1
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Thiery J, Fahrner M. Integration of proteomics in the molecular tumor board. Proteomics 2024; 24:e2300002. [PMID: 38143279 DOI: 10.1002/pmic.202300002] [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: 07/24/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 12/26/2023]
Abstract
Cancer remains one of the most complex and challenging diseases in mankind. To address the need for a personalized treatment approach for particularly complex tumor cases, molecular tumor boards (MTBs) have been initiated. MTBs are interdisciplinary teams that perform in-depth molecular diagnostics to cooperatively and interdisciplinarily advise on the best therapeutic strategy. Current molecular diagnostics are routinely performed on the transcriptomic and genomic levels, aiming to identify tumor-driving mutations. However, these approaches can only partially capture the actual phenotype and the molecular key players of tumor growth and progression. Thus, direct investigation of the expressed proteins and activated signaling pathways provide valuable complementary information on the tumor-driving molecular characteristics of the tissue. Technological advancements in mass spectrometry-based proteomics enable the robust, rapid, and sensitive detection of thousands of proteins in minimal sample amounts, paving the way for clinical proteomics and the probing of oncogenic signaling activity. Therefore, proteomics is currently being integrated into molecular diagnostics within MTBs and holds promising potential in aiding tumor classification and identifying personalized treatment strategies. This review introduces MTBs and describes current clinical proteomics, its potential in precision oncology, and highlights the benefits of multi-omic data integration.
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Affiliation(s)
- Johanna Thiery
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Matthias Fahrner
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
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2
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Cai YH, Wang CC, Hsiao CH, Wang YS. Experimental Validation of Comprehensive Calculation for High-Resolution Linear MALDI-TOF Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:992-998. [PMID: 38634762 PMCID: PMC11066958 DOI: 10.1021/jasms.4c00018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024]
Abstract
This work discusses the effectiveness of the previously developed comprehensive calculation model to optimize linear MALDI-TOF mass spectrometers. The model couples space- and velocity-focusing to precisely analyze the flight-time distribution of ions and predict optimal experimental parameters for the highest mass resolving power. Experimental validation was conducted using a laboratory-made instrument to analyze CsI3 and angiotensin I ions in low to medium m/z range. The results indicate that the predicted optimal extraction voltage and delay were reasonably accurate and effective. In the low m/z range, the peak width obtained using optimal parameters reached the sub nanosecond range, corresponding to a mass resolving power of 10 000-17 000, or 20 000-34 000 if shot-to-shot random fluctuations were minimized by the dynamic data correction method. The observed optimal mass resolving power in the current experiment is 4.8-7.8 times that of commercial instruments. Practical limitations resulting in the gap between the observed and theoretical ultimate mass resolving power are discussed.
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Affiliation(s)
- Yi-Hong Cai
- Genomics
Research Center, Academia Sinica, Taipei 115, Taiwan ROC
| | - Chia-Chen Wang
- Instrumentation
Center, National Taiwan Normal University, Taipei 106, Taiwan ROC
| | - Chih-Hao Hsiao
- Genomics
Research Center, Academia Sinica, Taipei 115, Taiwan ROC
| | - Yi-Sheng Wang
- Genomics
Research Center, Academia Sinica, Taipei 115, Taiwan ROC
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3
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Dev MJ, Mahajan GB, Warke RG, Warke GM, Patil TA, Satardekar MR, Dalvi RC, Singhal RS. Mutagenesis enhances gellan gum production by a novel Sphingomonas spp.: upstream optimization, kinetic modeling, and structural and physico-functional evaluation. Int Microbiol 2024; 27:459-476. [PMID: 37495894 DOI: 10.1007/s10123-023-00399-1] [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: 02/24/2023] [Revised: 06/11/2023] [Accepted: 07/07/2023] [Indexed: 07/28/2023]
Abstract
Gellan gum (GG) has gained tremendous attention owing to its diversified applications. However, its high production and hence market cost are still a bottleneck in its widespread utilization. In the present study, high GG producing mutant of Sphingomonas spp. was developed by random mutagenesis using ethyl methylsulphonate (EMS) for industrial fermentation and identified as Sphingomonas trueperi after 16S rRNA and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS) analysis. The fermentation conditions such as pH, temperature, and inoculum ratio were optimized by one factor at a time (OFAT) followed by screening of medium components by the Plackett-Burman statistical design. The most critical nutrients were further optimized by response surface methodology for maximizing GG production. The effect of dissolved oxygen tension in bioreactor on cell growth, substrate consumption, GG production, and batch productivity was elucidated. The highest GG titer (23 ± 2.4 g/L) was attained in optimized medium at 10% inoculum (6.45 ± 0.5 log cfu/mL) under controlled fermentation conditions of pH (7), temperature (30 °C), agitation (300-600 rpm), and aeration (0.5-2.0 SLPM) at 22 ± 2% dissolved oxygen tension in a 10-L bioreactor. Kinetic modeling of optimized batch process revealed that logistic growth model could best explain biomass accumulation, while GG formation and substrate consumption were best explained by Luedeking-Piret and exponential decay model, respectively. Structural and physico-functional features of GG produced by mutant Sphingomonas spp. were characterized by HPLC, FTIR, NMR, DSC, TGA, GPC, SEM, and rheological analysis. The higher productivity (0.51 g/L/h) under optimized fermentation conditions suggests potential consideration of mutant and process for commercial utilization.
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Affiliation(s)
- Manoj J Dev
- Food Engineering and Technology Department, Institute of Chemical Technology, Mumbai, 400019, India
- Department of Microbiology, HiMedia Laboratories Pvt. Ltd, Mumbai, India
| | - Girish B Mahajan
- Department of Microbiology, HiMedia Laboratories Pvt. Ltd, Mumbai, India
| | - Rahul G Warke
- Department of Microbiology, HiMedia Laboratories Pvt. Ltd, Mumbai, India
| | - Gangadhar M Warke
- Department of Microbiology, HiMedia Laboratories Pvt. Ltd, Mumbai, India
| | - Tanuja A Patil
- Department of Microbiology, HiMedia Laboratories Pvt. Ltd, Mumbai, India
| | - Milan R Satardekar
- Department of Microbiology, HiMedia Laboratories Pvt. Ltd, Mumbai, India
| | - Rachana C Dalvi
- Department of Microbiology, HiMedia Laboratories Pvt. Ltd, Mumbai, India
| | - Rekha S Singhal
- Food Engineering and Technology Department, Institute of Chemical Technology, Mumbai, 400019, India.
