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Tarfeen N, Nisa KU, Nisa Q. MALDI-TOF MS: application in diagnosis, dereplication, biomolecule profiling and microbial ecology. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2022. [PMCID: PMC9340741 DOI: 10.1007/s43538-022-00085-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized scientific research over the past few decades and has provided a unique platform in ongoing technological developments. Undoubtedly, there has been a bloom chiefly in the field of biological sciences with this emerging technology, and has enabled researchers to generate critical data in the field of disease diagnoses, drug development, dereplication. It has received well acceptance in the field of microbial identification even at strain level, as well as diversified field like biomolecule profiling (proteomics and lipidomics) has evolved tremendously. Additionally, this approach has received a lot more attention over conventional technologies due to its high throughput, speed, and cost effectiveness. This review aims to provide a detailed insight regarding the application of MALDI-TOF MS in the context of medicine, biomolecule profiling, dereplication, and microbial ecology. In general, the expansion in the application of this technology and new advancements it has made in the field of science and technology has been highlighted.
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Antibiotic and Heavy Metal Susceptibility of Non-Cholera Vibrio Isolated from Marine Sponges and Sea Urchins: Could They Pose a Potential Risk to Public Health? Antibiotics (Basel) 2021; 10:antibiotics10121561. [PMID: 34943773 PMCID: PMC8698511 DOI: 10.3390/antibiotics10121561] [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: 11/30/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 11/19/2022] Open
Abstract
Vibrio is an important human and animal pathogen that can carry clinically relevant antibiotic resistance genes and is present in different aquatic environments. However, there is a knowledge gap between antibiotic and heavy metal resistance and virulence potential when it is part of the microbiota from marine invertebrates. Here, we aimed to evaluate these characteristics and the occurrence of mobile genetic elements. Of 25 non-cholera Vibrio spp. from marine sponges and sea urchins collected at the coastlines of Brazil and France analyzed in this study, 16 (64%) were non-susceptible to antibiotics, and two (8%) were multidrug-resistant. Beta-lactam resistance (blaSHV) and virulence (vhh) genes were detected in sponge-associated isolates. The resistance gene for copper and silver (cusB) was detected in one sea urchin isolate. Plasmids were found in 11 (44%) of the isolates. This new information allows a better comprehension of antibiotic resistance in aquatic environments, since those invertebrates host resistant Vibrio spp. Thus, Vibrio associated with marine animals may pose a potential risk to public health due to carrying these antibiotic-resistant genes.
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Pinar-Méndez A, Fernández S, Baquero D, Vilaró C, Galofré B, González S, Rodrigo-Torres L, Arahal DR, Macián MC, Ruvira MA, Aznar R, Caudet-Segarra L, Sala-Comorera L, Lucena F, Blanch AR, Garcia-Aljaro C. Rapid and improved identification of drinking water bacteria using the Drinking Water Library, a dedicated MALDI-TOF MS database. WATER RESEARCH 2021; 203:117543. [PMID: 34433109 DOI: 10.1016/j.watres.2021.117543] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/23/2021] [Accepted: 08/07/2021] [Indexed: 06/13/2023]
Abstract
According to the European Directives (UE) 2020/2184 and 2009/54/EC, which establishes the sanitary criteria for water intended for human consumption in Europe, water suitable for human consumption must be free of the bacterial indicators Escherichia coli, Clostridium perfringens and Enterococcus spp. Drinking water is also monitored for heterotrophic bacteria, which are not a human health risk, but can serve as an index of bacteriological water quality. Therefore, a rapid, accurate, and cost-effective method for the identification of these colonies would improve our understanding of the culturable bacteria of drinking water and facilitate the task of water management by treatment facilities. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is potentially such a method, although most of the currently available mass spectral libraries have been developed in a clinical setting and have limited environmental applicability. In this work, a MALDI-TOF MS drinking water library (DWL) was defined and developed by targeting bacteria present in water intended for human consumption. This database, made up of 319 different bacterial strains, can contribute to the routine microbiological control of either treated drinking water or mineral bottled water carried out by water treatment and distribution operators, offering a faster identification rate compared to a clinical sample-based library. The DWL, made up of 96 bacterial genera, 44 of which are not represented in the MALDI-TOF MS bacterial Bruker Daltonics (BDAL) database, was found to significantly improve the identification of bacteria present in drinking water.
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Affiliation(s)
- Anna Pinar-Méndez
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, General Batet 1-7, Barcelona 08028, Spain; Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain.
| | - Sonia Fernández
- Cetaqua, Water technology center, Cornellà de Llobregat, Spain
| | - David Baquero
- Cetaqua, Water technology center, Cornellà de Llobregat, Spain
| | - Carles Vilaró
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, General Batet 1-7, Barcelona 08028, Spain
| | - Belén Galofré
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, General Batet 1-7, Barcelona 08028, Spain
| | - Susana González
- Cetaqua, Water technology center, Cornellà de Llobregat, Spain
| | - Lidia Rodrigo-Torres
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - David R Arahal
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - M Carmen Macián
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - María A Ruvira
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - Rosa Aznar
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - Laia Caudet-Segarra
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - Laura Sala-Comorera
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - Francisco Lucena
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - Anicet R Blanch
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain.
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AlMasoud N, Muhamadali H, Chisanga M, AlRabiah H, Lima CA, Goodacre R. Discrimination of bacteria using whole organism fingerprinting: the utility of modern physicochemical techniques for bacterial typing. Analyst 2021; 146:770-788. [DOI: 10.1039/d0an01482f] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review compares and contrasts MALDI-MS, FT-IR spectroscopy and Raman spectroscopy for whole organism fingerprinting and bacterial typing.
