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Pauter-Iwicka K, Railean V, Złoch M, Pomastowski P, Szultka-Młyńska M, Błońska D, Kupczyk W, Buszewski B. Characterization of the salivary microbiome before and after antibiotic therapy via separation technique. Appl Microbiol Biotechnol 2023; 107:2515-2531. [PMID: 36843196 PMCID: PMC10033590 DOI: 10.1007/s00253-023-12371-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 02/28/2023]
Abstract
In the present research, the MALDI-TOF MS technique was applied as a tool to rapidly identify the salivary microbiome. In this fact, it has been monitored the changes occurred in molecular profiles under different antibiotic therapy. Significant changes in the composition of the salivary microbiota were noticed not only in relation to the non antibiotic (non-AT) and antibiotic treatment (AT) groups, but also to the used media, the antibiotic therapy and co-existed microbiota. Each antibiotic generates specific changes in molecular profiles. The highest number of bacterial species was isolated in the universal culture medium (72%) followed by the selective medium (48% and 38%). In the case of non-AT patients, the prevalence of Streptococcus salivarius (25%), Streptococcus vestibularis (19%), Streptococcus oralis (13%), and Staphylococcus aureus (6%) was identified while in the case of AT, Streptococcus salivarius (11%), Streptococcus parasanguinis (11%), Staphylococcus epidermidis (12%), Enterococcus faecalis (9%), Staphylococcus hominis (8%), and Candida albicans (6%) were identified. Notable to specified that the Candida albicans was noticed only in AT samples, indicating a negative impact on the antibiotic therapy. The accuracy of the MALDI-TOF MS technique was performed by the 16S rRNA gene sequencing analysis-as a reference method. Conclusively, such an approach highlighted in the present study can help in developing the methods enabling a faster diagnosis of disease changes at the cellular level before clinical changes occur. Once the MALDI tool allows for the distinguishing of the microbiota of non-AT and AT, it may enable to monitor the diseases treatment and develop a treatment regimen for individual patients in relation to each antibiotic. KEY POINTS: The salivary microbiota of antibiotic-treated patients was more bacteria variety MALDI-TOF MS is a promising tool for recording of reproducible molecular profiles Our data can allow to monitor the treatment of bacterial diseases for patients.
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Affiliation(s)
- Katarzyna Pauter-Iwicka
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100, Torun, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100, Torun, Poland
| | - Viorica Railean
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100, Torun, Poland
- Department of Infectious, Invasive Diseases and Veterinary Administration, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100, Toruń, Poland
| | - Michał Złoch
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100, Torun, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100, Torun, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100, Torun, Poland
| | - Małgorzata Szultka-Młyńska
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100, Torun, Poland
| | - Dominika Błońska
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100, Torun, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100, Torun, Poland
| | - Wojciech Kupczyk
- Department of General, Gastroenterological&Oncological Surgery Collegium Medicum, Nicolaus Copernicus University, Torun, Poland
| | - Bogusław Buszewski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100, Torun, Poland.
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100, Torun, Poland.
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Pauter K, Szultka-Młyńska M, Buszewski B. Determination and Identification of Antibiotic Drugs and Bacterial Strains in Biological Samples. Molecules 2020; 25:E2556. [PMID: 32486359 PMCID: PMC7321139 DOI: 10.3390/molecules25112556] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/22/2022] Open
Abstract
Antibiotics were initially natural substances. However, nowadays, they also include synthetic drugs, which show their activity against bacteria, killing or inhibiting their growth and division. Thanks to these properties, many antibiotics have quickly found practical application in the fight against infectious diseases such as tuberculosis, syphilis, gastrointestinal infections, pneumonia, bronchitis, meningitis and septicemia. Antibiotic resistance is currently a detrimental problem; therefore, in addition to the improvement of antibiotic therapy, attention should also be paid to active metabolites in the body, which may play an important role in exacerbating the existing problem. Taking into account the clinical, cognitive and diagnostic purposes of drug monitoring, it is important to select an appropriate analytical method that meets all the requirements. The detection and identification of the microorganism responsible for the infection is also an essential factor in the implementation of appropriate antibiotic therapy. In recent years, clinical microbiology laboratories have experienced revolutionary changes in the way microorganisms are identified. The MALDI-TOF MS technique may be interesting, especially in some areas where a quick analysis is required, as is the case with clinical microbiology. This method is not targeted, which means that no prior knowledge of the infectious agent is required, since identification is based on a database match.
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Affiliation(s)
- Katarzyna Pauter
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarin 7, 87-100 Torun, Poland; (K.P.); (B.B.)
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100 Torun, Poland
| | - Małgorzata Szultka-Młyńska
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarin 7, 87-100 Torun, Poland; (K.P.); (B.B.)
| | - Bogusław Buszewski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarin 7, 87-100 Torun, Poland; (K.P.); (B.B.)