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4
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Carpenter JM, Hynds HM, Bimpeh K, Hines KM. HILIC-IM-MS for Simultaneous Lipid and Metabolite Profiling of Bacteria. ACS MEASUREMENT SCIENCE AU 2024; 4:104-116. [PMID: 38404491 PMCID: PMC10885331 DOI: 10.1021/acsmeasuresciau.3c00051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 02/27/2024]
Abstract
Although MALDI-ToF platforms for microbial identifications have found great success in clinical microbiology, the sole use of protein fingerprints for the discrimination of closely related species, strain-level identifications, and detection of antimicrobial resistance remains a challenge for the technology. Several alternative mass spectrometry-based methods have been proposed to address the shortcomings of the protein-centric approach, including MALDI-ToF methods for fatty acid/lipid profiling and LC-MS profiling of metabolites. However, the molecular diversity of microbial pathogens suggests that no single "ome" will be sufficient for the accurate and sensitive identification of strain- and susceptibility-level profiling of bacteria. Here, we describe the development of an alternative approach to microorganism profiling that relies upon both metabolites and lipids rather than a single class of biomolecule. Single-phase extractions based on butanol, acetonitrile, and water (the BAW method) were evaluated for the recovery of lipids and metabolites from Gram-positive and -negative microorganisms. We found that BAW extraction solutions containing 45% butanol provided optimal recovery of both molecular classes in a single extraction. The single-phase extraction method was coupled to hydrophilic interaction liquid chromatography (HILIC) and ion mobility-mass spectrometry (IM-MS) to resolve similar-mass metabolites and lipids in three dimensions and provide multiple points of evidence for feature annotation in the absence of tandem mass spectrometry. We demonstrate that the combined use of metabolites and lipids can be used to differentiate microorganisms to the species- and strain-level for four of the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Acinetobacter baumannii, and Pseudomonas aeruginosa) using data from a single ionization mode. These results present promising, early stage evidence for the use of multiomic signatures for the identification of microorganisms by liquid chromatography, ion mobility, and mass spectrometry that, upon further development, may improve upon the level of identification provided by current methods.
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Affiliation(s)
- Jana M. Carpenter
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Hannah M. Hynds
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Kingsley Bimpeh
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Kelly M. Hines
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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5
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Gant MS, Chamot-Rooke J. Present and future perspectives on mass spectrometry for clinical microbiology. Microbes Infect 2024:105296. [PMID: 38199266 DOI: 10.1016/j.micinf.2024.105296] [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: 07/03/2023] [Revised: 12/01/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
In the last decade, MALDI-TOF Mass Spectrometry (MALDI-TOF MS) has been introduced and broadly accepted by clinical laboratory laboratories throughout the world as a powerful and efficient tool for rapid microbial identification. During the MALDI-TOF MS process, microbes are identified using either intact cells or cell extracts. The process is rapid, sensitive, and economical in terms of both labor and costs involved. Whilst MALDI-TOF MS is currently the gold-standard, it suffers from several shortcomings such as lack of direct information on antibiotic resistance, poor depth of analysis and insufficient discriminatory power for the distinction of closely related bacterial species or for reliably sub-differentiating isolates to the level of clones or strains. Thus, new approaches targeting proteins and allowing a better characterization of bacterial strains are strongly needed, if possible, on a very short time scale after sample collection in the hospital. Bottom-up proteomics (BUP) is a nice alternative to MALDI-TOF MS, offering the possibility for in-depth proteome analysis. Top-down proteomics (TDP) provides the highest molecular precision in proteomics, allowing the characterization of proteins at the proteoform level. A number of studies have already demonstrated the potential of these techniques in clinical microbiology. In this review, we will discuss the current state-of-the-art of MALDI-TOF MS for the rapid microbial identification and detection of resistance to antibiotics and describe emerging approaches, including bottom-up and top-down proteomics as well as ambient MS technologies.
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Affiliation(s)
- Megan S Gant
- Institut Pasteur, Université Paris Cité, CNRS UAR 2024, Mass Spectrometry for Biology 75015 Paris, France
| | - Julia Chamot-Rooke
- Institut Pasteur, Université Paris Cité, CNRS UAR 2024, Mass Spectrometry for Biology 75015 Paris, France.
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6
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Birhanu AG. Mass spectrometry-based proteomics as an emerging tool in clinical laboratories. Clin Proteomics 2023; 20:32. [PMID: 37633929 PMCID: PMC10464495 DOI: 10.1186/s12014-023-09424-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/03/2023] [Indexed: 08/28/2023] Open
Abstract
Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these advanced tests more accessible and affordable will have the greatest healthcare benefit.This review article highlights the new paradigms MS-based clinical proteomics has created in microbiology laboratories, cancer research and diagnosis of metabolic disorders. The technique is preferred over conventional methods in disease detection and therapy monitoring for its combined advantages in multiplexing capacity, remarkable analytical specificity and sensitivity and low turnaround time.Despite the achievements in the development and adoption of a number of MS-based clinical proteomics practices, more are expected to undergo transition from bench to bedside in the near future. The review provides insights from early trials and recent progresses (mainly covering literature from the NCBI database) in the application of proteomics in clinical laboratories.
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7
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Sakagianni A, Koufopoulou C, Feretzakis G, Kalles D, Verykios VS, Myrianthefs P, Fildisis G. Using Machine Learning to Predict Antimicrobial Resistance-A Literature Review. Antibiotics (Basel) 2023; 12:antibiotics12030452. [PMID: 36978319 PMCID: PMC10044642 DOI: 10.3390/antibiotics12030452] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/30/2023] Open
Abstract
Machine learning (ML) algorithms are increasingly applied in medical research and in healthcare, gradually improving clinical practice. Among various applications of these novel methods, their usage in the combat against antimicrobial resistance (AMR) is one of the most crucial areas of interest, as increasing resistance to antibiotics and management of difficult-to-treat multidrug-resistant infections are significant challenges for most countries worldwide, with life-threatening consequences. As antibiotic efficacy and treatment options decrease, the need for implementation of multimodal antibiotic stewardship programs is of utmost importance in order to restrict antibiotic misuse and prevent further aggravation of the AMR problem. Both supervised and unsupervised machine learning tools have been successfully used to predict early antibiotic resistance, and thus support clinicians in selecting appropriate therapy. In this paper, we reviewed the existing literature on machine learning and artificial intelligence (AI) in general in conjunction with antimicrobial resistance prediction. This is a narrative review, where we discuss the applications of ML methods in the field of AMR and their value as a complementary tool in the antibiotic stewardship practice, mainly from the clinician's point of view.