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Affiliation(s)
- Najla AlMasoud
- Department of Chemistry
- College of Science
- Princess Nourah bint Abdulrahman University
- Riyadh 11671
- Saudi Arabia
| | - Howbeer Muhamadali
- Department of Biochemistry and Systems Biology
- Institute of Systems
- Molecular and Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
| | - Malama Chisanga
- School of Chemistry and Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
| | - Haitham AlRabiah
- Department of Pharmaceutical Chemistry
- College of Pharmacy
- King Saud University
- Riyadh
- Saudi Arabia
| | - Cassio A. Lima
- Department of Biochemistry and Systems Biology
- Institute of Systems
- Molecular and Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology
- Institute of Systems
- Molecular and Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
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5
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Mougin J, Flahaut C, Roquigny R, Bonnin-Jusserand M, Grard T, Le Bris C. Rapid Identification of Vibrio Species of the Harveyi Clade Using MALDI-TOF MS Profiling With Main Spectral Profile Database Implemented With an In-House Database: Luvibase. Front Microbiol 2020; 11:586536. [PMID: 33162963 PMCID: PMC7581793 DOI: 10.3389/fmicb.2020.586536] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/17/2020] [Indexed: 12/02/2022] Open
Abstract
Vibrio bacteria, and particularly members of the Harveyi clade, are the causative agents of vibriosis. This disease is responsible for mass mortality events and important economic losses on aquaculture farms. Improvements in surveillance and diagnosis are needed to successfully manage vibriosis outbreaks. 16S rRNA gene sequencing is generally considered to be the gold standard for bacterial identification but the cost and long processing time make it difficult to apply for routine identification. In contrast, MALDI-TOF MS offers rapid diagnosis and is commonly used in veterinary laboratories today. The major limiting factor for using this technique is the low environmental bacterial diversity in the commonly available databases. Here, we demonstrate that the sole use of the commercially available Bruker BioTyper database is not fully adequate for identifying Vibrio bacteria isolated from aquaculture farms. We therefore developed a new in-house database named Luvibase, composed of 23 reference MALDI-TOF mass spectra profiles obtained from Vibrio collection strains, mostly belonging to the Harveyi clade. The comparison of the accuracy of MALDI-TOF MS profiling and 16S rRNA gene sequencing revealed a lack of resolution for 16S rRNA gene sequencing. In contrast, MALDI-TOF MS profiling proved to be a more reliable tool for resolving species-level variations within the Harveyi clade. Finally, combining the Luvibase with the Bruker ver.9.0.0.0 database, led to successful identification of 47 Vibrio isolates obtained from moribund abalone, seabass and oysters. Thus, the use of Luvibase allow for increased confidence in identifying Vibrio species belonging to the Harveyi clade.
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Affiliation(s)
- Julia Mougin
- Université du Littoral Côte d'Opale, UMR 1158 BioEcoAgro, Institut Charles Viollette, Unité Sous Contrat ANSES, INRAe, Université d'Artois, Université de Lille, Université de Picardie Jules Verne, Université de Liège, Yncréa, Boulogne-sur-Mer, France
| | - Christophe Flahaut
- Université du Littoral Côte d'Opale, UMR 1158 BioEcoAgro, Institut Charles Viollette, Unité Sous Contrat ANSES, INRAe, Université d'Artois, Université de Lille, Université de Picardie Jules Verne, Université de Liège, Yncréa, Boulogne-sur-Mer, France
| | - Roxane Roquigny
- Université du Littoral Côte d'Opale, UMR 1158 BioEcoAgro, Institut Charles Viollette, Unité Sous Contrat ANSES, INRAe, Université d'Artois, Université de Lille, Université de Picardie Jules Verne, Université de Liège, Yncréa, Boulogne-sur-Mer, France
| | - Maryse Bonnin-Jusserand
- Université du Littoral Côte d'Opale, UMR 1158 BioEcoAgro, Institut Charles Viollette, Unité Sous Contrat ANSES, INRAe, Université d'Artois, Université de Lille, Université de Picardie Jules Verne, Université de Liège, Yncréa, Boulogne-sur-Mer, France
| | - Thierry Grard
- Université du Littoral Côte d'Opale, UMR 1158 BioEcoAgro, Institut Charles Viollette, Unité Sous Contrat ANSES, INRAe, Université d'Artois, Université de Lille, Université de Picardie Jules Verne, Université de Liège, Yncréa, Boulogne-sur-Mer, France
| | - Cédric Le Bris
- Université du Littoral Côte d'Opale, UMR 1158 BioEcoAgro, Institut Charles Viollette, Unité Sous Contrat ANSES, INRAe, Université d'Artois, Université de Lille, Université de Picardie Jules Verne, Université de Liège, Yncréa, Boulogne-sur-Mer, France
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6
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Håkonsholm F, Lunestad BT, Aguirre Sánchez JR, Martinez‐Urtaza J, Marathe NP, Svanevik CS. Vibrios from the Norwegian marine environment: Characterization of associated antibiotic resistance and virulence genes. Microbiologyopen 2020; 9:e1093. [PMID: 32558371 PMCID: PMC7520990 DOI: 10.1002/mbo3.1093] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 05/20/2020] [Accepted: 05/27/2020] [Indexed: 12/19/2022] Open
Abstract
A total of 116 Vibrio isolates comprising V. alginolyticus (n = 53), V. metschnikovii (n = 38), V. anguillarum (n = 21), V. antiquarius (n = 2), and V. fujianensis (n = 2) were obtained from seawater, fish, or bivalve molluscs from temperate Oceanic and Polar Oceanic area around Norway. Antibiotic sensitivity testing revealed resistance or reduced susceptibility to ampicillin (74%), oxolinic acid (33%), imipenem (21%), aztreonam (19%), and tobramycin (17%). Whole-genome sequence analysis of eighteen drug-resistant isolates revealed the presence of genes like β-lactamases, chloramphenicol-acetyltransferases, and genes conferring tetracycline and quinolone resistance. The strains also carried virulence genes like hlyA, tlh, rtxA to D and aceA, E and F. The genes for cholerae toxin (ctx), thermostable direct hemolysin (tdh), or zonula occludens toxin (zot) were not detected in any of the isolates. The present study shows low prevalence of multidrug resistance and absence of virulence genes of high global concern among environmental vibrios in Norway. However, in the light of climate change, and projected rising sea surface temperatures, even in the cold temperate areas, there is a need for frequent monitoring of resistance and virulence in vibrios to be prepared for future public health challenges.