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100 Torun, Poland
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Yuan Y, Wu X, Liu Z, Ning Q, Fu L, Wu S. A signal cascade amplification strategy based on RT-PCR triggering of a G-quadruplex DNAzyme for a novel electrochemical detection of viable Cronobacter sakazakii. Analyst 2020; 145:4477-4483. [PMID: 32391531 DOI: 10.1039/d0an00270d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cronobacter sakazakii is an important opportunistic food-borne pathogen, and it can cause severe diseases with main symptoms including neonatal meningitis, necrotizing enterocolitis, and sepsis. For the achievement of practical and convenient detection of viable C. sakazakii, a simple and robust strategy based on the cascade signal amplification of RT-PCR triggered G-quadruplex DNAzyme catalyzed reaction was firstly used to develop an effective and sensitive DNAzyme electrochemical assay. Without viable C. sakazakii in the samples there are no RT-PCR and DNAzyme products, which can cause a weak electrochemical response. Once viable C. sakazakii exists in the samples, an obvious enhancement of the electrochemical response can be achieved after the target signal is amplified by RT-PCR and the resulting DNAzyme, which catalyze the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) by H2O2 with the assistance of the cofactor hemin. Our novel assay can be performed in a range of 2.4 × 107 CFU mL-1 to 3.84 × 104 CFU mL-1 (R2 = 0.9863), with a detection limit of 5.01 × 102 CFU mL-1. Through the assay of 15 real samples, electrochemical detection assay provided the same results as conventional detection methods. Therefore, detection of viable C. sakazakii based on G-quadruplex DNAzyme electrochemical assay with RT-PCR demonstrates the significant advantages of high sensitivity, low cost and simple manipulation over existing approaches and offers an opportunity for potential application in pathogen detection.
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Affiliation(s)
- Yuanyuan Yuan
- School of Life Sciences, Shanghai University, Shanghai, 200444, P.R. China.
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Identification of Cronobacter species by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry with an optimized analysis method. J Microbiol Methods 2017; 139:172-180. [DOI: 10.1016/j.mimet.2017.05.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/25/2017] [Accepted: 05/27/2017] [Indexed: 11/23/2022]
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Novel Method for Reliable Identification of Siccibacter and Franconibacter Strains: from "Pseudo-Cronobacter" to New Enterobacteriaceae Genera. Appl Environ Microbiol 2017; 83:AEM.00234-17. [PMID: 28455327 DOI: 10.1128/aem.00234-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/12/2017] [Indexed: 11/20/2022] Open
Abstract
In the last decade, strains of the genera Franconibacter and Siccibacter have been misclassified as first Enterobacter and later Cronobacter Because Cronobacter is a serious foodborne pathogen that affects premature neonates and elderly individuals, such misidentification may not only falsify epidemiological statistics but also lead to tests of powdered infant formula or other foods giving false results. Currently, the main ways of identifying Franconibacter and Siccibacter strains are by biochemical testing or by sequencing of the fusA gene as part of Cronobacter multilocus sequence typing (MLST), but in relation to these strains the former is generally highly difficult and unreliable while the latter remains expensive. To address this, we developed a fast, simple, and most importantly, reliable method for Franconibacter and Siccibacter identification based on intact-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Our method integrates the following steps: data preprocessing using mMass software; principal-component analysis (PCA) for the selection of mass spectrum fingerprints of Franconibacter and Siccibacter strains; optimization of the Biotyper database settings for the creation of main spectrum projections (MSPs). This methodology enabled us to create an in-house MALDI MS database that extends the current MALDI Biotyper database by including Franconibacter and Siccibacter strains. Finally, we verified our approach using seven previously unclassified strains, all of which were correctly identified, thereby validating our method.IMPORTANCE We show that the majority of methods currently used for the identification of Franconibacter and Siccibacter bacteria are not able to properly distinguish these strains from those of Cronobacter While sequencing of the fusA gene as part of Cronobacter MLST remains the most reliable such method, it is highly expensive and time-consuming. Here, we demonstrate a cost-effective and reliable alternative that correctly distinguishes between Franconibacter, Siccibacter, and Cronobacter bacteria and identifies Franconibacter and Siccibacter at the species level. Using intact-cell MALDI-TOF MS, we extend the current MALDI Biotyper database with 11 Franconibacter and Siccibacter MSPs. In addition, the use of our approach is likely to lead to a more reliable identification scheme for Franconibacter and Siccibacter strains and, consequently, a more trustworthy epidemiological picture of their involvement in disease.
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Roosaare M, Vaher M, Kaplinski L, Möls M, Andreson R, Lepamets M, Kõressaar T, Naaber P, Kõljalg S, Remm M. StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees. PeerJ 2017; 5:e3353. [PMID: 28533988 PMCID: PMC5438578 DOI: 10.7717/peerj.3353] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/26/2017] [Indexed: 12/20/2022] Open
Abstract
Background Fast, accurate and high-throughput identification of bacterial isolates is in great demand. The present work was conducted to investigate the possibility of identifying isolates from unassembled next-generation sequencing reads using custom-made guide trees. Results A tool named StrainSeeker was developed that constructs a list of specific k-mers for each node of any given Newick-format tree and enables the identification of bacterial isolates in 1–2 min. It uses a novel algorithm, which analyses the observed and expected fractions of node-specific k-mers to test the presence of each node in the sample. This allows StrainSeeker to determine where the isolate branches off the guide tree and assign it to a clade whereas other tools assign each read to a reference genome. Using a dataset of 100 Escherichia coli isolates, we demonstrate that StrainSeeker can predict the clades of E. coli with 92% accuracy and correct tree branch assignment with 98% accuracy. Twenty-five thousand Illumina HiSeq reads are sufficient for identification of the strain. Conclusion StrainSeeker is a software program that identifies bacterial isolates by assigning them to nodes or leaves of a custom-made guide tree. StrainSeeker’s web interface and pre-computed guide trees are available at http://bioinfo.ut.ee/strainseeker. Source code is stored at GitHub: https://github.com/bioinfo-ut/StrainSeeker.
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Affiliation(s)
- Märt Roosaare
- Department of Bioinformatics, University of Tartu, Tartu, Estonia
| | - Mihkel Vaher
- Department of Bioinformatics, University of Tartu, