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Üstükarcı H, Ozyilmaz G, Ozyilmaz AT. Marine antifouling properties of enzyme modified polyaniline coated stainless steel surface. Enzyme Microb Technol 2024; 172:110340. [PMID: 37857080 DOI: 10.1016/j.enzmictec.2023.110340] [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: 07/02/2023] [Revised: 09/27/2023] [Accepted: 10/04/2023] [Indexed: 10/21/2023]
Abstract
On solid surfaces immersed in a liquid medium, a biofilm layer which is called biofouling formed over time by organic molecules and microorganisms. It is important to produce new eco-friendly ideas can prevent this undesired phenome. In this study, we focused on the antifouling performance of polyaniline (PANI), whose anticorrosive properties have been already known. The main purpose of this study was to immobilize hydrolytic enzymes that could break down biomolecules and microorganisms and how this would contribute to the antifouling performance of the PANI coating. When α-amylase, DNAse, glucose oxidase, α-chymotrypsin, lipase and pectinase enzymes immobilized into PANI that was synthesized in ammonium oxalate (PANIAO) and sodium salicylate (PANISS) electrolytes, α-amylase containing film (PANISS-A) showed the highest performance (76.5% antifouling activity). The surface properties after keeping in the Mediterranean Sea for 12 days were compared by digital photography, Scanning Electron microscope (SEM) and fluorescence microscope images, also with Energy Dispersive X-Ray (EDX) analysis and crystal violet staining. Carbohydrate and protein amounts and CFU (Colony Forming Units) values of biofilms formed on the surface for bare, PANISS and PANISS-A coupons after keeping 12 days in the Mediterranean Sea were determined. Vibrio species (V.harveyi, V.alginolyticus, V.parahaemolyticus) were detected in the biofilms by Matrix- Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) analysis.
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Affiliation(s)
- Handan Üstükarcı
- University of Hatay Mustafa Kemal, Faculty of Arts & Sciences, Department of Chemistry, 31040 Hatay, Turkey
| | - Gul Ozyilmaz
- University of Hatay Mustafa Kemal, Faculty of Arts & Sciences, Department of Chemistry, 31040 Hatay, Turkey.
| | - Ali Tuncay Ozyilmaz
- University of Hatay Mustafa Kemal, Faculty of Arts & Sciences, Department of Chemistry, 31040 Hatay, Turkey
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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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Sharaf PH, El Backly RM, Sherif RA, Zaazou AM, Hafez SF. Microbial identification from traumatized immature permanent teeth with periapical lesions using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. BMC Oral Health 2022; 22:661. [PMID: 36587207 PMCID: PMC9805193 DOI: 10.1186/s12903-022-02562-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/03/2022] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND This study aims at identifying the microbiota in traumatized immature permanent teeth with periapical lesions using Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). METHODS The study included 16 immature maxillary central incisors with periapical lesions in 13 patients. Field decontamination and negative control samples were performed before and after access cavity preparation. Root canal samples were taken using sterile stainless-steel hand files following field decontamination. In-office inoculation and pure sub-cultures were performed. Bacterial isolates were prepared for MALDI-TOF MS (Bruker, Billerica, MA USA) analysis using the formic acid extraction method. A comparison of the prevalence of isolated microorganisms was done using a one-sample chi-square test. Comparisons between identified microbial species with the, cone beam computed tomography periapical index (CBCT PAI) scores and lesion volume were also conducted. The Chi-square test was applied to investigate the association between the categorical variables . RESULTS Out of the forty isolates recovered from the 16 traumatized teeth included in the present study with the mean patients' age of 10.93 ± 1.77, 37 isolates were reliably identified by MALDI-TOF MS. Twelve teeth (62.5%) were polymicrobial. The recovered bacteria belonged to five phyla, 15 genera and 25 species. Firmicutes were the predominant phylum (P < 0.001) over Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria. Gram positive bacteria were significantly more prevalent than Gram negative (p = 0.03). Facultative anaerobes were the most prevalent (P < 0.001) compared to the obligate anaerobes and the obligate aerobes. The latter were the least prevalent. Statistically, significant differences existed in the comparison between CBCT PAI scores according to bacterial gram staining. CONCLUSION Traumatized immature permanent teeth with periapical lesions showed a significant predominance of Gram-positive facultative anaerobes. MALDI-TOF MS provided accurate identification of numerous viable endodontic microbes.