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Affiliation(s)
| | | | | | - Jaime Martinez‐Urtaza
- Department of Genetics and MicrobiologyUniversitat Autònoma de Barcelona (UAB)BarcelonaSpain
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7
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Ashfaq MY, Al-Ghouti MA, Qiblawey H, Rodrigues DF, Hu Y, Zouari N. Isolation, identification and biodiversity of antiscalant degrading seawater bacteria using MALDI-TOF-MS and multivariate analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 656:910-920. [PMID: 30625677 DOI: 10.1016/j.scitotenv.2018.11.477] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/30/2018] [Accepted: 11/30/2018] [Indexed: 06/09/2023]
Abstract
Seawater reverse osmosis (SWRO) is a commonly used desalination technique owing to its lesser environmental and economic impacts as compared to thermal desalination techniques. Antiscalants are used in SWRO to reduce membrane scaling caused by the supersaturation of salts present in feed water. However, to remain effective in reducing membrane scaling, antiscalants should be highly stable and resistant to biological degradation by seawater microorganisms. In this research, several bacteria from Qatar's seawater were isolated and screened for their ability to use antiscalants as a carbon and energy source. The biodiversity of antiscalant degrading seawater bacteria was demonstrated through combining the techniques of MALDI-TOF MS and principle component analysis. It was found that the bacteria isolated from Qatar's seawater such as H. aquamarina, H. elongata, P. fragi, P. stutzeri and others can degrade antiscalants and use them as a carbon and energy source. It was observed that the growth rates varied based on the type of antiscalant and the bacteria used. Among the tested strains, H. aquamarina, which is also known for its potential to cause biofouling, demonstrated the highest growth rates in antiscalants media. Thus, it was concluded that there is wide variety of bacteria in Qatar's seawater that can biodegrade the antiscalants; reducing their efficiency to combat membrane scaling. Since, these antiscalants will be used as a source of carbon and energy, microbial growth will increase resulting in enhanced membrane biofouling in SWRO.
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Affiliation(s)
- Mohammad Y Ashfaq
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box: 2713, Doha, Qatar
| | - Mohammad A Al-Ghouti
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box: 2713, Doha, Qatar.
| | - Hazim Qiblawey
- Department of Chemical Engineering, College of Engineering, Qatar University, P.O. Box: 2713, Doha, Qatar
| | - Debora F Rodrigues
- Department of Civil and Environmental Engineering, Cullen College of Engineering, University of Houston, Houston, TX, USA
| | - Yandi Hu
- Department of Civil and Environmental Engineering, Cullen College of Engineering, University of Houston, Houston, TX, USA
| | - Nabil Zouari
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box: 2713, Doha, Qatar
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8
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Bauer J, Teitge F, Neffe L, Adamek M, Jung A, Peppler C, Steinhagen D, Jung-Schroers V. Recommendations for identifying pathogenic Vibrio spp. as part of disease surveillance programmes in recirculating aquaculture systems for Pacific white shrimps (Litopenaeus vannamei). JOURNAL OF FISH DISEASES 2018; 41:1877-1897. [PMID: 30311657 DOI: 10.1111/jfd.12897] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
Due to their pathogenic potential, identifying Vibrio species from recirculating aquaculture systems (RAS) for Pacific white shrimp (Litopenaeus vannamei) is of great importance to determine the risk for animal's as well as for the consumer's health. The present study compared identification results for a total of 93 Vibrio isolates, including type strains and isolates from shrimp aquaculture. Results from biochemical identifications, 16S rRNA sequencing, sequencing of the uridylate kinase encoding gene pyrH and analysis of the protein spectra assessed by MALDI-TOF MS were compared. The results achieved by these different methods were highly divergent for many of the analysed isolates and for several Vibrio spp difficulties in reliably identifying occurred. These difficulties mainly resulted from missing entries in digital databases, a low number of comparable isolates analysed so far, and high interspecific similarities of biochemical traits and nucleotide sequences between the closely related Vibrio species. Due to the presented data, it can be concluded that for identifying Vibrio spp. from samples in routine diagnostics, it is recommended to use MALDI-TOF MS analysis for a quick and reliable identification of pathogenic Vibrio sp. Nevertheless, editing the database, containing the main spectra of Vibrio is recommended to achieve reliable identification results.
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Affiliation(s)
- Julia Bauer
- Fish Disease Research Unit, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Felix Teitge
- Fish Disease Research Unit, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Lisa Neffe
- Fish Disease Research Unit, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Mikolaj Adamek
- Fish Disease Research Unit, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Arne Jung
- Clinic for Poultry, University of Veterinary Medicine Hannover, Hannover, Germany
| | | | - Dieter Steinhagen
- Fish Disease Research Unit, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Verena Jung-Schroers
- Fish Disease Research Unit, University of Veterinary Medicine Hannover, Hannover, Germany
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9
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Li P, Xin W, Xia S, Luo Y, Chen Z, Jin D, Gao S, Yang H, Ji B, Wang H, Yan Y, Kang L, Wang J. MALDI-TOF mass spectrometry-based serotyping of V. parahaemolyticus isolated from the Zhejiang province of China. BMC Microbiol 2018; 18:185. [PMID: 30424744 PMCID: PMC6234682 DOI: 10.1186/s12866-018-1328-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 10/29/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Vibrio parahaemolyticus is as an important food-borne pathogen circulating in China. Since 1996, the core serotype has become O3:K6, which has specific genetic markers. This serotype causes the majority of outbreaks worldwide. Until now, nearly 21 serotypes were considered as serovariants of O3:K6. Among these, O4:K68, O1:K25 and O1:KUT have caused pandemic outbreaks. O4:K8, a serovariant of O3:K6, has become the second most dominant serotype circulating in China after O3:K6. In this study, we report the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze and characterize 146 V. parahaemolyticus isolates belonging to 23 serotypes. RESULTS Upon mass spectral analysis, isolates belonging to O4:K8 formed a distinct group among the five main pandemic groups (O3:K6, O4:K8, O4:K68, O1:K25 and O1:KUT). Two major protein peaks (m/z 4383 and 4397) were significantly different between serotype O4:K8 and the four other pandemic strains. Both of these peaks were present in 32 out of 36 O4:K8 isolates, but were absent in 105 out of 110 non-O4:K8 isolates. These peaks were also absent in all 74 pandemic serotypes (O3:K6, O4:K68, O1:K25 and O1:KUT). CONCLUSION Our results highlight the threat of O4:K8 forming a distinct group, which differs significantly from pandemic serotypes on the proteomic level. The use of MALDI-TOF MS has not been reported before in a study of this nature. Mass spectrum peaks at m/z 4383 and 4397 may be specific for O4:K8. However, we cannot conclude that MALDI-TOF MS can be used to serotype V. parahaemolyticus.
