant analysis (LDA), support vector machine, and Ensemble were used as ML algorithms and applied to training data set. RESULTS The accuracies for the training phase with 200 isolates were found to be 99.3%, 93.1%, and 88.3% for LDA, support vector machine, and Ensemble models, respectively. Accuracy, sensitivity, specificity, and precision values for LDA in the application test set with 60 K. pneumoniae isolates were 81.6%, 66.7%, 91.7%, and 84.2%, respectively. CONCLUSION This study provides a rapid and accurate MALDI-TOF MS screening assay for clinical practice in identifying colistin resistance in K. pneumoniae.
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Affiliation(s)
- Secil Iskender
- Department of Medical Microbiology, Istanbul University-Cerrahpasa, Cerrahpasa Medical Faculty, Istanbul, Turkey
| | - Saddam Heydarov
- Electronics Technologies, Istanbul Gelisim University, Istanbul, Turkey
| | - Metin Yalcin
- Department of Medical Microbiology, Istanbul University-Cerrahpasa, Cerrahpasa Medical Faculty, Istanbul, Turkey
| | - Cagri Faydaci
- Electronics Technologies, Istanbul Gelisim University, Istanbul, Turkey
| | - Ozge Kurt
- Department of Medical Microbiology, Istanbul University-Cerrahpasa, Cerrahpasa Medical Faculty, Istanbul, Turkey
| | - Serkan Surme
- Department of Medical Microbiology, Istanbul University-Cerrahpasa, Cerrahpasa Medical Faculty, Istanbul, Turkey
| | - Omer Kucukbasmaci
- Department of Medical Microbiology, Istanbul University-Cerrahpasa, Cerrahpasa Medical Faculty, Istanbul, Turkey.
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Wang Z, Zhou Y, Guo G, Li Q, Yu Y, Zhang W. Promising potential of machine learning-assisted MALDI-TOF MS as an effective detector for Streptococcus suis serotype 2 and virulence thereof. Appl Environ Microbiol 2023; 89:e0128423. [PMID: 37861326 PMCID: PMC10686076 DOI: 10.1128/aem.01284-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/01/2023] [Indexed: 10/21/2023] Open
Abstract
IMPORTANCE To the best of our knowledge, this study reveals a strong correlation between mass spectra pattern and virulence phenotype among S. suis for the first time. In order to make the findings applicable and to excavate the intrinsic information in the spectra, the classifiers based on the machine learning algorithms were established, and RF (Random Forest)-based models have achieved an accuracy of over 90%. Overall, this study will pave the way for virulent SS2 (Streptococcus suis serotype 2) rapid detection, and the important findings on the association between genotype and mass spectrum may provide a new idea for the genotype-dependent detection of specific pathogens.
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Affiliation(s)
- Zhuohao Wang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- The Sanya Institute of Nanjing Agriculture University, Sanya, China
| | - Yu Zhou
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- The Sanya Institute of Nanjing Agriculture University, Sanya, China
| | - Genglin Guo
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- The Sanya Institute of Nanjing Agriculture University, Sanya, China
| | - Quan Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Yanfei Yu
- Key Laboratory of Veterinary Biological Engineering and Technology of Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Wei Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- The Sanya Institute of Nanjing Agriculture University, Sanya, China
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Elbehiry A, Marzouk E, Moussa I, Anagreyyah S, AlGhamdi A, Alqarni A, Aljohani A, Hemeg HA, Almuzaini AM, Alzaben F, Abalkhail A, Alsubki RA, Najdi A, Algohani N, Abead B, Gazzaz B, Abu-Okail A. Using Protein Fingerprinting for Identifying and Discriminating Methicillin Resistant Staphylococcus aureus Isolates from Inpatient and Outpatient Clinics. Diagnostics (Basel) 2023; 13:2825. [PMID: 37685363 PMCID: PMC10486511 DOI: 10.3390/diagnostics13172825] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/25/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
In hospitals and other clinical settings, Methicillin-resistant Staphylococcus aureus (MRSA) is a particularly dangerous pathogen that can cause serious or even fatal infections. Thus, the detection and differentiation of MRSA has become an urgent matter in order to provide appropriate treatment and timely intervention in infection control. To ensure this, laboratories must have access to the most up-to-date testing methods and technology available. This study was conducted to determine whether protein fingerprinting technology could be used to identify and distinguish MRSA recovered from both inpatients and outpatients. A total of 326 S. aureus isolates were obtained from 2800 in- and outpatient samples collected from King Faisal Specialist Hospital and Research Centre in Riyadh, Saudi Arabia, from October 2018 to March 2021. For the phenotypic identification of 326 probable S. aureus cultures, microscopic analysis, Gram staining, a tube coagulase test, a Staph ID 32 API system, and a Vitek 2 Compact system were used. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), referred to as protein fingerprinting, was performed on each bacterial isolate to determine its proteomic composition. As part of the analysis, Principal Component Analysis (PCA) and a single-peak analysis of MALDI-TOF MS software were also used to distinguish between Methicillin-sensitive Staphylococcus aureus (MSSA) and MRSA. According to the results, S. aureus isolates constituted 326 out of 2800 (11.64%) based on the culture technique. The Staph ID 32 API system and Vitek 2 Compact System were able to correctly identify 262 (80.7%) and 281 (86.2%) S. aureus strains, respectively. Based on the Oxacillin Disc Diffusion Method, 197 (62.23%) of 326 isolates of S. aureus exhibited a cefoxitin inhibition zone of less than 21 mm and an oxacillin inhibition zone of less than 10 mm, and were classified as MRSA under Clinical Laboratory Standards Institute guidelines. MALDI-TOF MS was able to correctly identify 100% of all S. aureus isolates with a score value equal to or greater than 2.00. In addition, a close relationship was found between S. aureus isolates and higher peak intensities in the mass ranges of 3990 Da, 4120 Da, and 5850 Da, which were found in MRSA isolates but absent in MSSA isolates. Therefore, protein fingerprinting has the potential to be used in clinical settings to rapidly detect and differentiate MRSA isolates, allowing for more targeted treatments and improved patient outcomes.
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Affiliation(s)
- Ayman Elbehiry
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32511, Egypt
| | - Eman Marzouk
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Ihab Moussa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Sulaiman Anagreyyah
- Family Medicine Department, King Fahad Armed Forces Hospital, Jeddah 23311, Saudi Arabia
| | - Abdulaziz AlGhamdi
- Medical Director Office, North Area Armed Forces Hospital, King Khalid Military City 39747, Saudi Arabia
| | - Ali Alqarni
- Respiratory Therapy Department, Armed Forces Hospital Dhahran, Dhahran 34641, Saudi Arabia
| | - Ahmed Aljohani
- Patient Affairs Department, Sharourah Armed Forces Hospital, Sharourah 68372, Saudi Arabia
| | - Hassan A. Hemeg
- Department of Medical Technology/Microbiology, College of Applied Medical Science, Taibah University, Madina 30001, Saudi Arabia
| | - Abdulaziz M. Almuzaini
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52571, Saudi Arabia
| | - Feras Alzaben
- Department of Food Service, King Fahad Armed Forces Hospital, Jeddah 23311, Saudi Arabia
| | - Adil Abalkhail
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Roua A. Alsubki
- Department of Clinical Laboratory Science, College of Applied Medical Science, King Saud University, Riyadh 11433, Saudi Arabia
| | - Ali Najdi
- Northern Area Armed Forces Hospital, King Khalid Military City 39748, Saudi Arabia
| | - Nawaf Algohani
- Consultant Forensic Medicine, Forensic Medicine Center, Madina 42319, Saudi Arabia
| | - Banan Abead
- Support Service Department, King Fahad Armed Forces Hospital, Jeddah 23311, Saudi Arabia;
| | - Bassam Gazzaz
- Patient Affairs Department, King Fahad Armed Forces Hospital, Jeddah 23311, Saudi Arabia
| | - Akram Abu-Okail
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52571, Saudi Arabia
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Farina C, Cacciabue E, Averara F, Ferri N, Vailati F, Del Castillo G, Serafini A, Fermi B, Doniselli N, Pezzoli F. Water Safety Plan, Monochloramine Disinfection and Extensive Environmental Sampling Effectively Control Legionella and Other Waterborne Pathogens in Nosocomial Settings: The Ten-Year Experience of an Italian Hospital. Microorganisms 2023; 11:1794. [PMID: 37512966 PMCID: PMC10384652 DOI: 10.3390/microorganisms11071794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Legionella contamination control is crucial in healthcare settings where patients suffer an increased risk of disease and fatal outcome. To ensure an effective management of this health hazard, the accurate application of a hospital-specific Water Safety Plan (WSP), the choice of a suitable water disinfection system and an extensive monitoring program are required. Here, the ten-year experience of an Italian hospital is reported: since its commissioning, Legionellosis risk management has been entrusted to a multi-disciplinary Working Group, applying the principles of the World Health Organization's WSP. The disinfection strategy to prevent Legionella and other waterborne pathogens relies on the treatment of domestic hot water with a system ensuring the in situ production and dosage of monochloramine. An average of 250 samples/year were collected and analyzed to allow an accurate assessment of the microbiological status of water network. With the aim of increasing the monitoring sensitivity, in addition to the standard culture method, an optimized MALDI-ToF MS-based strategy was applied, allowing the identification of Legionella species and other relevant opportunistic pathogens. Data collected so far confirmed the effectiveness of this multidisciplinary approach: the fraction of positive samples never overcame 1% on a yearly basis and Legionnaires' Disease cases never occurred.