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Affiliation(s)
- Pervine H. Sharaf
- grid.7155.60000 0001 2260 6941Conservative Dentistry Department, Faculty of Dentistry, Alexandria University, Alexandria, Egypt, Endodontic Specialist, Ministry of Health, Alexandria, Egypt
| | - Rania M. El Backly
- grid.7155.60000 0001 2260 6941Endodontics, Conservative Dentistry Department, Faculty of Dentistry, Alexandria University, Alexandria, Egypt
| | - Raef A. Sherif
- grid.7155.60000 0001 2260 6941Endodontics, Conservative Dentistry Department, Faculty of Dentistry, Alexandria University, Alexandria, Egypt
| | - Ashraf M. Zaazou
- grid.7155.60000 0001 2260 6941Endodontics, Conservative Dentistry Department, Faculty of Dentistry, Alexandria University, Alexandria, Egypt ,Faculty of Dentistry, King Abdel Aziz University, Jeddah, Saudi Arabia
| | - Soad F. Hafez
- grid.7155.60000 0001 2260 6941Medical Microbiology and Immunology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
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Feucherolles M, Frache G. MALDI Mass Spectrometry Imaging: A Potential Game-Changer in a Modern Microbiology. Cells 2022; 11:cells11233900. [PMID: 36497158 PMCID: PMC9738593 DOI: 10.3390/cells11233900] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/11/2022] Open
Abstract
Nowadays, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is routinely implemented as the reference method for the swift and straightforward identification of microorganisms. However, this method is not flawless and there is a need to upgrade the current methodology in order to free the routine lab from incubation time and shift from a culture-dependent to an even faster independent culture system. Over the last two decades, mass spectrometry imaging (MSI) gained tremendous popularity in life sciences, including microbiology, due to its ability to simultaneously detect biomolecules, as well as their spatial distribution, in complex samples. Through this literature review, we summarize the latest applications of MALDI-MSI in microbiology. In addition, we discuss the challenges and avenues of exploration for applying MSI to solve current MALDI-TOF MS limits in routine and research laboratories.
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Rajpal N, Ratan JK, Divya N, Hebbani AV. Bioremediation of greywater using a novel bacterial-fungal consortium: optimization and validation of the operating parameters in vitro. ENVIRONMENTAL TECHNOLOGY 2022; 43:2430-2442. [PMID: 33502283 DOI: 10.1080/09593330.2021.1882582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 01/22/2021] [Indexed: 06/12/2023]
Abstract
In the present study, removal of pollutants in greywater was investigated using a novel bacterial-fungal consortium. Response surface methodology was used for the optimization of process variables like pH, temperature, inoculum size, and Carbon/Nitrogen (C/N ratio) for degradation of pollutants. Experiments were based on Box Behnken statistical design and the results show a good fit with the quadratic model, coefficient of determination (R2) value of 0.9499. The reliability of the model was established by various statistical parameters like lack of fit, pure error, and residual sum of squares. The optimized conditions for maximum reduction in chemical oxygen demand, oil & grease and sulphate were found to be 78.7%, 82.6% and 89.7%, respectively after 96 h of incubation of the reaction mixture at pH 7; temperature 35°C; inoculum size 150 µl and C/N ratio of 1:2. Our results clearly demonstrate that the developed novel bacterial-fungal consortium can be a cost-effective, safe, and environment-friendly alternative for remediation of greywater.