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Affiliation(s)
- Ping Li
- Graduate College, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, Anhui, China.,Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, No.486 Wenqiao Road, Nanhu district, Jiaxing, 314050, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China
| | - Wenwen Xin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China
| | - Susu Xia
- Graduate College, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, Anhui, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China
| | - Yun Luo
- Department of Microbiology, Zhejiang Province Center for Disease Control and Prevention, No.3399 Binsheng Road, Hangzhou, 310000, China
| | - Zhongwen Chen
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, No.486 Wenqiao Road, Nanhu district, Jiaxing, 314050, China
| | - Dazhi Jin
- Department of Microbiology, Zhejiang Province Center for Disease Control and Prevention, No.3399 Binsheng Road, Hangzhou, 310000, China
| | - Shan Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China
| | - Hao Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China
| | - Bin Ji
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China
| | - Henghui Wang
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, No.486 Wenqiao Road, Nanhu district, Jiaxing, 314050, China
| | - Yong Yan
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, No.486 Wenqiao Road, Nanhu district, Jiaxing, 314050, China
| | - Lin Kang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China.
| | - Jinglin Wang
- Graduate College, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, Anhui, China. .,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China.
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10
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Jang KS, Kim YH. Rapid and robust MALDI-TOF MS techniques for microbial identification: a brief overview of their diverse applications. J Microbiol 2018; 56:209-216. [PMID: 29492868 DOI: 10.1007/s12275-018-7457-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/23/2018] [Accepted: 01/24/2018] [Indexed: 10/25/2022]
Abstract
in mass spectrometry have enabled the investigation of various biological systems by directly analyzing diverse sets of biomolecules (i.e., proteins, lipids, and carbohydrates), thus making a significant impact on the life sciences field. Over the past decade, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been widely utilized as a rapid and reliable method for the identification of microorganisms. MALDI-TOF MS has come into widespread use despite its relatively low resolving power (full width at half maximum, FWHM: < 5,000) and its incompatibility with tandem MS analysis, features with which other high-resolution mass spectrometers are equipped. Microbial identification is achieved by searching databases containing mass spectra of peptides and proteins extracted from microorganisms of interest, using scoring algorithms to match analyzed spectra with reference spectra. In this paper, we give a brief overview of the diverse applications of rapid and robust MALDI-TOF MS-based techniques for microbial identification in a variety of fields, such as clinical diagnosis and environmental and food monitoring. We also describe the fundamental principles of MALDI-TOF MS. The general specifications of the two major MS-based microbial identification systems available in the global market (BioTyper® and VITEK® MS Plus) and the distribution of these instruments in Republic of Korea are also discussed. The current review provides an understanding of this emerging microbial identification and classification technology and will help bacteriologists and cell biologists take advantage of this powerful technique.
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Affiliation(s)
- Kyoung-Soon Jang
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea. .,Department of Bio-Analytical Science, University of Science and Technology, Daejeon, 34113, Republic of Korea.
| | - Young Hwan Kim
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea.,Department of Bio-Analytical Science, University of Science and Technology, Daejeon, 34113, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
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11
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Zhao H, Jia J, Chen Y, Tang J, Jiang Y, Wang J, Li Z, Zhao L. Strain-level characterization of cold-stressed Listeria monocytogenes
using maldi-tof mass fingerprinting. J Food Saf 2017. [DOI: 10.1111/jfs.12339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Han Zhao
- Technological Center; Shandong Entry-Exit Inspection and Quarantine Bureau; Qingdao China
| | - Juntao Jia
- Technological Center; Shandong Entry-Exit Inspection and Quarantine Bureau; Qingdao China
| | - Ying Chen
- Research Institute for Food Safety; Chinese Academy of Inspection and Quarantine; Beijing China
| | - Jing Tang
- Technological Center; Shandong Entry-Exit Inspection and Quarantine Bureau; Qingdao China
| | - Yinghui Jiang
- Technological Center; Shandong Entry-Exit Inspection and Quarantine Bureau; Qingdao China
| | - Jing Wang
- Technological Center; Shandong Entry-Exit Inspection and Quarantine Bureau; Qingdao China
| | - Zhengyi Li
- Technological Center; Shandong Entry-Exit Inspection and Quarantine Bureau; Qingdao China
| | - Liqing Zhao
- Technological Center; Shandong Entry-Exit Inspection and Quarantine Bureau; Qingdao China
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12
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Santos IC, Hildenbrand ZL, Schug KA. Mass Spectrometry for the Study of Microbial Communities in Environmental Waters. ADVANCES IN CHEMICAL POLLUTION, ENVIRONMENTAL MANAGEMENT AND PROTECTION 2017. [DOI: 10.1016/bs.apmp.2017.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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13
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Mégraud F, Musso D, Drancourt M, Lehours P. Curved and Spiral Bacilli. Infect Dis (Lond) 2017. [DOI: 10.1016/b978-0-7020-6285-8.00182-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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14
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Popović NT, Kazazić SP, Strunjak-Perović I, Čož-Rakovac R. Differentiation of environmental aquatic bacterial isolates by MALDI-TOF MS. ENVIRONMENTAL RESEARCH 2017; 152:7-16. [PMID: 27741451 DOI: 10.1016/j.envres.2016.09.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 09/20/2016] [Accepted: 09/24/2016] [Indexed: 05/20/2023]
Abstract
Identification of bacteria in aquatic and environmental applications, for monitoring purposes and research, for health assessments and therapy considerations of farmed and free-living aquatic organisms, still relies on conventional phenotypic and biochemical protocols. Although molecular techniques based on DNA amplification and sequencing are finding ways into diagnostic laboratories, they are time-consuming, costly and difficult in the case of multiplex assays. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is a rapid and accurate proteomic method reliable for identification of unknown bacteria to the genus and species level. Upon extension of databases, it will certainly find its position in environmental sciences. The paper presents an overview of the principle of the method, its effectiveness in comparison with conventional and molecular identification procedures, and applicability on environmental and aquatic isolates, discussing its advantages and shortcomings, as well as possible future implementations.