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Affiliation(s)
| | - Christina Koufopoulou
- 1st Anesthesiology Department, Aretaieio Hospital, National and Kapodistrian University of Athens Medical School, 11528 Athens, Greece
| | - Georgios Feretzakis
- School of Science and Technology, Hellenic Open University, 26335 Patras, Greece
- Department of Quality Control, Research and Continuing Education, Sismanogleio General Hospital, 15126 Marousi, Greece
| | - Dimitris Kalles
- School of Science and Technology, Hellenic Open University, 26335 Patras, Greece
| | - Vassilios S Verykios
- School of Science and Technology, Hellenic Open University, 26335 Patras, Greece
| | - Pavlos Myrianthefs
- Faculty of Nursing, School of Health Sciences, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Georgios Fildisis
- Faculty of Nursing, School of Health Sciences, National and Kapodistrian University of Athens, 11527 Athens, Greece
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8
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Larson EA, Rensner JJ, Larsen KR, Bellaire B, Lee YJ. Rapid Antibiotic Susceptibility Testing by Deuterium Labeling of Bacterial Lipids in On-Target Microdroplet Cultures. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1221-1228. [PMID: 35623100 PMCID: PMC9264383 DOI: 10.1021/jasms.2c00056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Antimicrobial resistance is a serious challenge facing human and veterinary health. Current methods of detecting resistance are limited in turn-around time or universal detection. In this work, a new antimicrobial susceptibility test is developed and validated, which utilizes deuterium labeling of membrane lipids to track the growth of bacterial cells. We hypothesize that deuterium uptake and subsequent labeling of lipids can be detected using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Additionally, bacteria growth is performed on the MALDI target, minimizing sample preparation materials and time. When two Escherichia coli strains are grown in the presence of deuterium oxide, labeling can be detected in as little as 30 min to 2 h. The labeling efficiency, or the ratio of labeled to unlabeled lipid peaks, provides information about the growth rate of bacteria. This growth ratio can differentiate between resistant and susceptible strains of bacteria as a resistant strain will maintain ∼50% labeling efficiency between untreated and treated cultures. In comparison, a susceptible strain will see a decrease in fractional abundance of deuterium from ∼50% in the untreated to ∼10% in the treated. This approach is applied to measure the minimum inhibitory concentration (MIC) of the resistant and susceptible strains from on-target microdroplet culture in a range of antibiotic concentrations. The first antibiotic concentration with a significant decrease in fractional abundance of deuterium correlates well with a traditionally obtained MIC using broth dilution, indicating the clinical relevance of the results.
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Affiliation(s)
- Evan A. Larson
- Department
of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Josiah J. Rensner
- Department
of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Kristina R. Larsen
- Department
of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa 50011, United States
| | - Bryan Bellaire
- Department
of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa 50011, United States
| | - Young Jin Lee
- Department
of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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9
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Limitation of
ctrA
as a Target for Neisseria meningitidis Identification and Potential Alternative Targets. J Clin Microbiol 2022; 60:e0015222. [DOI: 10.1128/jcm.00152-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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10
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Chen XF, Hou X, Xiao M, Zhang L, Cheng JW, Zhou ML, Huang JJ, Zhang JJ, Xu YC, Hsueh PR. Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) Analysis for the Identification of Pathogenic Microorganisms: A Review. Microorganisms 2021; 9:microorganisms9071536. [PMID: 34361971 PMCID: PMC8304613 DOI: 10.3390/microorganisms9071536] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/03/2021] [Accepted: 07/10/2021] [Indexed: 12/13/2022] Open
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been used in the field of clinical microbiology since 2010. Compared with the traditional technique of biochemical identification, MALDI-TOF MS has many advantages, including convenience, speed, accuracy, and low cost. The accuracy and speed of identification using MALDI-TOF MS have been increasing with the development of sample preparation, database enrichment, and algorithm optimization. MALDI-TOF MS has shown promising results in identifying cultured colonies and rapidly detecting samples. MALDI-TOF MS has critical research applications for the rapid detection of highly virulent and drug-resistant pathogens. Here we present a scientific review that evaluates the performance of MALDI-TOF MS in identifying clinical pathogenic microorganisms. MALDI-TOF MS is a promising tool in identifying clinical microorganisms, although some aspects still require improvement.
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Affiliation(s)
- Xin-Fei Chen
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Xin Hou
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Meng Xiao
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Li Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Jing-Wei Cheng
- Center of Clinical Laboratory, Beijing Friendship Hospital, Capital Medical University, Beijing 100053, China;
| | - Meng-Lan Zhou
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Jing-Jing Huang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Jing-Jia Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Ying-Chun Xu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
- Correspondence: (Y.-C.X.); (P.-R.H.)
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, China Medical University Hospital, School of Medicine, China Medical University, Taichung 40447, Taiwan;
- Departments of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei 100, Taiwan
- Correspondence: (Y.-C.X.); (P.-R.H.)