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Affiliation(s)
- Claudio Farina
- Microbiology and Virology Laboratory, ASST "Papa Giovanni XXIII", 24127 Bergamo, Italy
| | - Eleonora Cacciabue
- Health Care Coordination Offices, ASST "Papa Giovanni XXIII", 24127 Bergamo, Italy
| | - Franca Averara
- Department of Health Care Professions, ASST "Papa Giovanni XXIII", 24127 Bergamo, Italy
| | - Nadia Ferri
- Microbiology and Virology Laboratory, ASST "Papa Giovanni XXIII", 24127 Bergamo, Italy
| | - Francesca Vailati
- Microbiology and Virology Laboratory, ASST "Papa Giovanni XXIII", 24127 Bergamo, Italy
| | | | | | - Beatrice Fermi
- Sanipur S.p.A., 25020 Flero, Italy
- ESCMID Study Group for Legionella Infections (ESGLI), 4001 Basel, Switzerland
| | - Nicola Doniselli
- Sanipur S.p.A., 25020 Flero, Italy
- ESCMID Study Group for Legionella Infections (ESGLI), 4001 Basel, Switzerland
| | - Fabio Pezzoli
- Health Care Coordination Offices, ASST "Papa Giovanni XXIII", 24127 Bergamo, Italy
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Mohammad N, Normand AC, Nabet C, Godmer A, Brossas JY, Blaize M, Bonnal C, Fekkar A, Imbert S, Tannier X, Piarroux R. Improving the Detection of Epidemic Clones in Candida parapsilosis Outbreaks by Combining MALDI-TOF Mass Spectrometry and Deep Learning Approaches. Microorganisms 2023; 11:microorganisms11041071. [PMID: 37110493 PMCID: PMC10146746 DOI: 10.3390/microorganisms11041071] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/11/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Identifying fungal clones propagated during outbreaks in hospital settings is a problem that increasingly confronts biologists. Current tools based on DNA sequencing or microsatellite analysis require specific manipulations that are difficult to implement in the context of routine diagnosis. Using deep learning to classify the mass spectra obtained during the routine identification of fungi by MALDI-TOF mass spectrometry could be of interest to differentiate isolates belonging to epidemic clones from others. As part of the management of a nosocomial outbreak due to Candida parapsilosis in two Parisian hospitals, we studied the impact of the preparation of the spectra on the performance of a deep neural network. Our purpose was to differentiate 39 otherwise fluconazole-resistant isolates belonging to a clonal subset from 56 other isolates, most of which were fluconazole-susceptible, collected during the same period and not belonging to the clonal subset. Our study carried out on spectra obtained on four different machines from isolates cultured for 24 or 48 h on three different culture media showed that each of these parameters had a significant impact on the performance of the classifier. In particular, using different culture times between learning and testing steps could lead to a collapse in the accuracy of the predictions. On the other hand, including spectra obtained after 24 and 48 h of growth during the learning step restored the good results. Finally, we showed that the deleterious effect of the device variability used for learning and testing could be largely improved by including a spectra alignment step during preprocessing before submitting them to the neural network. Taken together, these experiments show the great potential of deep learning models to identify spectra of specific clones, providing that crucial parameters are controlled during both culture and preparation steps before submitting spectra to a classifier.
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Affiliation(s)
- Noshine Mohammad
- Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie Mycologie, AP-HP, 75013 Paris, France
- INSERM, Institut Pierre-Louis d'Épidémiologie et de Santé Publique, Sorbonne Université, 75013 Paris, France
| | - Anne-Cécile Normand
- Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie Mycologie, AP-HP, 75013 Paris, France
| | - Cécile Nabet
- Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie Mycologie, AP-HP, 75013 Paris, France
- INSERM, Institut Pierre-Louis d'Épidémiologie et de Santé Publique, Sorbonne Université, 75013 Paris, France
| | - Alexandre Godmer
- CIMI-Paris, Centre d'Immunologie et des Maladies Infectieuses, UMR 1135, Sorbonne Université, 75013 Paris, France
- Département de Bactériologie, Hôpital Saint-Antoine, AP-HP, Sorbonne Université, 75012 Paris, France
| | - Jean-Yves Brossas
- Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie Mycologie, AP-HP, 75013 Paris, France
| | - Marion Blaize
- Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie Mycologie, AP-HP, 75013 Paris, France
- CIMI-Paris, Centre d'Immunologie et des Maladies Infectieuses, CNRS, INSERM, Sorbonne Université, 75013 Paris, France
| | - Christine Bonnal
- Service de Parasitologie Mycologie, Hôpital Bichat-Claude Bernard, AP-HP, 75018 Paris, France
| | - Arnaud Fekkar
- Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie Mycologie, AP-HP, 75013 Paris, France
- CIMI-Paris, Centre d'Immunologie et des Maladies Infectieuses, CNRS, INSERM, Sorbonne Université, 75013 Paris, France
| | - Sébastien Imbert
- Service de Parasitologie Mycologie, Centre Hospitalier Universitaire de Bordeaux, 33075 Bordeaux, France
| | - Xavier Tannier
- Sorbonne Université, Inserm, Laboratoire d'Informatique Médicale et d'Ingénierie des Connaissances en e-Santé, LIMICS, 75013 Paris, France
| | - Renaud Piarroux
- Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie Mycologie, AP-HP, 75013 Paris, France
- INSERM, Institut Pierre-Louis d'Épidémiologie et de Santé Publique, Sorbonne Université, 75013 Paris, France
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9
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Zhang C, Wu Z, Gao X, Wang X, Li H, Lin JM. Ion Addition by Electrolysis to Improve the Quantitative Analysis of Bacteria with MALDI-TOF MS. Anal Chem 2023; 95:739-746. [PMID: 36542088 DOI: 10.1021/acs.analchem.2c02813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is commonly applied to the identification of bacteria but rarely used for quantitative detection due to the inhomogeneous crystallization of the matrix leading to the unsatisfactory linear relationship between the sample amount and the mass spectrum signals. Herein, we proposed a noninterference ion addition (NIA) method by electrolysis to improve homogeneous crystallization during the evaporation progress of sample droplets on the target plates. The active metal wire was inserted in the droplet as the anode electrode, and metal ions were released through electrolysis. The directional migration of metal ions under the electric field can hinder the migration of matrix molecules to the boundary and homogenize the matrix crystals by forming spherical crystals. Simultaneously, trace cationic surfactant was added to the droplet for pinning the contact surface to define the circle crystallization region. The metal ions from the anode electrode wire were deposited on the surface of the target plates which served as the cathode. Therefore, ion addition has no interference effect on ionization during MALDI-MS detection. This NIA method benefits the homogeneous crystallization and so improves the quantitative analysis. NIA is suitable for biological samples with different matrices, and bacterial samples could be quantitatively analyzed.
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Affiliation(s)
- Chaoying Zhang
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, P. R. China
| | - Zengnan Wu
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, P. R. China
| | - Xinchang Gao
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, P. R. China
| | - Xia Wang
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, P. R. China
| | - Haifang Li
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, P. R. China
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, P. R. China
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Elbehiry A, Aldubaib M, Abalkhail A, Marzouk E, ALbeloushi A, Moussa I, Ibrahem M, Albazie H, Alqarni A, Anagreyyah S, Alghamdi S, Rawway M. How MALDI-TOF Mass Spectrometry Technology Contributes to Microbial Infection Control in Healthcare Settings. Vaccines (Basel) 2022; 10:1881. [PMID: 36366389 PMCID: PMC9699604 DOI: 10.3390/vaccines10111881] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 08/01/2023] Open
Abstract
Healthcare settings have been utilizing matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) since 2010. MALDI-TOF MS has various benefits over the conventional method of biochemical identification, including ease of use, speed, accuracy, and low cost. This approach can solve many of the obstacles to identifying bacteria, fungi and viruses. As technology advanced, more and more databases kept track of spectra, allowing species with similar morphological, genotypic, and biochemical traits to be identified. Using MALDI-TOF MS for identification has become more accurate and quicker due to advances in sample preparation and database enrichment. Rapid sample detection and colony identification using MALDI-TOF MS have produced promising results. A key application of MALDI-TOF MS is quickly identifying highly virulent and drug-resistant diseases. Here, we present a review of the scientific literature assessing the effectiveness of MALDI-TOF MS for locating clinically relevant pathogenic bacteria, fungi, and viruses. MALDI-TOF MS is a useful strategy for locating clinical pathogens, however, it also has some drawbacks. A small number of spectra in the database and inherent similarities among organisms can make it difficult to distinguish between different species, which can result in misidentifications. The majority of the time additional testing may correct these problems, which happen very seldom. In conclusion, infectious illness diagnosis and clinical care are being revolutionized by the use of MALDI-TOF MS in the clinical microbiology laboratory.
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Affiliation(s)
- Ayman Elbehiry
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32511, Egypt
| | - Musaad Aldubaib
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52571, Saudi Arabia
| | - Adil Abalkhail
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Eman Marzouk
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Ahmad ALbeloushi
- Al Bukayriyah General Hospital, Qassim, Al Bukayriyah 52725, Saudi Arabia
| | - Ihab Moussa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mai Ibrahem
- Department of Public Health, College of Applied Medical Science, King Khalid University, Abha 61421, Saudi Arabia
- Department of Aquatic Animal Medicine and Management, Faculty of Veterinary Medicine, Cairo University, Cairo 12211, Egypt
| | - Hamad Albazie
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Abdullah Alqarni
- Department of Support Service, King Fahad Armed Hospital, Jeddah 23311, Saudi Arabia
| | - Sulaiman Anagreyyah
- Department of Preventive Medicine, King Fahad Armed Hospital, Jeddah 23311, Saudi Arabia
| | - Saleh Alghamdi
- Department of Biomedical Engineering, King Fahad Armed Hospital, Jeddah 23311, Saudi Arabia
| | - Mohammed Rawway
- Biology Department, College of Science, Jouf University, Sakaka 42421, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, AL-Azhar University, Assiut 71524, Egypt
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11
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“Omic” Approaches to Bacteria and Antibiotic Resistance Identification. Int J Mol Sci 2022; 23:ijms23179601. [PMID: 36077000 PMCID: PMC9455953 DOI: 10.3390/ijms23179601] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/28/2022] Open
Abstract
The quick and accurate identification of microorganisms and the study of resistance to antibiotics is crucial in the economic and industrial fields along with medicine. One of the fastest-growing identification methods is the spectrometric approach consisting in the matrix-assisted laser ionization/desorption using a time-of-flight analyzer (MALDI-TOF MS), which has many advantages over conventional methods for the determination of microorganisms presented. Thanks to the use of a multiomic approach in the MALDI-TOF MS analysis, it is possible to obtain a broad spectrum of data allowing the identification of microorganisms, understanding their interactions and the analysis of antibiotic resistance mechanisms. In addition, the literature data indicate the possibility of a significant reduction in the time of the sample preparation and analysis time, which will enable a faster initiation of the treatment of patients. However, it is still necessary to improve the process of identifying and supplementing the existing databases along with creating new ones. This review summarizes the use of “-omics” approaches in the MALDI TOF MS analysis, including in bacterial identification and antibiotic resistance mechanisms analysis.