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Affiliation(s)
- Natalija Topić Popović
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Rudjer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
| | - Snježana P Kazazić
- Laboratory for Mass Spectrometry, Division of Physical Chemistry, Rudjer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia.
| | - Ivančica Strunjak-Perović
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Rudjer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
| | - Rozelindra Čož-Rakovac
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Rudjer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
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15
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Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry: A New Guide to Infectious Disease. ARCHIVES OF PEDIATRIC INFECTIOUS DISEASES 2016. [DOI: 10.5812/pedinfect.31816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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16
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Santos IC, Hildenbrand ZL, Schug KA. Applications of MALDI-TOF MS in environmental microbiology. Analyst 2016; 141:2827-37. [DOI: 10.1039/c6an00131a] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is an emerging technique for microbial identification, characterization, and typing.
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Affiliation(s)
- Inês C. Santos
- Department of Chemistry and Biochemistry
- The University of Texas at Arlington
- Arlington
- USA
| | - Zacariah L. Hildenbrand
- Inform Environmental
- LLC
- Dallas
- USA
- Affiliate of the Collaborative Laboratories for Environmental Analysis and Remediation
| | - Kevin A. Schug
- Department of Chemistry and Biochemistry
- The University of Texas at Arlington
- Arlington
- USA
- Affiliate of the Collaborative Laboratories for Environmental Analysis and Remediation
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17
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Topić Popović N, Strunjak-Perović I, Klobučar RS, Barišić J, Babić S, Jadan M, Kepec S, Kazazić SP, Matijatko V, Beer Ljubić B, Car I, Repec S, Stipaničev D, Klobučar GIV, Čož-Rakovac R. Impact of treated wastewater on organismic biosensors at various levels of biological organization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 538:23-37. [PMID: 26298246 DOI: 10.1016/j.scitotenv.2015.08.044] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 08/07/2015] [Accepted: 08/10/2015] [Indexed: 06/04/2023]
Abstract
Relating the treated wastewater quality and its impact on organismic biosensors (Prussian carp, Carassius gibelio and earthworm, Eisenia fetida) was the main objective of the study. The impact on health status of fish living downstream, microbiological contamination and antimicrobial resistance, fish tissue structure, blood biochemistry, oxidative stress, genotoxic effects, as well as multixenobiotic resistance mechanism (MXR) was assessed. Treated wastewater discharged from the WWTP modified the environmental parameters and xenobiotic concentrations of the receiving surface waters. Potential bacterial pathogens from fish and respective waters were found in relatively low numbers, although they comprised aeromonads with a zoonotic potential. High resistance profiles were determined towards the tested antimicrobial compounds, mostly sulfamethoxazole and erythromycin. Histopathology primarily revealed gill lamellar fusion and reduction of interlamellar spaces of effluent fish. A significant increase in plasma values of urea, total proteins, albumins and triglycerides and a significant decrease in the activity of plasma superoxide dismutase were noted in carp from the effluent-receiving canal. Micronucleus test did not reveal significant differences between the examined groups, but a higher frequency of erythrocyte nuclear abnormalities was found in fish sampled from the effluent-receiving canal. Earthworms indicated to the presence of MXR inhibitors in water and sludge samples, thus proving as a sensitive sentinel organism for environmental pollutants. The integrative approach of this study could serve as a guiding principle in conducting evaluations of the aquatic habitat health in complex bio-monitoring studies.
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Affiliation(s)
- Natalija Topić Popović
- Laboratory for Ichthyopathology-Biological Materials, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia.