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11
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Quantification and Characterization of Antimicrobial Resistance in Greywater Discharged to the Environment. WATER 2020. [DOI: 10.3390/w12051460] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In disenfranchised communities, untreated greywater (wastewater without sewage) is often environmentally discharged, resulting in potential human exposure to antimicrobial-resistant bacteria (ARB), including extended-spectrum beta-lactamase (ESBL) producers. We sought to examine the abundance of ARB, specifically ESBLs, and antimicrobial resistance genes (ARGs) in greywater from off-grid, pastoral Bedouin villages in Southern Israel. Greywater samples (n = 21) collected from five villages were analyzed to enumerate fecal coliforms and Escherichia coli. ESBL producers were recovered on CHROMagar ESBL and confirmed by VITEK®2 (bioMerieux, Marcy l’Etoile, France) for identification and antimicrobial susceptibility testing. Total genomic DNA was extracted from greywater samples and quantitative PCR (qPCR) was used to determine relative abundance (gene copies/16S rRNA gene) of class 1 integron-integrase intI1, blaTEM, blaCTX-M-32, sul1, and qnrS. The mean count of presumptive ESBL-producing isolates was 4.5 × 106 CFU/100 mL. Of 81 presumptive isolates, 15 ESBL producers were recovered. Phenotypically, 86.7% of ESBL producers were multi-drug resistant. Results from qPCR revealed a high abundance of intI1 (1.4 × 10−1 gene copies/16S rRNA), sul1 (5.2 × 10−2 gene copies/16S rRNA), and qnrS (1.7 × 10−2 gene copies/16S rRNA) followed by blaTEM (3.5 × 10−3 gene copies/16S rRNA) and blaCTX-M-32 (2.2 × 10−5 gene copies/16S rRNA). Results from our study indicate that greywater can be a source of ARB, including ESBL producers, in settings characterized by low sanitary conditions and inadequate wastewater management.
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12
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Papalia M, Figueroa-Espinosa R, Steffanowski C, Barberis C, Almuzara M, Barrios R, Vay C, Gutkind G, Di Conza J, Radice M. Expansion and improvement of MALDI-TOF MS databases for accurate identification of Achromobacter species. J Microbiol Methods 2020; 172:105889. [PMID: 32171844 DOI: 10.1016/j.mimet.2020.105889] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 10/24/2022]
Abstract
Different MALDI-TOF MS databases were evaluated for the identification of Achromobacter species. The in-house and extended database generated in this study rendered more accurate identification (58/64 and 57/64 isolates, respectively) in comparison with the Bruker commercial database (42/64 isolates), especially in those infrequent species that are not available or poorly represented.
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Affiliation(s)
- Mariana Papalia
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, IBaViM, Laboratorio de Resistencia Bacteriana, Junín 956, 8vo. Piso, Ciudad Autónoma de Buenos Aires, CP 1113, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Roque Figueroa-Espinosa
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, IBaViM, Laboratorio de Resistencia Bacteriana, Junín 956, 8vo. Piso, Ciudad Autónoma de Buenos Aires, CP 1113, Argentina
| | - Carla Steffanowski
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, IBaViM, Laboratorio de Resistencia Bacteriana, Junín 956, 8vo. Piso, Ciudad Autónoma de Buenos Aires, CP 1113, Argentina
| | - Claudia Barberis
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Laboratorio de Bacteriología Clínica, Av. Córdoba 2351, 1er. piso, Ciudad Autónoma de Buenos Aires CP1113, Argentina
| | - Marisa Almuzara
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Laboratorio de Bacteriología Clínica, Av. Córdoba 2351, 1er. piso, Ciudad Autónoma de Buenos Aires CP1113, Argentina
| | | | - Carlos Vay
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Laboratorio de Bacteriología Clínica, Av. Córdoba 2351, 1er. piso, Ciudad Autónoma de Buenos Aires CP1113, Argentina
| | - Gabriel Gutkind
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, IBaViM, Laboratorio de Resistencia Bacteriana, Junín 956, 8vo. Piso, Ciudad Autónoma de Buenos Aires, CP 1113, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - José Di Conza
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, IBaViM, Laboratorio de Resistencia Bacteriana, Junín 956, 8vo. Piso, Ciudad Autónoma de Buenos Aires, CP 1113, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Marcela Radice
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, IBaViM, Laboratorio de Resistencia Bacteriana, Junín 956, 8vo. Piso, Ciudad Autónoma de Buenos Aires, CP 1113, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
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13
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Piamsomboon P, Jaresitthikunchai J, Hung TQ, Roytrakul S, Wongtavatchai J. Identification of bacterial pathogens in cultured fish with a custom peptide database constructed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). BMC Vet Res 2020; 16:52. [PMID: 32046727 PMCID: PMC7014616 DOI: 10.1186/s12917-020-2274-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 02/04/2020] [Indexed: 12/19/2022] Open
Abstract
Background The majority of infectious diseases of cultured fish is caused by bacteria. Rapid identification of bacterial pathogens is necessary for immediate management. The present study developed a custom Main Spectra Profile (MSP) database and validate the method using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for rapid identification of fish bacterial pathogens. Streptococcus agalactiae, Streptococcus iniae, Aeromonas hydrophila, Aeromonas veronii, and Edwardsiella tarda obtained from diseased fish were used as representative bacterial pathogens in this study. Bacterial peptides were extracted to create a Main Spectra Profile (MSP), and the MSPs of each bacterial species was added into the MALDI Biotyper database. Fifteen additional isolates of each bacterial species were tested to validate the utilized technique. Results The MSPs of all field isolates were clearly distinguishable, and the MSPs of the same species were clustered together. The identification methodology was validated with 75 bacterial isolates. The reliability and specificity of the method were determined with MALDI Biotyper log score values and matching results with 16 s rDNA sequencing. The species identification using the public MALDI Biotyper library (Bruker MALDI Biotyper) showed unreliable results (log score < 2.000) with 42.67% matching result with the reference method. In contrast, accurate identification was obtained when using the custom-made database, giving log score > 2.115, and a 100% matching result. Conclusion This study demonstrates an effective identification of fish bacterial pathogens when a complete custom-made MSP database is applied. Further applications require a broad, well-established database to accommodate prudent identification of many fish bacterial pathogens by MALDI-TOF MS.
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Affiliation(s)
- Patharapol Piamsomboon
- Department of Veterinary Medicine, Faculty of Veterinary Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Janthima Jaresitthikunchai
- Proteomics Research Laboratory, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Tran Quang Hung
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25, Vodňany, Czech Republic
| | - Sittiruk Roytrakul
- Proteomics Research Laboratory, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Janenuj Wongtavatchai
- Department of Veterinary Medicine, Faculty of Veterinary Sciences, Chulalongkorn University, Bangkok, Thailand.