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Affiliation(s)
- Nikita Rajpal
- Department of Chemical Engineering, Dr. B.R. Ambedkar National Institute of Technology, Jalandhar, India
| | - Jatinder K Ratan
- Department of Chemical Engineering, Dr. B.R. Ambedkar National Institute of Technology, Jalandhar, India
| | - Neetu Divya
- Department of Chemical Engineering, Dr. B.R. Ambedkar National Institute of Technology, Jalandhar, India
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Ryu SY. Likelihood-based bacterial identification approach for bimicrobial mass spectrometry data. Ann Appl Stat 2022. [DOI: 10.1214/21-aoas1520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- So Young Ryu
- School of Public Health, University of Nevada, Reno
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Re-classification of Streptomyces venezuelae strains and mining secondary metabolite biosynthetic gene clusters. iScience 2021; 24:103410. [PMID: 34877485 PMCID: PMC8627960 DOI: 10.1016/j.isci.2021.103410] [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: 07/07/2021] [Revised: 09/05/2021] [Accepted: 11/04/2021] [Indexed: 11/20/2022] Open
Abstract
Streptomyces species have attracted considerable interest as a reservoir of medically important secondary metabolites, which are even diverse and different between strains. Here, we reassess ten Streptomyces venezuelae strains by presenting the highly resolved classification, using 16S rRNA sequencing, MALDI-TOF MS protein profiling, and whole-genome sequencing. The results revealed that seven of the ten strains were misclassified as S. venezuelae species. Secondary metabolite biosynthetic gene cluster (smBGC) mining and targeted LC-MS/MS based metabolite screening of S. venezuelae and misclassified strains identified in total 59 secondary metabolites production. In addition, a comparison of pyrrolamide-type antibiotic BGCs of four misclassified strains, followed by functional genomics, revealed that athv28 is critical in the synthesis of the anthelvencin precursor, 5-amino-3,4-dihydro-2H-pyrrole-2-carboxylate (ADPC). Our findings illustrate the importance of the accurate classification and better utilization of misclassified Streptomyces strains to discover smBGCs and their secondary metabolite products.
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Taguchi T, Ishikawa M, Ichikawa M, Tadenuma T, Hirakawa Y, Yoshino T, Maeda Y, Takeuchi H, Nojima D, Tanaami T, Matsunaga T, Tanaka T. Amplification-free detection of bacterial genes using a signaling probe-based DNA microarray. Biosens Bioelectron 2021; 194:113659. [PMID: 34571443 DOI: 10.1016/j.bios.2021.113659] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/31/2021] [Accepted: 09/20/2021] [Indexed: 11/29/2022]
Abstract
In this study, we developed a novel DNA microarray system that does not require fluorophore-labeling, amplification, or washing of the target nucleic acid fragments. Two types of DNA probes (so-called "signaling probes") labeled with a fluorescence dye (Cy3) and quencher molecule (BHQ2) were spotted on the DNA microarray such that fluorescent signals of Cy3 could be quenched by BHQ2 due to duplex formation between the probes. The addition of the target DNA or RNA fragments disrupted the duplex formed by the probes, resulting in the generation of fluorescence signals. We examined the assay conditions of the signaling probe-based DNA microarray, including the design of the probes, hybridization temperatures, and methods for fragmentation of target molecules. Since this approach does not require time-consuming processes, including labeling, amplification, and washing, the assay achieved specific detection of 16S rDNA and 16S rRNA extracted from Escherichia coli within 60 min, which was significantly rapid compared to conventional PCR-dependent DNA microarrays.
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Affiliation(s)
- Tomoyuki Taguchi
- Yokogawa Electric Corporation, 2-9-32, Naka-cho, Musashino-shi, Tokyo, 180-8750, Japan
| | - Machi Ishikawa
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Momoko Ichikawa
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Takashi Tadenuma
- Yokogawa Electric Corporation, 2-9-32, Naka-cho, Musashino-shi, Tokyo, 180-8750, Japan
| | - Yuko Hirakawa
- Yokogawa Electric Corporation, 2-9-32, Naka-cho, Musashino-shi, Tokyo, 180-8750, Japan; Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Tomoko Yoshino
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Yoshiaki Maeda
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Hiyori Takeuchi
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Daisuke Nojima
- Yokogawa Electric Corporation, 2-9-32, Naka-cho, Musashino-shi, Tokyo, 180-8750, Japan
| | - Takeo Tanaami
- Yokogawa Electric Corporation, 2-9-32, Naka-cho, Musashino-shi, Tokyo, 180-8750, Japan
| | - Tadashi Matsunaga
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan; Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15, Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Tsuyoshi Tanaka
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan.