| | - Ivančica Strunjak-Perović
- Laboratory for Ichthyopathology-Biological Materials, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Roberta Sauerborn Klobučar
- Laboratory for Ichthyopathology-Biological Materials, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Josip Barišić
- Laboratory for Ichthyopathology-Biological Materials, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Sanja Babić
- Laboratory for Ichthyopathology-Biological Materials, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Margita Jadan
- Laboratory for Ichthyopathology-Biological Materials, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Slavko Kepec
- Virkom d.o.o, Public Water Supply and Wastewater Services, Kralja Petra Krešimira IV 30, Virovitica. Croatia
| | - Snježana P Kazazić
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Vesna Matijatko
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, Zagreb, Croatia
| | - Blanka Beer Ljubić
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, Zagreb, Croatia
| | - Ivan Car
- Laboratory for Ichthyopathology-Biological Materials, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Siniša Repec
- Croatian Waters, Main Water Management Laboratory, Ul. grada Vukovara 220, Zagreb, Croatia
| | - Draženka Stipaničev
- Croatian Waters, Main Water Management Laboratory, Ul. grada Vukovara 220, Zagreb, Croatia
| | - Goran I V Klobučar
- Division of Zoology, Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, Zagreb, Croatia
| | - Rozelindra Čož-Rakovac
- Laboratory for Ichthyopathology-Biological Materials, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
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18
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Topic Popovic N, Kazazic SP, Strunjak-Perovic I, Barisic J, Sauerborn Klobucar R, Kepec S, Coz-Rakovac R. Detection and diversity of aeromonads from treated wastewater and fish inhabiting effluent and downstream waters. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2015; 120:235-242. [PMID: 26092555 DOI: 10.1016/j.ecoenv.2015.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 05/27/2015] [Accepted: 06/08/2015] [Indexed: 06/04/2023]
Abstract
A two-season investigation of the wastewater treatment plant (WWTP) effluent, of related waters, sludge and fish across a wide area and 11 stations, with emphasis on Aeromonas spp. was conducted. Aeromonas veronii was the prevailing aeromonad isolated by MALDI TOF MS in the summer period. A rise of Aeromonas hydrophila was observed in summer in raw sewage, treated wastewater and effluent-carrying canal. The ratio of aeromonad species retrieved from fish tissues did not correspond with the water and sludge findings, as in spring in the effluent-carrying canal fish carried Aeromonas salmonicida ssp. salmonicida and Aeromonas bestiarum, while in summer mainly A. veronii and Acinetobacter johnsonii were isolated from fish tissues in the same location. No correlation was established between fecal coliforms/enterococci and aeromonad occurrence. All retrieved Aeromonas species demonstrated a distinct spectral pattern, with peaks showing unique mass distribution ranging from 4000 to 10,000Da. Hierarchical clustering separated aeromonads of all isolated species and clustered closely related strains together. Resistance was determined towards amoxicillin, and frequently towards sulfamethoxazole and erythromycin. In summer, a high proportion of water and sludge Aeromonas species demonstrated multiple resistance patterns towards five or more antimicrobials. The quinolone resistance of water aeromonads was mostly related to A. veronii. There are potential health concerns regarding aeromonad exposure amongst recreational fishermen who come into contact with fish inhabiting waters downstream from the WWTP, and WWTP workers who are occupationally exposed to wastewaters and their aerosols.
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Affiliation(s)
- Natalija Topic Popovic
- Laboratory for Ichthyopathology-Biological Materials, Rudjer Boskovic Institute, Zagreb, Croatia.
| | - Snjezana P Kazazic
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Rudjer Boskovic Institute, Zagreb, Croatia
| | | | - Josip Barisic
- Laboratory for Ichthyopathology-Biological Materials, Rudjer Boskovic Institute, Zagreb, Croatia
| | | | - Slavko Kepec
- Virkom d.o.o., Public Water Supply and Wastewater Services, Virovitica, Croatia
| | - Rozelinda Coz-Rakovac
- Laboratory for Ichthyopathology-Biological Materials, Rudjer Boskovic Institute, Zagreb, Croatia
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Singhal N, Kumar M, Kanaujia PK, Virdi JS. MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis. Front Microbiol 2015; 6:791. [PMID: 26300860 PMCID: PMC4525378 DOI: 10.3389/fmicb.2015.00791] [Citation(s) in RCA: 770] [Impact Index Per Article: 85.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/21/2015] [Indexed: 01/13/2023] Open
Abstract
Currently microorganisms are best identified using 16S rRNA and 18S rRNA gene sequencing. However, in recent years matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a potential tool for microbial identification and diagnosis. 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. The technology has been readily imbibed by microbiologists who have reported usage of MALDI-TOF MS for a number of purposes like, microbial identification and strain typing, epidemiological studies, detection of biological warfare agents, detection of water- and food-borne pathogens, detection of antibiotic resistance and detection of blood and urinary tract pathogens etc. The limitation of the technology is that identification of new isolates is possible only if the spectral database contains peptide mass fingerprints of the type strains of specific genera/species/subspecies/strains. This review provides an overview of the status and recent applications of mass spectrometry for microbial identification. It also explores the usefulness of this exciting new technology for diagnosis of diseases caused by bacteria, viruses, and fungi.
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Affiliation(s)
- Neelja Singhal
- Department of Microbiology, University of Delhi New Delhi, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi New Delhi, India
| | - Pawan K Kanaujia
- Department of Microbiology, University of Delhi New Delhi, India
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20
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Ersoy Omeroglu E. Determination of the Genetic Diversity of Different Bioluminescent Bacteria by Pulsed-Field Gel Electrophoresis (PFGE). Jundishapur J Microbiol 2015; 8:e28378. [PMID: 26421141 PMCID: PMC4584076 DOI: 10.5812/jjm.28378v2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/26/2015] [Accepted: 05/21/2015] [Indexed: 11/16/2022] Open
Abstract
Background: There are 4 different genera (i.e. Vibrio, Aliivibrio, Photobacterium, and Shewanella) in the new classification of bioluminescent bacteria. The mechanism of bioluminescence has yet to be fully elucidated. Therefore, the determination of physiological and genetic characteristics of bioluminescent bacteria isolated from different sources is very important. Pulsed-Field Gel Electrophoresis (PFGE) has the highest discriminatory power among the different molecular typing methods for the investigation of the clonal relationships between bacteria. For the PFGE analysis of bioluminescent bacteria, the NotI-HF™ is the method of choice among the restriction enzymes. Objectives: The present study aimed to determine genetic relatedness via PFGE in 41 bioluminescent bacteria (belonging to 10 different species) isolated and identified from various marine sources. Materials and Methods: Different bioluminescent bacteria (i.e. Vibrio gigantis, V. azureus, V. harveyi, V. lentus, V. crassostreae, V. orientalis, Aliivibrio logei, A. fischeri, Shewanella woodyi, and Photobacterium kishitanii) were analyzed by PFGE using the NotI-HF™ restriction enzyme. The whole DNA of the strains embedded into the agarose plugs was digested with enzyme at 37°C for 30 minutes. CHEF-Mapper PFGE system was used for electrophoresis and band profile of the strains for the NotI-HF™ restriction enzyme were analyzed by Bio-Profil-1D++ software (Vilber Lourmat) at 10% homology coefficient. Results: Although all experiments were performed three times, four of forty-one bioluminescent strains (V. gigantis E-16, H-16 and S3W46 strains and A. fischeri E-4 strain) could not be typed by PFGE technique with NotI-HF™ enzyme. While only two strains (V. crassostreae H-12 and H-19 strains) were exhibiting same band pattern profiles (100% genome homology), thirty-six different PFGE band patterns were obtained. Pattern homologies changed between 66% - 92%, 73% - 83% and 49% - 100% for V. gigantis, V. harveyi and other strains, respectively. Conclusions: The obtained results revealed that there has been a high rate of genetic diversity in bioluminescent strains isolated from Gulf of Izmir and V. lentus and V. crassostreae strains could be also bioluminescent for the first report. At the same time, PFGE analysis of bioluminescent bacteria including four different genera and ten different species were shown for the first time by this study. It is considered that data acquired by this study will contribute evolution and mechanism of bioluminescence to further works to be done.