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12
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Wang X, Chen C, Yang Y, Wang L, Li M, Zhang P, Deng S, Liang S. Proteome-Based Serotyping of the Food-Borne Pathogens Salmonella Enterica by Label-Free Mass Spectrometry. Molecules 2022; 27:molecules27144334. [PMID: 35889206 PMCID: PMC9321705 DOI: 10.3390/molecules27144334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/27/2022] [Accepted: 07/01/2022] [Indexed: 11/16/2022] Open
Abstract
Food-borne diseases caused by Salmonella enterica of 2500 serovars represent a serious public health problem worldwide. A quick identification for the pathogen serovars is critical for controlling food pollution and disease spreading. Here, we applied a mass spectrum-based proteomic profiling for identifying five epidemiologically important Salmonella enterica subsp. enterica serovars (Enteritidis, Typhimurium, London, Rissen and Derby) in China. By label-free analysis, the 53 most variable serovar-related peptides, which were almost all enzymes related to nucleoside phosphate and energy metabolism, were screened as potential peptide biomarkers, and based on which a C5.0 predicted model for Salmonella enterica serotyping with four predictor peptides was generated with the accuracy of 94.12%. In comparison to the classic gene patterns by PFGE analysis, the high-throughput proteomic fingerprints were also effective to determine the genotypic similarity among Salmonella enteric isolates according to each strain of proteome profiling, which is indicative of the potential breakout of food contamination. Generally, the proteomic dissection on Salmonella enteric serovars provides a novel insight and real-time monitoring of food-borne pathogens.
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Affiliation(s)
- Xixi Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and National Collaborative Innovation Center for Biotherapy, Chengdu 610041, China;
- Chengdu Center for Disease Control and Prevention, Chengdu 610041, China; (Y.Y.); (L.W.); (M.L.)
| | - Chen Chen
- Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu 610041, China;
| | - Yang Yang
- Chengdu Center for Disease Control and Prevention, Chengdu 610041, China; (Y.Y.); (L.W.); (M.L.)
| | - Lian Wang
- Chengdu Center for Disease Control and Prevention, Chengdu 610041, China; (Y.Y.); (L.W.); (M.L.)
| | - Ming Li
- Chengdu Center for Disease Control and Prevention, Chengdu 610041, China; (Y.Y.); (L.W.); (M.L.)
| | - Peng Zhang
- Department of Urinary Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China; (P.Z.); (S.D.)
| | - Shi Deng
- Department of Urinary Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China; (P.Z.); (S.D.)
| | - Shufang Liang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and National Collaborative Innovation Center for Biotherapy, Chengdu 610041, China;
- Correspondence:
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13
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Sarvestani HK, Ramandi A, Getso MI, Razavyoon T, Javidnia J, Golrizi MB, Saboor-Yaraghi AA, Ansari S. Mass spectrometry in research laboratories and clinical diagnostic: a new era in medical mycology. Braz J Microbiol 2022; 53:689-707. [PMID: 35344203 PMCID: PMC9151960 DOI: 10.1007/s42770-022-00715-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 02/14/2022] [Indexed: 02/01/2023] Open
Abstract
Diagnosis by clinical mycology laboratory plays a critical role in patient care by providing definitive knowledge of the cause of infection and antimicrobial susceptibility data to physicians. Rapid diagnostic methods are likely to improve patient. Aggressive resuscitation bundles, adequate source control, and appropriate antibiotic therapy are cornerstones for success in the treatment of patients. Routine methods for identifying clinical specimen fungal pathogen are based on the cultivation on different media with the subsequent examination of its phenotypic characteristics comprising a combination of microscopic and colony morphologies. As some fungi cannot be readily identified using these methods, molecular diagnostic methods may be required. These methods are fast, but it can cost a lot. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is suitable for high-throughput and rapid diagnostics at low costs. It can be considered an alternative for conventional biochemical and molecular identification systems in a microbiological laboratory. The reliability and accuracy of this method have been scrutinized in many surveys and have been compared with several methods including sequencing and molecular methods. According to these findings, the reliability and accuracy of this method are very high and can be trusted. With all the benefits of this technique, the libraries of MALDI-TOF MS need to be strengthened to enhance its performance. This review provides an overview of the most recent research literature that has investigated the applications and usage of MT-MS to the identification of microorganisms, mycotoxins, antifungal susceptibility examination, and mycobiome research.
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Affiliation(s)
- Hasti Kamali Sarvestani
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Ramandi
- Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Muhammad Ibrahim Getso
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Department of Medical Microbiology and Parasitology, College of Health Sciences, Bayero University, PMB, Kano, 3011, Nigeria
| | - Taraneh Razavyoon
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Javad Javidnia
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Miaad Banay Golrizi
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ali-Akbar Saboor-Yaraghi
- Department of Nutrition and Biochemistry, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Saham Ansari
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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14
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Tsai H, Phinney BS, Grigorean G, Salemi MR, Rashidi HH, Pepper J, Tran NK. Identification of Endogenous Peptides in Nasal Swab Transport Media used in MALDI-TOF-MS Based COVID-19 Screening. ACS OMEGA 2022; 7:17462-17471. [PMID: 35600141 PMCID: PMC9113002 DOI: 10.1021/acsomega.2c01864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/18/2022] [Indexed: 06/15/2023]
Abstract
Mass spectrometry (MS) based diagnostic detection of 2019 novel coronavirus infectious disease (COVID-19) has been postulated to be a useful alternative to classical PCR based diagnostics. These MS based approaches have the potential to be both rapid and sensitive and can be done on-site without requiring a dedicated laboratory or depending on constrained supply chains (i.e., reagents and consumables). Matrix-assisted laser desorption ionization (MALDI)-time-of-flight (TOF) MS has a long and established history of microorganism detection and systemic disease assessment. Previously, we have shown that automated machine learning (ML) enhanced MALDI-TOF-MS screening of nasal swabs can be both sensitive and specific for COVID-19 detection. The underlying molecules responsible for this detection are generally unknown nor are they required for this automated ML platform to detect COVID-19. However, the identification of these molecules is important for understanding both the mechanism of detection and potentially the biology of the underlying infection. Here, we used nanoscale liquid chromatography tandem MS to identify endogenous peptides found in nasal swab saline transport media to identify peptides in the same the mass over charge (m/z) values observed by the MALDI-TOF-MS method. With our peptidomics workflow, we demonstrate that we can identify endogenous peptides and endogenous protease cut sites. Further, we show that SARS-CoV-2 viral peptides were not readily detected and are highly unlikely to be responsible for the accuracy of MALDI based SARS-CoV-2 diagnostics. Further analysis with more samples will be needed to validate our findings, but the methodology proves to be promising.
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Affiliation(s)
- Helen Tsai
- Proteomics
Core, University of California, Davis, 451 E. Health Sciences Dr., Davis, California 95616, United States
| | - Brett S. Phinney
- Proteomics
Core, University of California, Davis, 451 E. Health Sciences Dr., Davis, California 95616, United States
| | - Gabriela Grigorean
- Proteomics
Core, University of California, Davis, 451 E. Health Sciences Dr., Davis, California 95616, United States
| | - Michelle R. Salemi
- Proteomics
Core, University of California, Davis, 451 E. Health Sciences Dr., Davis, California 95616, United States
| | - Hooman H. Rashidi
- Department
of Pathology and Laboratory Medicine, University
of California, Davis, 4400 V St., Sacramento, California 95817, United States
| | - John Pepper
- SpectraPass,
LLC, 1980 Festival Plaza,
Suite 770, Las Vegas, Nevada 89135, United States
- Allegiant
Air, 1201 North Town
Center Drive, Las Vegas, Nevada 89144, United
States
| | - Nam K. Tran
- Department
of Pathology and Laboratory Medicine, University
of California, Davis, 4400 V St., Sacramento, California 95817, United States
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15
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MALDI-Based Mass Spectrometry in Clinical Testing: Focus on Bacterial Identification. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12062814] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The term “proteome” refers to the total of all proteins expressed in an organism. The term “proteomics” refers to the field of research that includes not only information on the expression levels of individual proteins, but also their higher-order structures, intermolecular interactions, and post-translational modifications. The core technology, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), is available for protein analysis thanks to the work of Koichi Tanaka and John Fenn, who were awarded the Nobel Prize in Chemistry in 2002. The most successful proteome analysis in clinical practice is rapid microbial identification. This method determines the bacterial species by comparing the proteome profile of the bacteria obtained by matrix-assisted laser desorption ionization-time of flight MS (MALDI-TOF MS) with a database. MS is superior in simplicity, speed, and accuracy to classic speciation by staining and phenotyping. In clinical microbiology, MS has had a large impact on the diagnosis and treatment of infectious disease. Early diagnosis and treatment of infectious disease are important, and rapid identification by MALDI-TOF MS has made a major contribution to this field.
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16
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Detection of Frozen-Thawed Duck Fatty Liver by MALDI-TOF Mass Spectrometry: A Chemometrics Study. Molecules 2021; 26:molecules26123508. [PMID: 34207540 PMCID: PMC8229872 DOI: 10.3390/molecules26123508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 11/17/2022] Open
Abstract
The marketing of poultry livers is only authorized as fresh, frozen, or deep-frozen. The higher consumer demand for these products for a short period of time may lead to the marketing of frozen–thawed poultry livers: this constitutes fraud. The aim of this study was to design a method for distinguishing frozen–thawed livers from fresh livers. For this, the spectral fingerprint of liver proteins was acquired using Matrix-Assisted Laser Dissociation Ionization-Time-Of-Flight mass spectrometry. The spectra were analyzed using the chemometrics approach. First, principal component analysis studied the expected variability of commercial conditions before and after freezing–thawing. Then, the discriminant power of spectral fingerprint of liver proteins was assessed using supervised model generation. The combined approach of mass spectrometry and chemometrics successfully described the evolution of protein profile during storage time, before and after freezing-thawing, and successfully discriminated the fresh and frozen–thawed livers. These results are promising in terms of fraud detection, providing an opportunity for implementation of a reference method for agencies to fight fraud.
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17
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Effect of humidity during sample preparation on bacterial identification using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1176:122780. [PMID: 34052563 DOI: 10.1016/j.jchromb.2021.122780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 01/08/2023]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a highly reliable and efficient technology for the identification of microbial pathogens. We previously found that 40% humidity was the optimal condition for the preparation of samples (co-crystallization of the sample and matrix) for serum peptidomic analysis via MALDI-TOF MS profiling. This optimum temperature was applied to obtain the highest reproducibility and throughput and greatest number of peaks. We therefore hypothesized that humidity control was also essential for MALDI-TOF MS bacterial identification. In this study, we constructed a simple sample preparation device that enables humidity control and used it for co-crystallization of the sample and matrix. Identification scores for five Gram-negative bacteria and six Gram-positive bacteria were determined using the MALDI BioTyper® system at three humidity ranges (10-20%, 30-40%, and 50-60%). As a result, higher identification scores were obtained at 30-40% humidity than at 10-20% or 50-60% humidity. At 30-40% humidity, 517/550 (94.0%) isolates scored greater than 2.0, indicating the success of species-level identification. Similarly, 537/550 (97.6%) isolates scored greater than 1.7, indicating the success of genus-level identification. Thus, 30-40% humidity generated optimal MALDI-TOF MS identification scores and the highest percentage of correct identifications. These results could lead to further improvements in the accuracy of MALDI-TOF MS bacterial identification.