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14
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Lellman SE, Cramer R. Bacterial identification by lipid profiling using liquid atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry. ACTA ACUST UNITED AC 2019; 58:930-938. [DOI: 10.1515/cclm-2019-0908] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/25/2019] [Indexed: 12/16/2022]
Abstract
Abstract
Background
In recent years, mass spectrometry (MS) has been applied to clinical microbial biotyping, exploiting the speed of matrix-assisted laser desorption/ionization (MALDI) in recording microbe-specific MS profiles. More recently, liquid atmospheric pressure (AP) MALDI has been shown to produce extremely stable ion flux from homogenous samples and ‘electrospray ionization (ESI)-like’ multiply charged ions for larger biomolecules, whilst maintaining the benefits of traditional MALDI including high tolerance to contaminants, low analyte consumption and rapid analysis. These and other advantages of liquid AP-MALDI MS have been explored in this study to investigate its potential in microbial biotyping.
Methods
Genetically diverse bacterial strains were analyzed using liquid AP-MALDI MS, including clinically relevant species such as Escherichia coli, Staphylococcus aureus and Klebsiella pneumoniae. Bacterial cultures were subjected to a simple and fast extraction protocol using ethanol and formic acid. Extracts were spotted with a liquid support matrix (LSM) and analyzed using a Synapt G2-Si mass spectrometer with an in-house built AP-MALDI source.
Results
Each species produces a unique lipid profile in the m/z range of 400–1100, allowing species discrimination. Traditional (solid) MALDI MS produced spectra containing a high abundance of matrix-related clusters and an absence of lipid peaks. The MS profiles of the bacterial species tested form distinct clusters using principle component analysis (PCA) with a classification accuracy of 98.63% using a PCA-based prediction model.
Conclusions
Liquid AP-MALDI MS profiles can be sufficient to distinguish clinically relevant bacterial pathogens and other bacteria, based on their unique lipid profiles. The analysis of the lipid MS profiles is typically excluded from commercial instruments approved for clinical diagnostics.
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Affiliation(s)
- Sophie E. Lellman
- Department of Chemistry , University of Reading , Whiteknights, Reading , UK
| | - Rainer Cramer
- Department of Chemistry , University of Reading , Whiteknights, Reading , UK
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15
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Multidrug-resistant Gram-negative Bacterial Bloodstream Infections in Children's Hospitals in Japan, 2010-2017. Pediatr Infect Dis J 2019; 38:653-659. [PMID: 30672891 DOI: 10.1097/inf.0000000000002273] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND The risk factors of multidrug-resistant (MDR) Gram-negative bacilli (GNB) bloodstream infection (BSI) are not yet known in children. Our aim was to evaluate risk factors and outcomes associated with MDR GNB BSI in children. METHODS Patients with GNB BSI were enrolled between April 2010 and March 2017 at 8 children's hospitals in Japan. Clinical and microbiologic data were collected retrospectively. The risk factors and outcomes of MDR and non-MDR GNB BSI were compared. RESULTS In total, 629 GNB BSI episodes met the case definition. The median age and proportion of males were 2 years (interquartile range, 0.3-8.7) and 50.7%, respectively. An underlying disease was found in 94% of patients. The proportion of BSI cases that developed >48 hours after admission was 76.2%. MDR comprised 24.5% of BSI cases. The MDR rate did not change over time (P = 0.540). The effective coverage rate of the initial empiric therapy for the MDR and non-MDR BSI cases was 60.4% and 83.4%, respectively (P < 0.001). The all-cause mortality rate at 28 days for all BSI, MDR-BSI and non-MDR BSI cases was 10.7%, 13.6% and 9.7%, respectively (P = 0.167). MDR BSI was independently associated with cancer chemotherapy within 30 days (odds ratio [OR] 43.90), older age (OR 1.05) and admission to the neonatal ward (OR 0.019). CONCLUSIONS One-fourth of GNB BSI cases were MDR. Cancer chemotherapy and older age were risk factors for MDR GNB BSI in children's hospitals. MDR did not increase the all-cause mortality rate.
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16
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Feucherolles M, Poppert S, Utzinger J, Becker SL. MALDI-TOF mass spectrometry as a diagnostic tool in human and veterinary helminthology: a systematic review. Parasit Vectors 2019; 12:245. [PMID: 31101120 PMCID: PMC6525464 DOI: 10.1186/s13071-019-3493-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/06/2019] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has become a widely used technique for the rapid and accurate identification of bacteria, mycobacteria and certain fungal pathogens in the clinical microbiology laboratory. Thus far, only few attempts have been made to apply the technique in clinical parasitology, particularly regarding helminth identification. METHODS We systematically reviewed the scientific literature on studies pertaining to MALDI-TOF MS as a diagnostic technique for helminths (cestodes, nematodes and trematodes) of medical and veterinary importance. Readily available electronic databases (i.e. PubMed/MEDLINE, ScienceDirect, Cochrane Library, Web of Science and Google Scholar) were searched from inception to 10 October 2018, without restriction on year of publication or language. The titles and abstracts of studies were screened for eligibility by two independent reviewers. Relevant articles were read in full and included in the systematic review. RESULTS A total of 84 peer-reviewed articles were considered for the final analysis. Most papers reported on the application of MALDI-TOF for the study of Caenorhabditis elegans, and the technique was primarily used for identification of specific proteins rather than entire pathogens. Since 2015, a small number of studies documented the successful use of MALDI-TOF MS for species-specific identification of nematodes of human and veterinary importance, such as Trichinella spp. and Dirofilaria spp. However, the quality of available data and the number of examined helminth samples was low. CONCLUSIONS Data on the use of MALDI-TOF MS for the diagnosis of helminths are scarce, but recent evidence suggests a potential role for a reliable identification of nematodes. Future research should explore the diagnostic accuracy of MALDI-TOF MS for identification of (i) adult helminths, larvae and eggs shed in faecal samples; and (ii) helminth-related proteins that are detectable in serum or body fluids of infected individuals.
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Affiliation(s)
- Maureen Feucherolles
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation, Belvaux, Luxembourg
| | - Sven Poppert
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jürg Utzinger
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany.