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Affiliation(s)
- Esra Ersoy Omeroglu
- Biology Department, Faculty of Science, Basic and Industrial Microbiology Section, Ege University, Bornova-Izmir, Turkey
- Corresponding author: Esra Ersoy Omeroglu, Biology Department, Faculty of Science, Basic and Industrial Microbiology Section, Ege University, Bornova-Izmir, Turkey. Tel: +90-2323112811, Fax: +90-2323881036, E-mail:
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21
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Determination of the Genetic Diversity of Different Bioluminescent Bacteria by Pulsed-Field Gel Electrophoresis (PFGE). Jundishapur J Microbiol 2015. [DOI: 10.5812/jjm.28378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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22
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Niyompanich S, Jaresitthikunchai J, Srisanga K, Roytrakul S, Tungpradabkul S. Source-identifying biomarker ions between environmental and clinical Burkholderia pseudomallei using whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). PLoS One 2014; 9:e99160. [PMID: 24914956 PMCID: PMC4051666 DOI: 10.1371/journal.pone.0099160] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Accepted: 05/12/2014] [Indexed: 11/18/2022] Open
Abstract
Burkholderia pseudomallei is the causative agent of melioidosis, which is an endemic disease in Northeast Thailand and Northern Australia. Environmental reservoirs, including wet soils and muddy water, serve as the major sources for contributing bacterial infection to both humans and animals. The whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (whole-cell MALDI-TOF MS) has recently been applied as a rapid, accurate, and high-throughput tool for clinical diagnosis and microbiological research. In this present study, we employed a whole-cell MALDI-TOF MS approach for assessing its potency in clustering a total of 11 different B. pseudomallei isolates (consisting of 5 environmental and 6 clinical isolates) with respect to their origins and to further investigate the source-identifying biomarker ions belonging to each bacterial group. The cluster analysis demonstrated that six out of eleven isolates were grouped correctly to their sources. Our results revealed a total of ten source-identifying biomarker ions, which exhibited statistically significant differences in peak intensity between average environmental and clinical mass spectra using ClinProTools software. Six out of ten mass ions were assigned as environmental-identifying biomarker ions (EIBIs), including, m/z 4,056, 4,214, 5,814, 7,545, 7,895, and 8,112, whereas the remaining four mass ions were defined as clinical-identifying biomarker ions (CIBIs) consisting of m/z 3,658, 6,322, 7,035, and 7,984. Hence, our findings represented, for the first time, the source-specific biomarkers of environmental and clinical B. pseudomallei.
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Affiliation(s)
- Suthamat Niyompanich
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Kitima Srisanga
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology, Pathumthani, Thailand
| | - Sumalee Tungpradabkul
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
- * E-mail:
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Zhang L, Borror CM, Sandrin TR. A designed experiments approach to optimization of automated data acquisition during characterization of bacteria with MALDI-TOF mass spectrometry. PLoS One 2014; 9:e92720. [PMID: 24662978 PMCID: PMC3963954 DOI: 10.1371/journal.pone.0092720] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 02/24/2014] [Indexed: 01/27/2023] Open
Abstract
MALDI-TOF MS has been shown capable of rapidly and accurately characterizing bacteria. Highly reproducible spectra are required to ensure reliable characterization. Prior work has shown that spectra acquired manually can have higher reproducibility than those acquired automatically. For this reason, the objective of this study was to optimize automated data acquisition to yield spectra with reproducibility comparable to those acquired manually. Fractional factorial design was used to design experiments for robust optimization of settings, in which values of five parameters (peak selection mass range, signal to noise ratio (S:N), base peak intensity, minimum resolution and number of shots summed) commonly used to facilitate automated data acquisition were varied. Pseudomonas aeruginosa was used as a model bacterium in the designed experiments, and spectra were acquired using an intact cell sample preparation method. Optimum automated data acquisition settings (i.e., those settings yielding the highest reproducibility of replicate mass spectra) were obtained based on statistical analysis of spectra of P. aeruginosa. Finally, spectrum quality and reproducibility obtained from non-optimized and optimized automated data acquisition settings were compared for P. aeruginosa, as well as for two other bacteria, Klebsiella pneumoniae and Serratia marcescens. Results indicated that reproducibility increased from 90% to 97% (p-value[Formula: see text]0.002) for P. aeruginosa when more shots were summed and, interestingly, decreased from 95% to 92% (p-value [Formula: see text] 0.013) with increased threshold minimum resolution. With regard to spectrum quality, highly reproducible spectra were more likely to have high spectrum quality as measured by several quality metrics, except for base peak resolution. Interaction plots suggest that, in cases of low threshold minimum resolution, high reproducibility can be achieved with fewer shots. Optimization yielded more reproducible spectra than non-optimized settings for all three bacteria.