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18
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Sogawa K, Takano S, Ishige T, Yoshitomi H, Kagawa S, Furukawa K, Takayashiki T, Kuboki S, Nomura F, Ohtsuka M. Usefulness of the MALDI-TOF MS technology with membrane filter protocol for the rapid identification of microorganisms in perioperative drainage fluids of hepatobiliary pancreatic surgery. PLoS One 2021; 16:e0246002. [PMID: 33539441 PMCID: PMC7861402 DOI: 10.1371/journal.pone.0246002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 01/12/2021] [Indexed: 12/04/2022] Open
Abstract
Surgical site infections (SSIs) are significant and frequent perioperative complications, occurring due to the contamination of the surgical site. The late detection of SSIs, especially organ/space SSIs which are the more difficult to treat, often leads to severe complications. An effective method that can identify bacteria with a high accuracy, leading to the early detection of organ/space SSIs, is needed. Ninety-eight drainage fluid samples obtained from 22 patients with hepatobiliary pancreatic disease were analyzed to identify microorganisms using matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) with a new membrane filtration protocol and rapid BACpro® pretreatment compared to sole rapid BACpro® pretreatment. The levels of detail of rapid BACpro® pretreatment with or without filtration were also evaluated for the accuracy of bacterial identification. We found that reliable scores for E. coli and E. faecalis were obtained by inoculation with 1.0 × 104 CFU/ml after preparation of the membrane filter with rapid BACpro®, indicating approximately 10-folds more sensitive compared to sole rapid BACpro® pretreatment in drainage fluid specimens. Among 60 bacterial positive colonies in drainage fluid specimens, the MALDI-TOF MS and the membrane filtration with rapid BACpro® identified 53 isolates (88.3%) with a significantly higher accuracy, compared to 25 isolates in the rapid BACpro® pretreatment group (41.7%) (p < 0.001). Among the 78 strains, 14 enteric Gram-negative bacteria (93.0%) and 55 Gram-positive cocci (87.3%) were correctly identified by the membrane filtration with rapid BACpro® with a high reliability. This novel protocol could identify bacterial species within 30 min, at $2-$3 per sample, thus leading to cost and time savings. MALDI-TOF MS with membrane filter and rapid BACpro® is a quick and reliable method for bacterial identification in drainage fluids. The shortened analysis time will enable earlier selection of suitable antibiotics for treatment of organ/space SSIs to improve patients' outcomes.
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Affiliation(s)
- Kazuyuki Sogawa
- Department of Biochemistry, School of Life and Environmental Science, Azabu University, Kanagawa, Japan
| | - Shigetsugu Takano
- Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takayuki Ishige
- Division of Laboratory Medicine, Chiba University Hospital, Chiba, Japan
| | - Hideyuki Yoshitomi
- Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shingo Kagawa
- Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Katsunori Furukawa
- Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tsukasa Takayashiki
- Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Satoshi Kuboki
- Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Fumio Nomura
- Divisions of Clinical Mass Spectrometry and Clinical Genetics, Chiba University Hospital, Chiba, Japan
| | - Masayuki Ohtsuka
- Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
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19
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Huang L, Gao K, Chen G, Zhong H, Li Z, Guan X, Deng Q, Xie Y, Ji W, McIver DJ, Chang CY, Liu H. Rapid Classification of Multilocus Sequence Subtype for Group B Streptococcus Based on MALDI-TOF Mass Spectrometry and Statistical Models. Front Cell Infect Microbiol 2021; 10:577031. [PMID: 33585264 PMCID: PMC7878539 DOI: 10.3389/fcimb.2020.577031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 12/11/2020] [Indexed: 11/13/2022] Open
Abstract
Group B Streptococcus (GBS) is an important etiological agent of maternal and neonatal infections as well as postpartum women and individuals with impaired immunity. We developed and evaluated a rapid classification method for sequence types (STs) of GBS based on statistic models with Matrix-Assisted Laser Desorption/Ionization Time-of Flight Mass Spectrometry (MALDI-TOF/MS). Whole-cell lysates MALDI-TOF/MS analysis was performed on 235 well-characterized GBS isolates from neonatal invasive infections in a multi-center study in China between 2015 and 2017. Mass spectra belonging to major STs (ST10, ST12, ST17, ST19, ST23) were selected for model generation and validation. Recognition and cross validation values were calculated by Genetic Algorithm-K Nearest Neighbor (GA-KNN), Supervised Neural Network (SNN), QuickClassifier (QC) to select models with the best performance for validation of diagnostic efficiency. Informative peaks were further screened through peak statistical analysis, ST subtyping MSP peak data and mass spectrum visualization. For major STs, the ML models generated by GA-KNN algorithms attained highest cross validation values in comparison to SNN and QC algorithms. GA-KNN models of ST10, ST17, and ST12/ST19 had good diagnostic efficiency, with high sensitivity (95–100%), specificity (91.46%–99.23%), accuracy (92.79–99.29%), positive prediction value (PPV, 80%–92.68%), negative prediction value (NPV, 94.32%–99.23%). Peak markers were firstly identified for ST10 (m/z 6250, 3125, 6891) and ST17 strains (m/z 2956, 5912, 7735, 5218). Statistical models for rapid GBS ST subtyping using MALDI-TOF/MS spectrometry contributes to easier epidemical molecular monitoring of GBS infection diseases.
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Affiliation(s)
- Lianfen Huang
- Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Kankan Gao
- Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Guanglian Chen
- Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Huamin Zhong
- Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Zixian Li
- Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiaoshan Guan
- Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Qiulian Deng
- Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yongqiang Xie
- Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wenjing Ji
- Department of Pharmacy Administration and Clinical Pharmacy, School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - David J McIver
- Global Health Group, Institute for Global Health Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Chien-Yi Chang
- School of Dental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Haiying Liu
- Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
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20
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Aljaafari MN, AlAli AO, Baqais L, Alqubaisy M, AlAli M, Molouki A, Ong-Abdullah J, Abushelaibi A, Lai KS, Lim SHE. An Overview of the Potential Therapeutic Applications of Essential Oils. Molecules 2021; 26:628. [PMID: 33530290 PMCID: PMC7866131 DOI: 10.3390/molecules26030628] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/07/2021] [Accepted: 01/10/2021] [Indexed: 12/27/2022] Open
Abstract
The emergence of antimicrobial resistance (AMR) has urged researchers to explore therapeutic alternatives, one of which includes the use of natural plant products such as essential oils (EO). In fact, EO obtained from clove, oregano, thymus, cinnamon bark, rosemary, eucalyptus, and lavender have been shown to present significant inhibitory effects on bacteria, fungi, and viruses; many studies have been done to measure EO efficacy against microorganisms. The strategy of combinatory effects via conventional and non-conventional methods revealed that the combined effects of EO-EO or EO-antibiotic exhibit enhanced efficacy. This paper aims to review the antimicrobial effects of EO, modes of EO action (membrane disruption, efflux inhibition, increase membrane permeability, and decrease in intracellular ATP), and their compounds' potential as effective agents against bacteria, fungi, and viruses. It is hoped that the integration of EO applications in this work can be used to consider EO for future clinical applications.
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Affiliation(s)
- Mariam Nasser Aljaafari
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, 41012 Abu Dhabi, UAE; (M.N.A.); (A.O.A.); (L.B.); (M.A.); (M.A.); (K.-S.L.)
| | - Asma Obaid AlAli
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, 41012 Abu Dhabi, UAE; (M.N.A.); (A.O.A.); (L.B.); (M.A.); (M.A.); (K.-S.L.)
| | - Laila Baqais
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, 41012 Abu Dhabi, UAE; (M.N.A.); (A.O.A.); (L.B.); (M.A.); (M.A.); (K.-S.L.)
| | - Maream Alqubaisy
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, 41012 Abu Dhabi, UAE; (M.N.A.); (A.O.A.); (L.B.); (M.A.); (M.A.); (K.-S.L.)
| | - Mudhi AlAli
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, 41012 Abu Dhabi, UAE; (M.N.A.); (A.O.A.); (L.B.); (M.A.); (M.A.); (K.-S.L.)
| | - Aidin Molouki
- Department of Avian Disease Research and Diagnostic, Razi Vaccine and Serum Research Institute, Agricultural Research Education and Extension Organization (AREEO), Karaj 31585-854, Iran;
| | - Janna Ong-Abdullah
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 Selangor, Malaysia;
| | | | - Kok-Song Lai
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, 41012 Abu Dhabi, UAE; (M.N.A.); (A.O.A.); (L.B.); (M.A.); (M.A.); (K.-S.L.)
| | - Swee-Hua Erin Lim
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, 41012 Abu Dhabi, UAE; (M.N.A.); (A.O.A.); (L.B.); (M.A.); (M.A.); (K.-S.L.)
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21
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LEI DERU, CHEN PEIYING, CHEN XUETING, ZONG YUJIE, LI XIANGYANG. Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry for Identification of Microorganisms in Clinical Urine Specimens after Two Pretreatments. Pol J Microbiol 2021; 70:1-7. [PMID: 34131429 PMCID: PMC8196241 DOI: 10.33073/pjm-2021-018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/29/2021] [Accepted: 04/06/2021] [Indexed: 02/06/2023] Open
Abstract
Rapid identification of microorganisms in urine is essential for patients with urinary tract infections (UTIs). Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been proposed as a method for the direct identification of urinary pathogens. Our purpose was to compare centrifugation-based MALDI-TOF MS and short-term culture combined with MALDI-TOF MS for the direct identification of pathogens in urine specimens. We collected 965 urine specimens from patients with suspected UTIs, 211/965 isolates were identified as positive by conventional urine culture. Compared with the conventional method, the results of centrifugation-based MALDI-TOF MS were consistent in 159/211 cases (75.4%), of which 135/159 (84.9%) had scores ≥ 2.00; 182/211 cases (86.3%) were detected using short-term culture combined with MALDI-TOF MS, of which 153/182 (84.1%) had scores ≥ 2.00. There were no apparent differences among the three methods (p = 0.135). MALDI-TOF MS appears to accelerate the microbial identification speed in urine and saves at least 24 to 48 hours compared with the routine urine culture. Centrifugation-based MALDI-TOF MS is characterized by faster identification speed; however, it is substantially affected by the number of bacterial colonies. In contrast, short-term culture combined with MALDI-TOF MS has a higher detection rate but a relatively slow identification speed. Combining these characteristics, the two methods may be effective and reliable alternatives to traditional urine culture.