- Swiss Tropical and Public Health Institute, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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17
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Hou TY, Chiang-Ni C, Teng SH. Current status of MALDI-TOF mass spectrometry in clinical microbiology. J Food Drug Anal 2019; 27:404-414. [PMID: 30987712 PMCID: PMC9296205 DOI: 10.1016/j.jfda.2019.01.001] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 01/11/2019] [Accepted: 01/18/2019] [Indexed: 11/16/2022] Open
Abstract
Mass spectrometry (MS) is a type of analysis used to determine what molecules make up a sample, based on the mass spectrum that are created by the ions. Mass spectrometers are able to perform traditional target analyte identification and quantitation; however, they may also be used within a clinical setting for the rapid identification of bacteria. The causative agent in sepsis is changed over time, and clinical decisions affecting the management of infections are often based on the outcomes of bacterial identification. Therefore, it is essential that such identifications are performed quickly and interpreted correctly. Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometer is one of the most popular MS instruments used in biology, due to its rapid and precise identification of genus and species of an extensive range of Gram-negative and-positive bacteria. Microorganism identification by Mass spectrometry is based on identifying a characteristic spectrum of each species and then matched with a large database within the instrument. The present review gives a contemporary perspective on the challenges and opportunities for bacterial identification as well as a written report of how technological innovation has advanced MS. Future clinical applications will also be addressed, particularly the use of MALDI-TOF MS in the field of microbiology for the identification and the analysis of antibiotic resistance.
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Affiliation(s)
- Tsung-Yun Hou
- Division of Rheumatology/Immunology/Allergy, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei,
Taiwan
- Division of Allergy, Immunology and Rheumatology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei,
Taiwan
- Division of Rheumatology/Immunology/Allergy, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei,
Taiwan
| | - Chuan Chiang-Ni
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan,
Taiwan
| | - Shih-Hua Teng
- Bruker Taiwan Co., Ltd., Taipei,
Taiwan
- Corresponding author. 4F, 107 Yanshou Street, Songshan District, Taipei City 105, Taiwan. Fax: +886 2 2761 5335. E-mail address: (S.-H. Teng)
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18
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Dieckmann R, Hammerl JA, Hahmann H, Wicke A, Kleta S, Dabrowski PW, Nitsche A, Stämmler M, Al Dahouk S, Lasch P. Rapid characterisation of Klebsiella oxytoca isolates from contaminated liquid hand soap using mass spectrometry, FTIR and Raman spectroscopy. Faraday Discuss 2018; 187:353-75. [PMID: 27053001 DOI: 10.1039/c5fd00165j] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Microbiological monitoring of consumer products and the efficiency of early warning systems and outbreak investigations depend on the rapid identification and strain characterisation of pathogens posing risks to the health and safety of consumers. This study evaluates the potential of three rapid analytical techniques for identification and subtyping of bacterial isolates obtained from a liquid hand soap product, which has been recalled and reported through the EU RAPEX system due to its severe bacterial contamination. Ten isolates recovered from two bottles of the product were identified as Klebsiella oxytoca and subtyped using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI TOF MS), near-infrared Fourier transform (NIR FT) Raman spectroscopy and Fourier transform infrared (FTIR) spectroscopy. Comparison of the classification results obtained by these phenotype-based techniques with outcomes of the DNA-based methods pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST) and single nucleotide polymorphism (SNP) analysis of whole-genome sequencing (WGS) data revealed a high level of concordance. In conclusion, a set of analytical techniques might be useful for rapid, reliable and cost-effective microbial typing to ensure safe consumer products and allow source tracking.
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Affiliation(s)
- Ralf Dieckmann
- Federal Institute for Risk Assessment, Department of Biological Safety, Max-Dohrn-Str. 8-10, D-10589 Berlin, Germany.
| | - Jens Andre Hammerl
- Federal Institute for Risk Assessment, Department of Biological Safety, Max-Dohrn-Str. 8-10, D-10589 Berlin, Germany.
| | - Hartmut Hahmann
- Landesamt für Verbraucherschutz Sachsen-Anhalt, Fachbereich Lebensmittelsicherheit, Freiimfelder Str. 68, D-06112 Halle, Germany
| | - Amal Wicke
- Landesamt für Verbraucherschutz Sachsen-Anhalt, Fachbereich Lebensmittelsicherheit, Freiimfelder Str. 68, D-06112 Halle, Germany
| | - Sylvia Kleta
- Federal Institute for Risk Assessment, Department of Biological Safety, Max-Dohrn-Str. 8-10, D-10589 Berlin, Germany.
| | | | - Andreas Nitsche
- Robert Koch-Institut, ZBS 1 - Highly Pathogenic Viruses, Seestraße 10, D-13353 Berlin, Germany
| | - Maren Stämmler
- Robert Koch-Institut, ZBS 6 - Proteomics and Spectroscopy, Seestraße 10, D-13353 Berlin, Germany
| | - Sascha Al Dahouk
- Federal Institute for Risk Assessment, Department of Biological Safety, Max-Dohrn-Str. 8-10, D-10589 Berlin, Germany.
| | - Peter Lasch
- Robert Koch-Institut, ZBS 6 - Proteomics and Spectroscopy, Seestraße 10, D-13353 Berlin, Germany
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19
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Wilson DA, Young S, Timm K, Novak-Weekley S, Marlowe EM, Madisen N, Lillie JL, Ledeboer NA, Smith R, Hyke J, Griego-Fullbright C, Jim P, Granato PA, Faron ML, Cumpio J, Buchan BW, Procop GW. Multicenter Evaluation of the Bruker MALDI Biotyper CA System for the Identification of Clinically Important Bacteria and Yeasts. Am J Clin Pathol 2017; 147:623-631. [PMID: 28505220 DOI: 10.1093/ajcp/aqw225] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVES A report on the multicenter evaluation of the Bruker MALDI Biotyper CA System (MBT-CA; Bruker Daltonics, Billerica, MA) for the identification of clinically important bacteria and yeasts. METHODS In total, 4,399 isolates of medically important bacteria and yeasts were assessed in the MBT-CA. These included 2,262 aerobic gram-positive (AGP) bacteria, 792 aerobic gram-negative (AGN) bacteria 530 anaerobic (AnA) bacteria, and 815 yeasts (YSTs). Three processing methods were assesed. RESULTS Overall, 98.4% (4,329/4,399) of all bacterial and yeast isolates were correctly identified to the genus and species/species complex level, and 95.7% of isolates were identified with a high degree of confidence. The percentage correctly identified and the percentage identified correctly with a high level of confidence, respectively, were as follows: AGP bacteria (98.6%/96.5%), AGN bacteria (98.5%/96.8%), AnA bacteria (98.5%/97.4%), and YSTs (97.8%/87.6%). The extended direct transfer method was only minimally superior to the direct transfer method for bacteria (89.9% vs 86.8%, respectively) but significantly superior for yeast isolates (74.0% vs 48.9%, respectively). CONCLUSIONS The Bruker MALDI Biotyper CA System accurately identifies most clinically important bacteria and yeasts and has optional processing methods to improve isolate characterization.