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Affiliation(s)
- Lin Zhang
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, Arizona, United States of America
| | - Connie M. Borror
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, Arizona, United States of America
| | - Todd R. Sandrin
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, Arizona, United States of America
- * E-mail:
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Arpornsuwan T, Buasakul B, Jaresitthikunchai J, Roytrakul S. Potent and rapid antigonococcal activity of the venom peptide BmKn2 and its derivatives against different Maldi biotype of multidrug-resistant Neisseria gonorrhoeae. Peptides 2014; 53:315-20. [PMID: 24184420 DOI: 10.1016/j.peptides.2013.10.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Revised: 10/18/2013] [Accepted: 10/18/2013] [Indexed: 11/27/2022]
Abstract
The emergence of multidrug-resistant strains of Neisseria gonorrhoeae constitutes a serious threat to public health and necessitates the discovery of new types of antimicrobial agents. Among the 18 clinical isolates of N. gonorrhoeae with susceptible to spectinomycin, ceftriaxone and cefixime, 14 isolates were resistance to penicillin, tetracycline and ciprofloxacin, while 2 isolates were susceptible to tetracycline and another was penicillin intermediate isolate. Significant differences between laboratory strain and multidrug resistant strains were revealed by means of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry profiling and bioinformatics examination using the MALDI BioTyper software. However, Maldi Biotyper was not successfully separated ciprofloxacin-penicillin resistance and ciprofloxacin-tetracycline resistance from ciprofloxacin-penicillin-tetracycline resistant N. gonorrhoeae isolates. BmKn2 is a basic, alpha-helical peptide with no disulfide-bridge venom peptides that was first isolated from Buthus martensii Kasch. A panel of BmKn2 scorpion venom peptide and its derivatives of varying length and characteristics were synthesized chemically and evaluated for their ability to inhibit the growth of clinical N. gonorrhoeae isolates. Synthetic BmKn2 displayed potent activity against 18 clinical isolates of N. gonorrhoeae with MIC50 values of 6.9-27.6 μM. BmKn2 exerted its antibacterial activity via a bactericidal mechanism. Cyclic BmKn1 did not show antigonococcal activity. Decreasing the cationicity and helix percentage at the C-terminus of BmKn2 reduced the potency against N. gonorrhoeae. Taken together, the BmKn1 peptide can be developed as a topical therapeutic agent for treating multidrug-resistant strains of N. gonorrhoeae infections.
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Affiliation(s)
- Teerakul Arpornsuwan
- Department of Medical Technology, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand.
| | - Brisana Buasakul
- Sexually Transmitted Infection Cluster, Bureau of AIDS TB and STIs, Department of Disease Control, Ministry of Public Health, Sathon, Bangkok, Thailand
| | - Janthima Jaresitthikunchai
- Genome Institute, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Klong Luang, Pathumthani, Thailand
| | - Sittiruk Roytrakul
- Genome Institute, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Klong Luang, Pathumthani, Thailand
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25
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Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology. Clin Microbiol Rev 2014; 26:547-603. [PMID: 23824373 DOI: 10.1128/cmr.00072-12] [Citation(s) in RCA: 511] [Impact Index Per Article: 51.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (MS). Historically, MS was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. Today, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) MS is adapted for use in microbiology laboratories, where it serves as a paradigm-shifting, rapid, and robust method for accurate microbial identification. Multiple instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases genetic sequence-based identification practices. This review summarizes the current position of MALDI-TOF MS in clinical research and in diagnostic clinical microbiology laboratories and serves as a primer to examine the "nuts and bolts" of MALDI-TOF MS, highlighting research associated with sample preparation, spectral analysis, and accuracy. Currently available MALDI-TOF MS hardware and software platforms that support the use of MALDI-TOF with direct and precultured specimens and integration of the technology into the laboratory workflow are also discussed. Finally, this review closes with a prospective view of the future of MALDI-TOF MS in the clinical microbiology laboratory to accelerate diagnosis and microbial identification to improve patient care.
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26
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Typing of nosocomial outbreaks of Acinetobacter baumannii by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2012; 51:603-6. [PMID: 23175257 DOI: 10.1128/jcm.01811-12] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been evaluated for the identification of multidrug-resistant Acinetobacter baumannii nosocomial outbreaks in comparison with the repetitive sequence-based PCR DiversiLab system. The results suggest that MALDI-TOF MS can be used for real-time detection of Acinetobacter outbreaks before results from DNA-based systems are available.
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Emami K, Askari V, Ullrich M, Mohinudeen K, Anil AC, Khandeparker L, Burgess JG, Mesbahi E. Characterization of bacteria in ballast water using MALDI-TOF mass spectrometry. PLoS One 2012; 7:e38515. [PMID: 22685576 PMCID: PMC3369924 DOI: 10.1371/journal.pone.0038515] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 05/07/2012] [Indexed: 11/29/2022] Open
Abstract
To evaluate a rapid and cost-effective method for monitoring bacteria in ballast water, several marine bacterial isolates were characterized by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Since International Maritime Organization (IMO) regulations are concerned with the unintended transportation of pathogenic bacteria through ballast water, emphasis was placed on detecting species of Vibrio, enterococci and coliforms. Seawater samples collected from the North Sea were incubated in steel ballast tanks and the presence of potentially harmful species of Pseudomonas was also investigated. At the genus-level, the identification of thirty six isolates using MALDI-TOF MS produced similar results to those obtained by 16S rRNA gene sequencing. No pathogenic species were detected either by 16S rRNA gene analysis or by MALDI-TOF MS except for the opportunistically pathogenic bacterium Pseudomonas aeruginosa. In addition, in house software that calculated the correlation coefficient values (CCV) of the mass spectral raw data and their variation was developed and used to allow the rapid and efficient identification of marine bacteria in ballast water for the first time.
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Affiliation(s)
- Kaveh Emami
- School of Biology, Newcastle University, Newcastle upon Tyne, United Kingdom.
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Potential of MALDI-TOF mass spectrometry as a rapid detection technique in plant pathology: identification of plant-associated microorganisms. Anal Bioanal Chem 2012; 404:1247-55. [DOI: 10.1007/s00216-012-6091-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 04/27/2012] [Accepted: 05/02/2012] [Indexed: 11/26/2022]
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