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Affiliation(s)
- DERU LEI
- The Center of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - PEIYING CHEN
- The Center of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - XUETING CHEN
- The Center of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - YUJIE ZONG
- The Center of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - XIANGYANG LI
- The Center of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
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22
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Lasch P, Schneider A, Blumenscheit C, Doellinger J. Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS 1) and in Silico Peptide Mass Libraries. Mol Cell Proteomics 2020; 19:2125-2139. [PMID: 32998977 PMCID: PMC7710138 DOI: 10.1074/mcp.tir120.002061] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 09/21/2020] [Indexed: 01/03/2023] Open
Abstract
Over the past decade, modern methods of MS (MS) have emerged that allow reliable, fast and cost-effective identification of pathogenic microorganisms. Although MALDI-TOF MS has already revolutionized the way microorganisms are identified, recent years have witnessed also substantial progress in the development of liquid chromatography (LC)-MS based proteomics for microbiological applications. For example, LC-tandem MS (LC-MS2) has been proposed for microbial characterization by means of multiple discriminative peptides that enable identification at the species, or sometimes at the strain level. However, such investigations can be laborious and time-consuming, especially if the experimental LC-MS2 data are tested against sequence databases covering a broad panel of different microbiological taxa. In this proof of concept study, we present an alternative bottom-up proteomics method for microbial identification. The proposed approach involves efficient extraction of proteins from cultivated microbial cells, digestion by trypsin and LC-MS measurements. Peptide masses are then extracted from MS1 data and systematically tested against an in silico library of all possible peptide mass data compiled in-house. The library has been computed from the UniProt Knowledgebase covering Swiss-Prot and TrEMBL databases and comprises more than 12,000 strain-specific in silico profiles, each containing tens of thousands of peptide mass entries. Identification analysis involves computation of score values derived from correlation coefficients between experimental and strain-specific in silico peptide mass profiles and compilation of score ranking lists. The taxonomic positions of the microbial samples are then determined by using the best-matching database entries. The suggested method is computationally efficient - less than 2 mins per sample - and has been successfully tested by a test set of 39 LC-MS1 peak lists obtained from 19 different microbial pathogens. The proposed method is rapid, simple and automatable and we foresee wide application potential for future microbiological applications.
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Affiliation(s)
- Peter Lasch
- Robert Koch-Institute, ZBS6, Proteomics and Spectroscopy, Berlin, Germany.
| | - Andy Schneider
- Robert Koch-Institute, ZBS6, Proteomics and Spectroscopy, Berlin, Germany
| | | | - Joerg Doellinger
- Robert Koch-Institute, ZBS6, Proteomics and Spectroscopy, Berlin, Germany
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23
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Grossegesse M, Hartkopf F, Nitsche A, Schaade L, Doellinger J, Muth T. Perspective on Proteomics for Virus Detection in Clinical Samples. J Proteome Res 2020; 19:4380-4388. [PMID: 33090795 PMCID: PMC7640980 DOI: 10.1021/acs.jproteome.0c00674] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Indexed: 12/29/2022]
Abstract
One of the most widely used methods to detect an acute viral infection in clinical specimens is diagnostic real-time polymerase chain reaction. However, because of the COVID-19 pandemic, mass-spectrometry-based proteomics is currently being discussed as a potential diagnostic method for viral infections. Because proteomics is not yet applied in routine virus diagnostics, here we discuss its potential to detect viral infections. Apart from theoretical considerations, the current status and technical limitations are considered. Finally, the challenges that have to be overcome to establish proteomics in routine virus diagnostics are highlighted.
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Affiliation(s)
- Marica Grossegesse
- Centre
for Biological Threats and Special Pathogens, Highly Pathogenic Viruses
(ZBS 1), Robert Koch Institute, Seestr. 10, Berlin 13353, Germany
| | - Felix Hartkopf
- Microbial
Genomics (NG 1), Robert Koch Institute, Berlin 13353, Germany
- Section
eScience (S.3), Federal Institute for Materials
Research and Testing, Unter den Eichen 87, Berlin 12205, Germany
| | - Andreas Nitsche
- Centre
for Biological Threats and Special Pathogens, Highly Pathogenic Viruses
(ZBS 1), Robert Koch Institute, Seestr. 10, Berlin 13353, Germany
| | - Lars Schaade
- Centre
for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin 13353, Germany
| | - Joerg Doellinger
- Centre
for Biological Threats and Special Pathogens, Proteomics and Spectroscopy
(ZBS 6), Robert Koch Institute, Berlin 13353, Germany
| | - Thilo Muth
- Section
eScience (S.3), Federal Institute for Materials
Research and Testing, Unter den Eichen 87, Berlin 12205, Germany
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24
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Abd El-Aziz NK, Gharib AA, Mohamed EAA, Hussein AH. Real-time PCR versus MALDI-TOF MS and culture-based techniques for diagnosis of bloodstream and pyogenic infections in humans and animals. J Appl Microbiol 2020; 130:1630-1644. [PMID: 33073430 DOI: 10.1111/jam.14862] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/10/2020] [Accepted: 09/16/2020] [Indexed: 12/18/2022]
Abstract
AIMS This study was applied to evaluate the usefulness of a high-throughput sample preparation protocol prior to the application of quantitative real-time PCR (qPCR) for the early diagnosis of bloodstream and pyogenic infections in humans and animals compared to matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and classical culture. METHODS AND RESULTS Saponin-mediated selective host cell lysis combined with DNase-1 was applied for processing of whole blood and pus clinical samples collected from suspected cases of septicaemia and pyogenic infections in humans and animals. The pre-PCR processing strategy enabled the recovery of microbial cells with no changes in their colony forming units immediately after the addition of saponin. DNase-1 was efficient for removing the DNAs from the host cells as well as dead cells with damaged cell membranes. The metagenomic qPCR and MALDI-TOF MS could identify the bacterial community of sepsis at species level with a concordance of 97·37% unlike the conventional culture. According to qPCR results, Staphylococcus aureus (24·24%) was predominated in animal pyogenic infections, whereas Klebsiella pneumonia (31·81%) was commonly detected in neonatal sepsis. CONCLUSIONS Saponin combined with DNase-1 allowed the efficient recovery of microbial DNA from blood and pus samples in sepsis using qPCR assay. SIGNIFICANCE AND IMPACT OF THE STUDY Metagenomic qPCR could identify a broad range of bacteria directly from blood and pus with more sensitivity, higher discriminatory power and shorter turnaround time than those using MALDI-TOF MS and conventional culture. This might allow a timely administration of a prompt treatment.
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Affiliation(s)
- N K Abd El-Aziz
- Microbiology Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - A A Gharib
- Microbiology Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - E A A Mohamed
- Microbiology Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - A H Hussein
- Avian and Rabbit Medicine Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
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25
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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: 81] [Impact Index Per Article: 20.3] [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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Doellinger J, Schneider A, Stark TD, Ehling-Schulz M, Lasch P. Evaluation of MALDI-ToF Mass Spectrometry for Rapid Detection of Cereulide From Bacillus cereus Cultures. Front Microbiol 2020; 11:511674. [PMID: 33329410 PMCID: PMC7709880 DOI: 10.3389/fmicb.2020.511674] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 09/16/2020] [Indexed: 12/20/2022] Open
Abstract
Bacillus cereus plays an often unrecognized role in food borne diseases. Food poisoning caused by this pathogen is manifested by either diarrhea or emesis. Due to the relatively high prevalence of emetic toxin cereulide associated food poisoning, methods for simple and reliable detection of cereulide producing strains are of utmost importance. Recently, two different studies reported on the application of MALDI-ToF MS for either the differentiation of emetic and non-emetic strains of B. cereus or for direct detection of cereulide from bacterial colony smears. However, for implementation of cereulide detection using MALDI-ToF MS in routine microbiological diagnostics additional investigations on the sensitivity and specificity as well as on the fitting into common workflows for bacterial identification are needed. These aspects prompted us to investigate open issues and to test sample preparation methods, commonly used for microbial identification for their suitability to detect the emetic toxin from bacteria. Based on our experimental findings we propose a workflow that allows identification of B. cereus and sensitive detection of cereulide in parallel, using linear-mode MALDI-ToF MS equipment. The protocol was validated in a blinded study and is based on the well-established ethanol/formic acid extraction method. Cereulide is detected in the ethanol wash solution of samples identified as B. cereus as peaks at m/z 1175 and 1191. Peak position difference of 16 Th (Thomson) indicates detection of the sodium and potassium adducts of cereulide. This sample treatment offers possibilities for further characterization by more sophisticated LC-MS-based methods. In summary, the ease of use and the achieved level of analytical sensitivity as well as the wide-spread availability of MALDI-ToF MS equipment in clinical microbiological laboratories provides a promising tool to improve and to facilitate routine diagnostics of B. cereus associated food intoxications.
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Affiliation(s)
- Joerg Doellinger
- Proteomics and Spectroscopy Unit (ZBS 6), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Andy Schneider
- Proteomics and Spectroscopy Unit (ZBS 6), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Timo D Stark
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Munich, Germany
| | - Monika Ehling-Schulz
- Functional Microbiology, Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Peter Lasch
- Proteomics and Spectroscopy Unit (ZBS 6), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
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27
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Ohtaki H, Takahashi A, Niwa A, Yonetamari J, Nakayama A, Kuchibiro T, Ohta H, Ito H, Baba H, Murakami N, Ohkusu K. Evaluation of presumptive identification of
Enterobacterales
using CHROMagar Orientation medium and rapid biochemical tests. J Clin Lab Anal 2020; 34:e23453. [PMID: 32594571 PMCID: PMC7595914 DOI: 10.1002/jcla.23453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/07/2020] [Accepted: 05/29/2020] [Indexed: 11/28/2022] Open
Abstract
Background The use of matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry is gradually spreading among large‐scale laboratories; however, this method is impractical for small‐scale laboratories. In laboratories without access to these rapid identification methods, problems related to them remain unsolved. In this study, we aimed to develop a rapid and inexpensive method to presumptively identify Enterobacterales using CHROMagar Orientation medium. Methods The algorithm for presumptive identification of Enterobacteriaceae using CHROMagar Orientation medium was based on our previous studies. Modified property tests for indole, lysine decarboxylase, ornithine decarboxylase, and hydrogen sulfide were performed to evaluate the differentiation of the bacterial species. Results Using the type strains and clinical isolates, it was possible to conduct the property tests at a low cost, within 4 hours. The spot indole test was performed without any nonspecific reactions for the bacteria forming colored colonies. The presumptive identification of bacteria was thereby possible within 24 hours after specimen submission. Conclusion All these results suggest that the rapid presumptive identification of Enterobacterales is possible with this new identification method using CHROMagar Orientation medium. This is therefore a prompt and economical method that can be used in routine laboratory work.