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Affiliation(s)
| | - Stephen Young
- Tricore Reference Laboratories, Albuquerque, NM
- Department of Pathology, The University of New Mexico Health Sciences Center, Albuquerque
| | - Karen Timm
- Tricore Reference Laboratories, Albuquerque, NM
| | - Susan Novak-Weekley
- Kaiser Permanente Southern California Permanente Medical Group Regional Reference Laboratories, North Hollywood, CA
| | - Elizabeth M Marlowe
- Kaiser Permanente Southern California Permanente Medical Group Regional Reference Laboratories, North Hollywood, CA
| | | | | | - Nathan A Ledeboer
- Wisconsin Diagnostic Laboratory, Milwaukee
- Medical College of Wisconsin, Milwaukee
| | | | - Josh Hyke
- Wisconsin Diagnostic Laboratory, Milwaukee
| | | | | | - Paul A Granato
- Laboratory Alliance of Central New York, Fayetteville
- SUNY Upstate Medical University, Syracuse, NY
| | | | - Joven Cumpio
- Kaiser Permanente Southern California Permanente Medical Group Regional Reference Laboratories, North Hollywood, CA
| | - Blake W Buchan
- Wisconsin Diagnostic Laboratory, Milwaukee
- Medical College of Wisconsin, Milwaukee
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20
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Klont F, Ten Hacken NHT, Horvatovich P, Bakker SJL, Bischoff R. Assuring Consistent Performance of an Insulin-Like Growth Factor 1 MALDImmunoassay by Monitoring Measurement Quality Indicators. Anal Chem 2017; 89:6188-6195. [PMID: 28467045 PMCID: PMC5463271 DOI: 10.1021/acs.analchem.7b01125] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Analytical
methods based on mass spectrometry (MS) have been successfully
applied in biomarker discovery studies, while the role of MS in translating
biomarker candidates to clinical diagnostics is less pronounced. MALDImmunoassays—methods
that combine immunoaffinity enrichment with matrix-assisted laser
desorption ionization time-of-flight (MALDI-TOF) mass spectrometric
detection—are attractive analytical approaches for large-scale
sample analysis by virtue of their ease of operation and high-throughput
capabilities. Despite this fact, MALDImmunoassays are not widely used
in clinical diagnostics, which is mainly due to the limited availability
of internal standards that can adequately correct for variability
in sample preparation and the MALDI process itself. Here we present
a novel MALDImmunoassay for quantification of insulin-like growth
factor 1 (IGF1) in human plasma. Reliable IGF1 quantification in the
range of 10–1000 ng/mL was achieved by employing 15N-IGF1 as internal standard, which proved to be an essential feature
of the IGF1 MALDImmunoassay. The method was validated according to
U.S. Food and Drug Administration (FDA) guidelines, which included
demonstrating the effectiveness of IGF1/IGF binding protein (IGF1/IGFBP)
complex dissociation using sodium dodecyl sulfate (SDS). Furthermore,
the MALDImmunoassay compared well with the IDS-iSYS IGF1 immunoassay
with high correlation (R2 = 0.99), although
substantially lower levels were reported by the MALDImmunoassay. The
method was tested on >1000 samples from a cohort of renal transplant
recipients to assess its performance in a clinical setting. On the
basis of this study, we identified readouts to monitor the quality
of the measurements. Our work shows that MALDI-TOF mass spectrometry
is suitable for quantitative biomarker analysis provided that an appropriate
internal standard is used and that readouts are monitored to assess
the quality of the measurements.
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Affiliation(s)
- Frank Klont
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | | | - Péter Horvatovich
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | | | - Rainer Bischoff
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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Abstract
In the last decade mass spectrometry imaging has developed rapidly, in terms of multiple new instrumentation innovations, expansion of target molecules, and areas of application. Mass spectrometry imaging has already had a substantial impact in cancer research, uncovering biomolecular changes associated with disease progression, diagnosis, and prognosis. Many new approaches are incorporating the use of readily available formalin-fixed paraffin-embedded cancer tissues from pathology centers, including tissue blocks, biopsy specimens, and tumor microarrays. It is also increasingly used in drug formulation development as an inexpensive method to determine the distributions of drugs and their metabolites. In this chapter, we offer a perspective in the current and future methodological developments and how these may open up new vistas for cancer research.
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Alsalhi MS, Devanesan S, Alfuraydi AA, Vishnubalaji R, Munusamy MA, Murugan K, Nicoletti M, Benelli G. Green synthesis of silver nanoparticles using Pimpinella anisum seeds: antimicrobial activity and cytotoxicity on human neonatal skin stromal cells and colon cancer cells. Int J Nanomedicine 2016; 11:4439-4449. [PMID: 27660438 PMCID: PMC5019319 DOI: 10.2147/ijn.s113193] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The present study focused on a simple and eco-friendly method for the synthesis of silver nanoparticles (AgNPs) with multipurpose anticancer and antimicrobial activities. MATERIALS AND METHODS We studied a green synthesis route to produce AgNPs by using an aqueous extract of Pimpinella anisum seeds (3 mM). Their antimicrobial activity and cytotoxicity on human neonatal skin stromal cells (hSSCs) and colon cancer cells (HT115) were assessed. RESULTS A biophysical characterization of the synthesized AgNPs was realized: the morphology of AgNPs was determined by transmission electron microscopy, energy dispersive spectroscopy, X-ray powder diffraction, and ultraviolet-vis absorption spectroscopy. Transmission electron microscopy showed spherical shapes of AgNPs of P. anisum seed extracts with a 3.2 nm minimum diameter and average diameter ranging from 3.2 to 16 nm. X-ray powder diffraction highlighted the crystalline nature of the nanoparticles, ultraviolet-vis absorption spectroscopy was used to monitor their synthesis, and Fourier transform infrared spectroscopy showed the main reducing groups from the seed extract. Energy dispersive spectroscopy was used to confirm the presence of elemental silver. We evaluated the antimicrobial potential of green-synthesized AgNPs against five infectious bacteria: Staphylococcus pyogenes (29213), Acinetobacter baumannii (4436), Klebsiella pneumoniae (G455), Salmonella typhi, and Pseudomonas aeruginosa. In addition, we focused on the toxicological effects of AgNPs against hSSC cells and HT115 cells by using in vitro proliferation tests and cell viability assays. Among the different tested concentrations of nanoparticles, doses < 10 µg showed few adverse effects on cell proliferation without variations in viability, whereas doses >10 µg led to increased cytotoxicity. CONCLUSION Overall, our results highlighted the capacity of P. anisum-synthesized AgNPs as novel and cheap bioreducing agents for eco-friendly nanosynthetical routes. The data confirm the multipurpose potential of plant-borne reducing and stabilizing agents in nanotechnology.