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Topić Popović N, Kazazić SP, Bojanić K, Strunjak-Perović I, Čož-Rakovac R. Sample preparation and culture condition effects on MALDI-TOF MS identification of bacteria: A review. MASS SPECTROMETRY REVIEWS 2021. [PMID: 34642960 DOI: 10.1002/mas.21739] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an excellent tool for bacterial identification. It allows high throughput, sensitive and specific applications in clinical diagnostics and environmental research. Currently, there is no optimal standardized protocol for sample preparation and culture conditions to profile bacteria. The performance of MALDI-TOF MS is affected by several variables, such as sample preparation, culture media and culture conditions, incubation time/growth stage, incubation temperature, high salt content, blood in the culture media, and others. This review thus aims to clarify why a uniformed protocol is not plausible, to assess the effects these factors have on MALDI-TOF MS identification score, and discuss possible optimizations for its methodology, in relation to specific bacterial representatives and strain requirements.
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Affiliation(s)
- Natalija Topić Popović
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Centre of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
| | - Snježana P Kazazić
- Laboratory for Mass Spectrometry and Functional Proteomics, Ruđer Bošković Institute, Zagreb, Croatia
| | - Krunoslav Bojanić
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Centre of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ivančica Strunjak-Perović
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Centre of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
| | - Rozelindra Čož-Rakovac
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Centre of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
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Yu Z, Zhao C, Hu S, Zhang H, Li W, Zhang R, Luo Q, Yang H. MALDI-MS-based biomarker analysis of extracellular vesicles from human lung carcinoma cells. RSC Adv 2021; 11:25375-25380. [PMID: 35478925 PMCID: PMC9037017 DOI: 10.1039/d1ra04305f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/12/2021] [Indexed: 12/19/2022] Open
Abstract
Extracellular vesicles (EVs) are actively secreted by mammalian cells. They are increasingly recognized as promising circulating biomarkers of disease progression. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is currently one of the most powerful techniques for the rapid analysis of biological samples, especially for discovering biomarkers for disease diagnosis and prognosis. It is unclear what cell culture medium components and EV isolation methods are suitable for MALDI-TOF MS analysis. Using a human lung carcinoma cell line (A549), we investigated and optimized the critical experimental conditions for EVs' protein profiling by combining differential ultracentrifugation and MALDI-TOF MS. The results demonstrated that medium components and ultracentrifugation procedures to extract EVs played important roles in MS detection. Compared with EV-depleted serum and normal serum medium, conditioned medium with 2% fetal bovine serum in this study maintained cell proliferation and displayed significant protein profiling of EVs. RPS27A (ribosomal protein), which plays an essential role in mRNA translation and ribosome assembly for the differentiation of cancer cells, was detected from the EVs of lung cancer cells associated with cancer cell migration and invasion. We also found the known tumor diagnosis marker, which is S100A10_S100 calcium-binding protein A10. Therefore, MALDI-TOF MS-based EV analysis with optimized experimental protocols can contribute to future development of rapid screening techniques of protein biomarkers associated with early cancer diagnosis.