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Affiliation(s)
- Hirofumi Ohtaki
- Department of Clinical Laboratory Science Graduate School of Kansai University of Health Sciences Osaka Japan
- Department of Informative Clinical Medicine Gifu University Graduate School of Medicine Gifu Japan
| | - Akifumi Takahashi
- Department of Clinical Laboratory Science Graduate School of Kansai University of Health Sciences Osaka Japan
| | - Ayumi Niwa
- Department of Clinical Laboratory Gifu University Hospital Gifu Japan
| | - Jun Yonetamari
- Department of Clinical Laboratory Gifu University Hospital Gifu Japan
| | - Asami Nakayama
- Department of Clinical Laboratory Yamagata University Hospital Yamagata Japan
| | - Tomokazu Kuchibiro
- Department of Clinical Laboratory Naga Municipal Hospital Kinokawa Japan
| | - Hirotoshi Ohta
- Department of Clinical Laboratory Gifu University Hospital Gifu Japan
| | - Hiroyasu Ito
- Department of Informative Clinical Medicine Gifu University Graduate School of Medicine Gifu Japan
| | - Hisashi Baba
- Center for Nutrition Support & Infection Control Gifu University Hospital Gifu Japan
| | - Nobuo Murakami
- Center for Nutrition Support & Infection Control Gifu University Hospital Gifu Japan
| | - Kiyofumi Ohkusu
- Department of Microbiology Tokyo Medical University Tokyo Japan
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28
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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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29
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Yee WLS, Drum CL. Increasing Complexity to Simplify Clinical Care: High Resolution Mass Spectrometry as an Enabler of AI Guided Clinical and Therapeutic Monitoring. ADVANCED THERAPEUTICS 2020. [DOI: 10.1002/adtp.201900163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Wei Loong Sherman Yee
- Yong Loo Lin School of MedicineDepartment of MedicineNational University of Singapore Singapore 119077 Singapore
- Cardiovascular Research Institute (CVRI)National University Health System Singapore 119228 Singapore
| | - Chester Lee Drum
- Yong Loo Lin School of MedicineDepartment of MedicineNational University of Singapore Singapore 119077 Singapore
- Cardiovascular Research Institute (CVRI)National University Health System Singapore 119228 Singapore
- Yong Loo Lin School of MedicineDepartment of BiochemistryNational University of Singapore Singapore 119077 Singapore
- The N.1 Institute for Health (N.1)National University of Singapore Singapore 119077 Singapore
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Rapid identification of microorganisms from positive blood cultures in pediatric patients by MALDI-TOF MS: Sepsityper kit versus short-term subculture. J Microbiol Methods 2020; 172:105894. [PMID: 32184161 DOI: 10.1016/j.mimet.2020.105894] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 03/13/2020] [Accepted: 03/13/2020] [Indexed: 01/18/2023]
Abstract
BACKGROUND AND AIM The rapid diagnosis of bloodstream infection (BSI) often leads to better clinical outcomes. The present study was conducted to compare two rapid protocols (Sepsityper kit and short-term subculture) for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based identification of microorganisms from positive blood cultures in pediatric patients. METHODS This study was conducted between May 1, 2018, and April 30, 2019, at a tertiary children's hospital in eastern China. Only monomicrobial blood cultures included in this study were used to conduct the Sepsityper kit protocol and short-term subculture protocol at the same time. RESULTS In total, 115 monomicrobial blood cultures were included in this study. For the Sepsityper kit protocol, 85.2% and 64.3% of microorganisms were correctly identified to the genus (score ≥ 1.700) and species levels (score ≥ 2.000), respectively. For the short-term subculture protocol, 89.6% and 70.4% of microorganisms were correctly identified to the genus and species levels, respectively. At the genus level (P = .321) or the species level (P = .325), there was no significant difference between the Sepsityper kit protocol and the short-term subculture protocol. Moreover, the short-term subculture protocol exhibited similar performance between Gram-positive bacteria (GPB) and Gram-negative bacteria (GNB) (the genus level: 93.7% (GPB) versus 87.9% (GNB), P = .518; the species level: 68.4% (GPB) versus 81.8% (GNB), P = .147). In addition, the Sepsityper kit protocol exhibited similar performance between GPB and GNB at the genus level (86.1% (GPB) versus 84.8% (GNB), P = 1.000). However, the Sepsityper kit protocol exhibited better performance in GNB at the species level (58.2% (GPB) versus 81.8% (GNB), P = .017). The rates of yeast-like fungi were correctly identified to the genus level (0.0%) or the species level (0.0%) for short-term subculture protocol were significantly lower than those of other microorganisms (the genus level: 92.0%, P = .001; the species level: 72.3%, P = .024). However, a similar result of identification was not found using the Sepsityper kit protocol (the genus level: P = .384; the species level: P = .599). In addition, the two rapid protocols both exhibited better performance at the genus level when the time to positivity (TTP) of blood cultures <19 h (the Sepsityper kit protocol: 91.8% (TTP < 19 h) versus 77.8% (TTP ≥ 19 h), P = .034; the short-term subculture protocol: 95.1% (TTP < 19 h) versus 83.3% (TTP ≥ 19 h), P = .040). In addition, the two rapid protocols both exhibited better performance at the species level when the TTP of blood cultures was <19 h (the Sepsityper kit protocol: 78.7% (TTP < 19 h) versus 48.1% (TTP ≥ 19 h), P = .000; the short-term subculture protocol: 83.6% (TTP < 19 h) versus 55.6% (TTP ≥ 19 h), P = .001). CONCLUSION The Sepsityper kit protocol and short-term subculture protocol are both reliable and rapid methods for the identification of most microorganisms from positive blood cultures in pediatric patients. The performance of these two rapid protocols is associated with the TTP of blood cultures.
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31
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Kyritsi MA, Kristo I, Hadjichristodoulou C. Serotyping and detection of pathogenecity loci of environmental isolates of Legionella pneumophila using MALDI-TOF MS. Int J Hyg Environ Health 2020; 224:113441. [DOI: 10.1016/j.ijheh.2019.113441] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 02/05/2023]
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Spivak-Lavrov I, Baisanov O, Yakushev E, Nazarenko L. Time-of-flight mass spectrometers based on a wedge-shaped electrostatic mirror with a two-dimensional field. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8590. [PMID: 31515849 DOI: 10.1002/rcm.8590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE For most of the last two decades, a considerable effort has been made towards improving time-of-flight mass spectrometry (TOF MS), which has become an irreplaceable instrumental platform for the purposes of performing analytical measurements in life sciences, such as molecular biology, proteomics, medicine, etc. This can primarily be attributed to the ability of TOF MS to rapidly detect and identify nearly any targeted chemical trace with both high precision and accuracy. However, multi-span TOF MS experiments are limited due to aberrations arising from multiple reflection; our proposed scheme will minimize these aberrations. METHODS The inhomogeneous accelerating field is generated without using meshes by changing the potentials on the electrodes of the mirror. The ions are extracted from the ion source by short impulse activation of the accelerating electric field. Since the ions are extracted from various points of the source, even ions with identical masses acquire different velocities during acceleration. RESULTS We have shown that the "rear" ions of the packet catch up with the "front" ions, and packets of ions with identical masses are compressed in the direction of their movement. It is concluded that, by placing the detector in a plane with the greatest compression of ion packets, an enhanced performance of a time-of-flight mass spectrometer is achieved. CONCLUSIONS We have shown that effective spatial-temporal focusing allows a small mass spectrometer to achieve high resolution and sensitivity. We also propose and numerically evaluate a new platform for designing multi-stage and multi-reflective time-of-flight analyzers with wedge-shaped mirrors. We applied the simulation results to the modernization of old equipment and showed that by simply replacing the electrostatic mirror with an optimized one, a significant increase in the analyzing power can be achieved.
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Affiliation(s)
- Igor Spivak-Lavrov
- Aktobe Regional State University named after K. Zhubanov, Aktobe, Kazakhstan
| | - Orda Baisanov
- Military Institute of Air Defense Forces named after T. Begeldinov, Aktobe, Kazakhstan
| | - Evgeniy Yakushev
- RSE Institute of Nuclear Physics of Ministry of Industry and New Technologies of Republic Kazakhstan, Almaty, Kazakhstan
| | - Leonid Nazarenko
- RSE Institute of Nuclear Physics of Ministry of Industry and New Technologies of Republic Kazakhstan, Almaty, Kazakhstan
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Rapid identification of respiratory bacterial pathogens from bronchoalveolar lavage fluid in cattle by MALDI-TOF MS. Sci Rep 2019; 9:18381. [PMID: 31804604 PMCID: PMC6895124 DOI: 10.1038/s41598-019-54599-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 11/18/2019] [Indexed: 02/07/2023] Open
Abstract
Respiratory tract infections are a major health problem and indication for antimicrobial use in cattle and in humans. Currently, most antimicrobial treatments are initiated without microbiological results, holding the risk of inappropriate first intention treatment. The main reason for this empirical treatment is the long turnaround time between sampling and availability of identification and susceptibility results. Therefore the objective of the present study was to develop a rapid identification procedure for pathogenic respiratory bacteria in bronchoalveolar lavage fluid (BALf) samples from cattle by MALDI-TOF MS, omitting the cultivation step on agar plates to reduce the turnaround time between sampling and identification of pathogens. The effects of two different liquid growth media and various concentrations of bacitracin were determined to allow optimal growth of Pasteurellaceae and minimise contamination. The best procedure was validated on 100 clinical BALf samples from cattle with conventional bacterial culture as reference test. A correct identification was obtained in 73% of the samples, with 59.1% sensitivity (Se) (47.2–71.0%) and 100% specificity (Sp) (100–100%) after only 6 hours of incubation. For pure and dominant culture samples, the procedure was able to correctly identify 79.2% of the pathogens, with a sensitivity (Se) of 60.5% (45.0–76.1%) and specificity (Sp) of 100% (100–100%). In mixed culture samples, containing ≥2 clinically relevant pathogens, one pathogen could be correctly identified in 57% of the samples with 57.1% Se (38.8–75.5%) and 100% Sp (100–100%). In conclusion, MALDI-TOF MS is a promising tool for rapid pathogen identification in BALf. This new technique drastically reduces turnaround time and may be a valuable decision support tool to rationalize antimicrobial use.