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Affiliation(s)
- Mohamad S Alsalhi
- Research Chair in Laser Diagnosis of Cancers
- Department of Physics and Astronomy
| | | | | | - Radhakrishnan Vishnubalaji
- Stem Cell Unit, Department of Anatomy, College of Medicine, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | | | - Kadarkarai Murugan
- Divisionof Entomology, Department of Zoology, School of Life Sciences, Bharathiar University, Coimbatore, India
| | | | - Giovanni Benelli
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
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Angeletti S. Matrix assisted laser desorption time of flight mass spectrometry (MALDI-TOF MS) in clinical microbiology. J Microbiol Methods 2016; 138:20-29. [PMID: 27613479 DOI: 10.1016/j.mimet.2016.09.003] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 09/01/2016] [Accepted: 09/03/2016] [Indexed: 10/21/2022]
Abstract
The microbiological management of patients with suspected bacterial infection includes the identification of the pathogen and the determination of the antibiotic susceptibility. These traditional approaches, based on the pure culture of the microorganism, require at least 36-48h. A new method, Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS), has been recently developed to profile bacterial proteins from whole cell extracts and obtain a bacterial fingerprint able to discriminate microorganisms from different genera and species. By whole cell-mass spectrometry, microbial identification can be achieved within minutes from cultured isolate, rather than traditional phenotypic or genotypic characterizations. From the year 2009 an explosion of applications of this technology has been observed with promising results. Several studies have been performed and showed that MALDI-TOF represents a reliable alternative method for rapid bacteria and fungi identification in clinical setting. A future area of expansion is represented by the application of MALDI-TOF technology to the antibiotic susceptibility test. In conclusion, the revision of the literature available up to date demonstrated that MALDI-TOF MS represents an innovative technology for the rapid and accurate identification of bacterial and fungal isolates in clinical settings. By an earlier microbiological diagnosis, MALDI-TOF MS contributes to a reduced mortality and hospitalization time of the patients and consequently has a significant impact on cost savings and public health.
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Affiliation(s)
- Silvia Angeletti
- Clinical Pathology and Microbiology Unit, University Campus Bio-Medico of Rome, Italy.
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24
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Fleurbaaij F, Kraakman MEM, Claas ECJ, Knetsch CW, van Leeuwen HC, van der Burgt YEM, Veldkamp KE, Vos MC, Goessens W, Mertens BJ, Kuijper EJ, Hensbergen PJ, Nicolardi S. Typing Pseudomonas aeruginosa Isolates with Ultrahigh Resolution MALDI-FTICR Mass Spectrometry. Anal Chem 2016; 88:5996-6003. [PMID: 27123572 DOI: 10.1021/acs.analchem.6b01037] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The introduction of standardized matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) platforms in the medical microbiological practice has revolutionized the way microbial species identification is performed on a daily basis. To a large extent, this is due to the ease of operation. Acquired spectra are compared to profiles obtained from cultured colonies present in a reference spectra database. It is fast and reliable, and costs are low compared to previous diagnostic approaches. However, the low resolution and dynamic range of the MALDI-TOF profiles have shown limited applicability for the discrimination of different bacterial strains, as achieved with typing based on genetic markers. This is pivotal in cases where certain strains are associated with, e.g., virulence or antibiotic resistance. Ultrahigh resolution MALDI-FTICR MS allows the measurement of small proteins at isotopic resolution and can be used to analyze complex mixtures with increased dynamic range and higher precision than MALDI-TOF MS, while still generating results in a similar time frame. Here, we propose to use ultrahigh resolution 15T MALDI-Fourier transform ion cyclotron resonance (FTICR) MS to discriminate clinically relevant bacterial strains after species identification performed by MALDI-TOF MS. We used a collection of well characterized Pseudomonas aeruginosa strains, featuring distinct antibiotic resistance profiles, and isolates obtained during hospital outbreaks. Following cluster analysis based on amplification fragment length polymorphism (AFLP), these strains were grouped into three different clusters. The same clusters were obtained using protein profiles generated by MALDI-FTICR MS. Subsequent intact protein analysis by electrospray ionization (ESI)-collision-induced dissociation (CID)-FTICR MS was applied to identify protein isoforms that contribute to the separation of the different clusters, illustrating the additional advantage of this analytical platform.
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Affiliation(s)
- Frank Fleurbaaij
- Department of Medical Microbiology, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
| | - Margriet E M Kraakman
- Department of Medical Microbiology, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
| | - Eric C J Claas
- Department of Medical Microbiology, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
| | - Cornelis W Knetsch
- Department of Medical Microbiology, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
| | - Hans C van Leeuwen
- Department of Medical Microbiology, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
| | - Yuri E M van der Burgt
- Center for Proteomics and Metabolomics, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
| | - Karin Ellen Veldkamp
- Department of Medical Microbiology, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
| | - Margreet C Vos
- Department of Medical Microbiology and Infectious Disease, Erasmus MC , 3015 CN Rotterdam, The Netherlands
| | - Wil Goessens
- Department of Medical Microbiology and Infectious Disease, Erasmus MC , 3015 CN Rotterdam, The Netherlands
| | - Bart J Mertens
- Department of Medical Statistics, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
| | - Paul J Hensbergen
- Center for Proteomics and Metabolomics, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
| | - Simone Nicolardi
- Center for Proteomics and Metabolomics, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
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