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Affiliation(s)
- Zitong Yu
- Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
| | - Chao Zhao
- Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
| | - Shi Hu
- Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
| | - Huitao Zhang
- Research Center for Medical Artificial Intelligence, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
| | - Wenbo Li
- Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
| | - Renjie Zhang
- Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
| | - Qian Luo
- Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
| | - Hui Yang
- Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China .,CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
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Kim E, Yang SM, Kim HY. Analysis of Cultivable Microbial Community during Kimchi Fermentation Using MALDI-TOF MS. Foods 2021; 10:foods10051068. [PMID: 34066045 PMCID: PMC8151656 DOI: 10.3390/foods10051068] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 04/28/2021] [Accepted: 05/08/2021] [Indexed: 12/31/2022] Open
Abstract
Kimchi, a traditional Korean fermented vegetable, has received considerable attention for its health-promoting effects. This study analyzes the cultivable microbial community in kimchi fermented at different temperatures using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to comprehensively understand the factors affecting the quality of kimchi. Of the 5204 strains isolated from kimchi, aligned with the in-house database, 4467 (85.8%) were correctly identified at the species level. The fermentation temperature affected the microbial community by varying the pH and acidity, which was mainly caused by temperature-dependent competition between the different lactic acid bacteria (LAB) species in kimchi. LAB, such as Levilactobacillus (Lb.) brevis and Lactiplantibacillus (Lpb.) plantarum associated with rancidity and tissue softening, proliferated faster at higher temperatures than at low temperature. In addition, LAB, such as Latilactobacillus (Lat.) sakei and Leuconostoc (Leu.) mesenteroides, which produce beneficial substances and flavor, were mainly distributed in kimchi fermented at 4 °C. This study shows as a novelty that MALDI-TOF MS is a robust and economically affordable method for investigating viable microbial communities in kimchi.
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Affiliation(s)
| | | | - Hae-Yeong Kim
- Correspondence: ; Tel.: +82-31-201-2600; Fax: +82-31-204-8116
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12
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Differentiation of Gastric Helicobacter Species Using MALDI-TOF Mass Spectrometry. Pathogens 2021; 10:pathogens10030366. [PMID: 33803832 PMCID: PMC8003121 DOI: 10.3390/pathogens10030366] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 02/07/2023] Open
Abstract
Gastric helicobacters (Helicobacter (H.) pylori and non-H. pylori Helicobacter species (NHPHs)) colonize the stomach of humans and/or animals. Helicobacter species identification is essential since many of them are recognized as human and/or animal pathogens. Currently, Helicobacter species can only be differentiated using molecular methods. Differentiation between NHPHs using MALDI-TOF MS has not been described before, probably because these species are poorly represented in current MALDI-TOF MS databases. Therefore, we identified 93 gastric Helicobacter isolates of 10 different Helicobacter species using MALDI-TOF MS in order to establish a more elaborate Helicobacter reference database. While the MALDI Biotyper database was not able to correctly identify any of the isolates, the in-house database correctly identified all individual mass spectra and resulted in 82% correct species identification based on the two highest log score matches (with log scores ≥2). In addition, a dendrogram was constructed using all newly created main spectrum profiles. Nine main clusters were formed, with some phylogenetically closely related Helicobacter species clustering closely together and well-defined subclusters being observed in specific species. Current results suggest that MALDI-TOF MS allows rapid differentiation between gastric Helicobacter species, provided that an extensive database is at hand and variation due to growth conditions and agar-medium-related peaks are taken into account.
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Lu JJ, Lo HJ, Lee CH, Chen MJ, Lin CC, Chen YZ, Tsai MH, Wang SH. The Use of MALDI-TOF Mass Spectrometry to Analyze Commensal Oral Yeasts in Nursing Home Residents. Microorganisms 2021; 9:microorganisms9010142. [PMID: 33435490 PMCID: PMC7828027 DOI: 10.3390/microorganisms9010142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/17/2020] [Accepted: 01/06/2021] [Indexed: 12/20/2022] Open
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a rapid and accurate method to identify microorganisms in clinical laboratories. This study isolates yeast-like microorganisms in the oral washes that are collected from non-bedridden nursing home residents, using CHROMagar Candida plates, and identifies them using Bruker MALDI-TOF MS. The ribosomal DNA sequences of the isolates are then examined. Three hundred and twenty yeast isolates are isolated from the oral washes. Candida species form the majority (78.1%), followed by Trichosporon/Cutaneotrichosporon species (8.8%). Bruker MALDI-TOF MS gives a high-level confidence, with a log(score) value of ≥1.8, and identifies 96.9% of the isolates. There are six inconclusive results (1.9%), and those sequences are verified as rare clinical species, including Candida ethanolica, Cutaneotrichosporon jirovecii, Exophiala dermatitidis, and Fereydounia khargensis. Almost all of the isolates have a regular color on the CHROMagar Candida plates. If the colonies are grouped by color on the plates, a specific dominant yeast species is present in each color group, except for purple or orange isolates. In conclusion, MALDI-TOF MS is verified as a fast, accurate and practical method to analyze oral yeasts in elderly subjects.