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Tsuchida S, Murata S, Miyabe A, Satoh M, Takiwaki M, Matsushita K, Nomura F. An in-house centrifugation and membrane filtration technique for identifying microorganisms from positive blood culture bottles with high identification rates using matrix-assisted laser desorption ionization-Time-of-flight mass spectrometry: A preliminary report. J Infect Chemother 2019; 26:266-271. [PMID: 31678054 DOI: 10.1016/j.jiac.2019.09.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 09/24/2019] [Accepted: 09/27/2019] [Indexed: 02/06/2023]
Abstract
Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) is one of the most promising technologies for the identification of microbial pathogens directly from positive blood culture bottles. As blood culture bottle medium contains various nonbacterial proteins, including those derived from blood cells, pretreatment to effectively remove host cells is key for successful proteome-based identification of microorganisms. Although the Sepsityper® kit is the most widely used pretreatment protocol, its performance is not satisfactory, particularly for gram-positive isolates. We developed a new in-house protocol, the centrifugation and membrane filtration technique (CMFT), in which vacuum-filtration is coupled with differential centrifugation. We prospectively evaluated the performance of this novel method compared with that of the Sepsityper®. For gram-negative bacterial isolates, the species-level identification rates obtained with the CMFT and the Sepsityper® were comparable (98.8% vs 92.9%). By contrast, for gram-positive isolates, the performance of the CMFT was significantly better than that of the Sepsityper® (P < 0.05). Using our new protocol, 81 (95.3%) isolates were identified with a score >2.0, and 85 (100%) isolates were identified with a score >1.7, versus 46 (54.1%) and 69 (81.2%), respectively, for the Sepsityper®. These results are preliminary, but considering that this novel protocol provides notably high species-level identification rates for gram-positive isolates, it deserves assessment in a larger-scale study with a variety of platforms for MS-based identification of microorganisms.
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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
| | - 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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Pais RJ, Zmuidinaite R, Butler S, Iles R. An automated workflow for MALDI-ToF mass spectra pattern identification on large data sets: An application to detect aneuploidies from pregnancy urine. INFORMATICS IN MEDICINE UNLOCKED 2019. [DOI: 10.1016/j.imu.2019.100194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Tsuchida S, Satoh M, Takiwaki M, Nomura F. Current Status of Proteomic Technologies for Discovering and Identifying Gingival Crevicular Fluid Biomarkers for Periodontal Disease. Int J Mol Sci 2018; 20:ijms20010086. [PMID: 30587811 PMCID: PMC6337088 DOI: 10.3390/ijms20010086] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 12/19/2018] [Accepted: 12/21/2018] [Indexed: 12/20/2022] Open
Abstract
Periodontal disease is caused by bacteria in dental biofilms. To eliminate the bacteria, immune system cells release substances that inflame and damage the gums, periodontal ligament, or alveolar bone, leading to swollen bleeding gums, which is a sign of gingivitis. Damage from periodontal disease can cause teeth to loosen also. Studies have demonstrated the proteomic approach to be a promising tool for the discovery and identification of biochemical markers of periodontal diseases. Recently, many studies have applied expression proteomics to identify proteins whose expression levels are altered by disease. As a fluid lying in close proximity to the periodontal tissue, the gingival crevicular fluid (GCF) is the principal target in the search for periodontal disease biomarkers because its protein composition may reflect the disease pathophysiology. Biochemical marker analysis of GCF is effective for objective diagnosis in the early and advanced stages of periodontal disease. Periodontal diseases are also promising targets for proteomics, and several groups, including ours, have applied proteomics in the search for GCF biomarkers of periodontal diseases. This search is of continuing interest in the field of experimental and clinical periodontal disease research. In this article, we summarize the current situation of proteomic technologies to discover and identify GCF biomarkers for periodontal diseases.
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Affiliation(s)
- Sachio Tsuchida
- Division of Clinical Mass Spectrometry, 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.
| | - Masaki Takiwaki
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8677, Japan.
| | - Fumio Nomura
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8677, Japan.
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Giordano C, Barnini S. Rapid detection of colistin-resistant Klebsiella pneumoniae using MALDI-TOF MS peak-based assay. J Microbiol Methods 2018; 155:27-33. [DOI: 10.1016/j.mimet.2018.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 11/09/2018] [Accepted: 11/11/2018] [Indexed: 12/19/2022]
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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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Zhang H, Zhao Z, Chen S, Kang P, Wang Y, Feng J, Jia J, Yan M, Wang Y, Xu L. Paracoccus versutus KS293 adaptation to aerobic and anaerobic denitrification: Insights from nitrogen removal, functional gene abundance, and proteomic profiling analysis. BIORESOURCE TECHNOLOGY 2018; 260:321-328. [PMID: 29631182 DOI: 10.1016/j.biortech.2018.03.123] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/23/2018] [Accepted: 03/27/2018] [Indexed: 06/08/2023]
Abstract
A novel strain KS293 exhibiting excellent aerobic and anaerobic denitrification performance was isolated and identified as Paracoccus versutus KS293. Nitrate nitrogen and total organic carbon could be effectively removed by P. versutus KS293 without nitrite accumulation, whilst 82% and 85% of total nitrogen was converted into gaseous products under aerobic and anaerobic conditions (P > .05), respectively. Based on the ratio of anaerobic to aerobic, relative abundance values were increased 1.41, 1.45, and 2.31 folds for nirS, nosZ, and narG, respectively. A comparison of the two-dimensional gel electrophoresis and principal component analysis showed significant differences in proteomic profiles between aerobic and anaerobic conditions. In total, 78 proteins that displayed fluctuations in relative expression were observed. 10 proteins including nitrate reductase, maintenance of cell membrane (TolA), and RNA polymerase-binding transcription factor (DksA) were differentially expressed. These findings demonstrated that P. versutus KS293 was effective for nitrogen removal under aerobic or anaerobic conditions.
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Affiliation(s)
- Haihan Zhang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China.
| | - Zhenfang Zhao
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Shengnan Chen
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Pengliang Kang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Yue Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Ji Feng
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Jingyu Jia
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Miaomiao Yan
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Yan Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
| | - Lei Xu
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China; Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi 710055, PR China
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Vrioni G, Tsiamis C, Oikonomidis G, Theodoridou K, Kapsimali V, Tsakris A. MALDI-TOF mass spectrometry technology for detecting biomarkers of antimicrobial resistance: current achievements and future perspectives. ANNALS OF TRANSLATIONAL MEDICINE 2018; 6:240. [PMID: 30069442 PMCID: PMC6046294 DOI: 10.21037/atm.2018.06.28] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The laboratory diagnosis of infections is based on pathogen identification and antimicrobial susceptibility determination. The gold standard of cultivation, isolation and susceptibility testing is a time-consuming procedure and in some cases this can be threatening for patients' outcome. In the current review the applications of mass spectrometry in pathogen identification and especially in detecting biomarkers of antimicrobial resistance are analyzed. MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry is a new technology that has revolutionized pathogen identification and has also proven to accelerate detection of antimicrobial resistance compared to the traditional antibiotic susceptibility tests (AST) as well as DNA amplification methodologies. The technology has incorporated up to know four different methodologies: (I) the detection of differences of mass spectra of susceptible and resistant isolates of a given microorganism using the classical strain typing methodology; (II) the analysis of bacterial induced hydrolysis of β-lactam antibiotics; (III) the detection of stable (non-radioactive) isotope-labeled amino acids; and (IV) the analysis of bacterial growth in the presence and absence of antibiotics using an internal standard. The implementation of MALDI-TOF methodologies has improved detection of resistance in aerobic, Gram-positive and Gram-negative bacteria, mycobacteria, anaerobic bacteria, fungi and viruses. The MALDI-TOF is an easy to use, rapid, reliable, economical, and environmentally friendly methodology. However, this technology needs further development of research protocols that will be validated for routine application.
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Affiliation(s)
- Georgia Vrioni
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Constantinos Tsiamis
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - George Oikonomidis
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Kalliopi Theodoridou
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Violeta Kapsimali
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Athanasios Tsakris
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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Florio W, Tavanti A, Barnini S, Ghelardi E, Lupetti A. Recent Advances and Ongoing Challenges in the Diagnosis of Microbial Infections by MALDI-TOF Mass Spectrometry. Front Microbiol 2018; 9:1097. [PMID: 29896172 PMCID: PMC5986882 DOI: 10.3389/fmicb.2018.01097] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/08/2018] [Indexed: 12/25/2022] Open
Abstract
Timeliness and accuracy in the diagnosis of microbial infections are associated with decreased mortality and reduced length of hospitalization, especially for severe, life-threatening infections. A rapid diagnosis also allows for early streamlining of empirical antimicrobial therapies, thus contributing to limit the emergence and spread of antimicrobial resistance. The introduction of matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) for routine identification of microbial pathogens has profoundly influenced microbiological diagnostics, and is progressively replacing biochemical identification methods. Compared to currently used identification methods, MALDI-TOF MS has the advantage of identifying bacteria and yeasts directly from colonies grown on culture plates for primary isolation in a few minutes and with considerable material and labor savings. The reliability and accuracy of MALDI-TOF MS in identification of clinically relevant bacteria and yeasts has been demonstrated by several studies showing that the performance of MALDI-TOF MS is comparable or superior to phenotypic methods currently in use in clinical microbiology laboratories, and can be further improved by database updates and analysis software upgrades. Besides microbial identification from isolated colonies, new perspectives are being explored for MALDI-TOF MS, such as identification of pathogens directly from positive blood cultures, sub-species typing, and detection of drug resistance determinants. In this review, we summarize the state of the art in routine identification of microbial pathogens by MALDI-TOF MS, and highlight recent advancements of this technology in special applications, such as strain typing, assessment of drug susceptibility, and detection of virulence factors.