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Affiliation(s)
- Jang-Jih Lu
- Department of Laboratory Medicine, Chang-Gung Memorial Hospital Linkou, Taoyuan City 333, Taiwan; (J.-J.L.); (C.-H.L.); (M.-J.C.)
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan City 333, Taiwan
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan City 333, Taiwan
| | - Hsiu-Jung Lo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County 350, Taiwan; (H.-J.L.); (C.-C.L.); (Y.-Z.C.)
- School of Dentistry, China Medical University, Taichung City 404, Taiwan
| | - Chih-Hua Lee
- Department of Laboratory Medicine, Chang-Gung Memorial Hospital Linkou, Taoyuan City 333, Taiwan; (J.-J.L.); (C.-H.L.); (M.-J.C.)
| | - Mei-Jun Chen
- Department of Laboratory Medicine, Chang-Gung Memorial Hospital Linkou, Taoyuan City 333, Taiwan; (J.-J.L.); (C.-H.L.); (M.-J.C.)
- Division of Neonatology and Pediatric Hematology/Oncology, Department of Pediatrics, Chang Gung Memorial Hospital, Yunlin County 638, Taiwan;
| | - Chih-Chao Lin
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County 350, Taiwan; (H.-J.L.); (C.-C.L.); (Y.-Z.C.)
| | - Yin-Zhi Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County 350, Taiwan; (H.-J.L.); (C.-C.L.); (Y.-Z.C.)
| | - Ming-Horng Tsai
- Division of Neonatology and Pediatric Hematology/Oncology, Department of Pediatrics, Chang Gung Memorial Hospital, Yunlin County 638, Taiwan;
| | - Shao-Hung Wang
- Department of Microbiology, Immunology and Biopharmaceuticals, National Chiayi University, Chiayi City 600, Taiwan
- Correspondence: ; Tel.: +886-5-2717225; Fax: +886-5-2717831
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Monopoli A, Nacci A, Cataldi TRI, Calvano CD. Synthesis and Matrix Properties of α-Cyano-5-phenyl-2,4-pentadienic Acid (CPPA) for Intact Proteins Analysis by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. Molecules 2020; 25:molecules25246054. [PMID: 33371472 PMCID: PMC7767571 DOI: 10.3390/molecules25246054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 01/06/2023] Open
Abstract
The effectiveness of a synthesized matrix, α-cyano-5-phenyl-2,4-pentadienic acid (CPPA), for protein analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in complex samples such as foodstuff and bacterial extracts, is demonstrated. Ultraviolet (UV) absorption along with laser desorption/ionization mass spectrometry (LDI-MS) experiments were systematically conducted in positive ion mode under standard Nd:YLF laser excitation with the aim of characterizing the matrix in terms of wavelength absorption and proton affinity. Besides, the results for standard proteins revealed that CPPA significantly enhanced the protein signals, reduced the spot-to-spot variability and increased the spot homogeneity. The CPPA matrix was successful employed to investigate intact microorganisms, milk and seed extracts for protein profiling. Compared to conventional matrices such as sinapinic acid (SA), α-cyano-4-hydroxycinnamic acid (CHCA) and 4-chloro-α-cyanocinnamic acid (CClCA), CPPA exhibited better signal-to-noise (S/N) ratios and a uniform response for most examined proteins occurring in milk, hazelnut and in intact bacterial cells of E. coli. These findings not only provide a reactive proton transfer MALDI matrix with excellent reproducibility and sensitivity, but also contribute to extending the battery of useful matrices for intact protein analysis.