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Affiliation(s)
- Walter Florio
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
| | | | | | - Emilia Ghelardi
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
| | - Antonella Lupetti
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
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Chu S, Baker MR, Leong G, Letcher RJ, Li QX. Covalent binding of the organophosphate insecticide profenofos to tyrosine on α- and β-tubulin proteins. CHEMOSPHERE 2018; 199:154-159. [PMID: 29433029 PMCID: PMC5847477 DOI: 10.1016/j.chemosphere.2018.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 06/08/2023]
Abstract
Organophosphorus (OP) compounds can bind covalently to many types of proteins and form protein adducts. These protein adducts can indicate the exposure to and neurotoxicity of OPs. In the present work, we studied adduction of tubulin with the OP insecticide profenofos in vitro and optimized the method for detection of adducted peptides. Porcine tubulin was incubated with profenofos and was then digested with trypsin, followed by mass spectrometric identification of the profenofos-modified tubulin and binding sites. With solvent-assisted digestion (80% acetonitrile in digestion solution), the protein was digested for peptide identification, especially for some peptides with low mass. The MALDI-TOF-MS and LC-ESI-TOF-MS analysis results showed that profenofos bound covalently to Tyr83 in porcine α-tubulin (TGTY*83R) and to Tyr281 in porcine β-tubulin (GSQQY*281R) with a mass increase of 166.02 Da from the original peptide fragments of porcine tubulin proteins. Tyrosine adduct sites were also confirmed by MALDI-TOF/TOF-MS analysis. This result may partially explain the neurotoxicity of profenofos at low doses and prolonged periods of exposure.
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Affiliation(s)
- Shaogang Chu
- Ecotoxicology and Wildlife Health Division, Wildlife and Landscape Science Directorate, National Wildlife Research Centre, Environment and Climate Change Canada, 1125 Colonel By Dr., Carleton University, Ottawa, ON, K1A 0H3, Canada
| | - Margaret R Baker
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East West Road, Honolulu, HI, 96822, USA
| | - Gladys Leong
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East West Road, Honolulu, HI, 96822, USA
| | - Robert J Letcher
- Ecotoxicology and Wildlife Health Division, Wildlife and Landscape Science Directorate, National Wildlife Research Centre, Environment and Climate Change Canada, 1125 Colonel By Dr., Carleton University, Ottawa, ON, K1A 0H3, Canada
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East West Road, Honolulu, HI, 96822, USA.
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Identification and Characterization of Clostridium difficile Sequence Type 37 Genotype by Matrix-Assisted Laser Desorption Ionization -Time of Flight Mass Spectrometry. J Clin Microbiol 2018; 56:JCM.01990-17. [PMID: 29467194 DOI: 10.1128/jcm.01990-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 02/15/2018] [Indexed: 01/05/2023] Open
Abstract
Clostridium difficile multilocus sequence type 37 (ST37), which mainly corresponds to ribotype 017, has been a dominant genotype circulating in China. In this study, we report the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) to analyze and characterize 204 C. difficile clinical isolates, including 49 ST37 and 155 non-ST37 isolates collected in China and other countries. The distributions of two major protein peaks (m/z 3,242 and 3,286) were significantly different between ST37 and non-ST37 prototype strains and clinical isolates. This difference was reproducible when analysis was performed on different colonies in different runs. This finding was repeated and confirmed by both bioMérieux Vitek MS and Bruker Microflex LT systems on isolates recovered from a variety of geographic regions worldwide. The combination of the two peaks was present in 47 of 49 ST37 isolates, resulting in a sensitivity of 95.9%. In contrast, the peak combination was absent in 153 of 155 non-ST37 isolates, resulting in a specificity of 98.7%. Our results suggest that MALDI-TOF MS is a rapid and reliable tool to identify C. difficile genotype ST37. Work is in progress to characterize the two molecules having peaks at m/z 3,242 and 3,286, which appear to be specific to C. difficile genotype ST37.
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Zhang D, Bi H, Liu B, Qiao L. Detection of Pathogenic Microorganisms by Microfluidics Based Analytical Methods. Anal Chem 2018; 90:5512-5520. [PMID: 29595252 DOI: 10.1021/acs.analchem.8b00399] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Microfluidics based biochemical analysis shows distinctive advantages for fast detection of pathogenic microorganisms. This Feature summarizes the progress in the past decade on microfluidic methods for purification and detection of pathogenic bacteria and viruses as well as their applications in food safety control, environmental monitoring, and clinical diagnosis.
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Affiliation(s)
- Dongxue Zhang
- Department of Chemistry, Shanghai Stomatological Hospital, and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials , Fudan University , Shanghai , China 200433
| | - Hongyan Bi
- College of Food Science and Engineering , Shanghai Ocean University , Shanghai , China 201306
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials , Fudan University , Shanghai , China 200433
| | - Liang Qiao
- Department of Chemistry, Shanghai Stomatological Hospital, and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials , Fudan University , Shanghai , China 200433
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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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Wang HY, Lee TY, Tseng YJ, Liu TP, Huang KY, Chang YT, Chen CH, Lu JJ. A new scheme for strain typing of methicillin-resistant Staphylococcus aureus on the basis of matrix-assisted laser desorption ionization time-of-flight mass spectrometry by using machine learning approach. PLoS One 2018. [PMID: 29534106 PMCID: PMC5849341 DOI: 10.1371/journal.pone.0194289] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA), one of the most important clinical pathogens, conducts an increasing number of morbidity and mortality in the world. Rapid and accurate strain typing of bacteria would facilitate epidemiological investigation and infection control in near real time. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry is a rapid and cost-effective tool for presumptive strain typing. To develop robust method for strain typing based on MALDI-TOF spectrum, machine learning (ML) is a promising algorithm for the construction of predictive model. In this study, a strategy of building templates of specific types was used to facilitate generating predictive models of methicillin-resistant Staphylococcus aureus (MRSA) strain typing through various ML methods. The strain types of the isolates were determined through multilocus sequence typing (MLST). The area under the receiver operating characteristic curve (AUC) and the predictive accuracy of the models were compared. ST5, ST59, and ST239 were the major MLST types, and ST45 was the minor type. For binary classification, the AUC values of various ML methods ranged from 0.76 to 0.99 for ST5, ST59, and ST239 types. In multiclass classification, the predictive accuracy of all generated models was more than 0.83. This study has demonstrated that ML methods can serve as a cost-effective and promising tool that provides preliminary strain typing information about major MRSA lineages on the basis of MALDI-TOF spectra.
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Affiliation(s)
- Hsin-Yao Wang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan
| | - Tzong-Yi Lee
- Department of Computer Science & Engineering, Yuan Ze University, Taoyuan City, Taiwan
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, China
| | - Yi-Ju Tseng
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan
- Department of Information Management, Chang Gung University, Taoyuan City, Taiwan
| | - Tsui-Ping Liu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan
| | - Kai-Yao Huang
- Department of Computer Science & Engineering, Yuan Ze University, Taoyuan City, Taiwan
| | - Yung-Ta Chang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan
| | - Chun-Hsien Chen
- Department of Information Management, Chang Gung University, Taoyuan City, Taiwan
- * E-mail: (CHC); (JJL)
| | - Jang-Jih Lu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City, Taiwan
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan City, Taiwan
- * E-mail: (CHC); (JJL)
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Pikina AP, Shkoporov AN, Kulagina EV, Khokhlova EV, Chaplin AV, Volodin NN, Kafarskaya LI, Korotkly NG, Efimov BA. [Comparative Genotyping of Staphylococcus aureus Strains Isolated from Skin Lesions, Nasal Cavities, and Feces of Children with Atopic Dermatitis]. ACTA ACUST UNITED AC 2018; 71:367-74. [PMID: 29297666 DOI: 10.15690/vramn695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Background The lesion of skin of the majority atopic dermatitis patients is chronically colonized by bacteria belonging to the species Staphylococcus aureus. Topical antibacterial and anti-inflammatory therapy treatment are often ineffective due to fast recolonization by S. aureus and exacerbation of allergic process. Aims Our aim was to determine a frequency of S. aureus colonization in skin lesions, mucous membranes of the nasal cavity and intestine of children with atopic dermatitis, to compare the genotypes of Staphylococcus aureus strains isolated from different biotopes of atopic dermatitis patients, and to clarify whether the intestinal and nasal cavities microbiota may act as a source of S. aureus recolonization of skin lesions. Materials and Methods Bacteriological examination of fecal samples, skin, and nasal swabs was conducted in 38 atopic dermatitis patients. The pure bacterial cultures of S. aureus were identified using API Staph (Biomerieux, France) and Vitek 2 MS (Biomerieux, France). Isolates of S. aureus were subjected to genotyping by analysis of rRNA internal 16S-23S rRNA spacer regions and high resolution melting analysis (HMR) of polymorphic spa X-regions. Results 99% S. aureus strains were successfully identified using MALDI-TOF mass-spectrometry. S. aureus cultures were isolated from all biotopes in 31,6% of children, from skin and nasal cavities — in 42% of cases, from skin and feces — in 2,6% of cases, only from skin — in 10,5%, from nasal cavities and feces — in 2,6%, and only from nasal cavities — in 2,6% of cases. In 8% of children, S. aureus was not detected in any of the biotopes. Genotyping of the isolates enabled the detection of 17 different genotypes. A match between the genotypes of skin and nasal strains, and skin and fecal strains was observed in 88% and 61% of the cases respectively. Conclusions The observed a high-frequency matching genotypes suggests the possibility of migration of S. aureus strains inside biotopes in humans and the absence of specialization to colonization of any of the niches.
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Rapid and robust analytical protocol for E. coli STEC bacteria subspecies differentiation using whole cell MALDI mass spectrometry. Talanta 2018; 182:164-170. [PMID: 29501136 DOI: 10.1016/j.talanta.2018.01.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 01/17/2018] [Accepted: 01/20/2018] [Indexed: 12/30/2022]
Abstract
Whole cell MALDI is regularly used for the identification of bacteria to species level in clinical Microbiology laboratories. However, there remains a need to rapidly characterize and differentiate isolates below the species level to support outbreak management. We describe the implementation of a modified preparative approach for MALDI-MS combined with a custom analytical computational pipeline as a rapid procedure for subtyping Shigatoxigenic E. coli (STEC) and accurately identifying strain-specifying biomarkers. The technique was able to differentiate E. coli O157:H7 from other STEC. Within O157 serotype O157:H7 isolates were readily distinguishable from Sorbitol Fermenting O157 isolates. Overall, nine homogeneous groups of isolates were distinguished, each exhibiting distinct profiles of defining mass spectra features. This offers a robust analytical tool useable in reference/diagnostic public health scenarios.
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Šalplachta J, Horká M, Růžička F, Šlais K. Identification of bacterial uropathogens by preparative isoelectric focusing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Chromatogr A 2018; 1532:232-237. [DOI: 10.1016/j.chroma.2017.11.072] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/20/2017] [Accepted: 11/30/2017] [Indexed: 01/25/2023]
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