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Affiliation(s)
- Antonio Monopoli
- Agenzia delle Dogane e dei Monopoli, Ufficio delle Dogane di Bari, Corso De Tullio, 70122 Bari, Italy;
| | - Angelo Nacci
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Via Orabona, 70126 Bari, Italy; (A.N.); (T.R.I.C.)
| | - Tommaso R. I. Cataldi
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Via Orabona, 70126 Bari, Italy; (A.N.); (T.R.I.C.)
- Centro Interdipartimentale di Ricerca S.M.A.R.T., 70126 Bari, Italy
| | - Cosima D. Calvano
- Centro Interdipartimentale di Ricerca S.M.A.R.T., 70126 Bari, Italy
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, Via Orabona, 70126 Bari, Italy
- Correspondence:
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Rapid direct detection of pathogens for diagnosis of joint infections by MALDI-TOF MS after liquid enrichment in the BacT/Alert blood culture system. PLoS One 2020; 15:e0243790. [PMID: 33306699 PMCID: PMC7732097 DOI: 10.1371/journal.pone.0243790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/25/2020] [Indexed: 11/19/2022] Open
Abstract
Pathogen identification is a critical step during diagnosis of infectious diseases. Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight mass spectrometry (MALDI-TOF-MS) has become the gold standard for identification of microorganisms cultured on solid media in microbiology laboratories. Direct identification of microbes from liquid specimen, circumventing the need for the additional overnight cultivation step, has been successfully established for blood culture, urine and liquor. Here, we evaluate the ability of MALDI-TOF MS for direct identification of pathogens in synovial fluid after liquid enrichment in BacT/Alert blood culture bottles. Influence of synovial specimen quality on direct species identification with the MALDI BioTyper/Sepsityper was tested with samples inoculated from pretested native synovia with concomitant inoculation of blood or pus, or highly viscous fluid. Here, we achieved >90% concordance with culture on solid medium, and only mixed-species samples posed significant problems. Performance in routine diagnostics was tested prospectively on bottles inoculated by treating physicians on ward. There, we achieved >70% concordance with culture on solid media. The major contributors to test failure were the absence of a measurable mass signal and mixed-specimen samples. The Sepsityper workflow worked well on samples derived from BacT/Alert blood culture bottles inoculated with synovial fluid, giving concordant results to identification from solid media. Host remnant material in the inoculum, such as blood or pus, had no detrimental effect on identification score values of the BioTyper system after processing with the Sepsityper workflow, and neither had the initial viscosity of the synovial sample.
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Araújo TMC, Pereira RDCL, Freitag IGR, Rusak LA, Botelho LAB, Hofer E, Hofer CB, Vallim DC. Evaluation of MALDI-TOF MS as a tool for detection of Listeria spp. directly from selective enrichment broth from food and stool samples. J Microbiol Methods 2020; 173:105936. [PMID: 32360382 DOI: 10.1016/j.mimet.2020.105936] [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: 03/04/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 12/29/2022]
Abstract
We evaluated the detection of Listeria spp. using MALDI-TOF MS directly in enrichment broths, without isolated colonies, with naturally contaminated food and stool samples. The success rate was 77%. Considering the reduced time for diagnosis and the success rate, this is a promising screening tool, but more tests are needed to determine its viability.
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Affiliation(s)
- Thais Martins Campos Araújo
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Zoonoses Bacterianas/Setor Listeria, Rio de Janeiro/RJ, Brazil
| | | | | | - Leonardo Alves Rusak
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Fisiologia Bacteriana, Rio de Janeiro/RJ, Brazil
| | - Larissa Alvarenga Batista Botelho
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Prof. Paulo de Góes, Laboratório de Investigação em Microbiologia Médica, Rio de Janeiro/RJ, Brazil
| | - Ernesto Hofer
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Zoonoses Bacterianas/Setor Listeria, Rio de Janeiro/RJ, Brazil
| | - Cristina Barroso Hofer
- Universidade Federal do Rio de Janeiro, Programa de Pós-Graduação em Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Rio de Janeiro/RJ, Brazil
| | - Deyse Christina Vallim
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Zoonoses Bacterianas/Setor Listeria, Rio de Janeiro/RJ, Brazil.
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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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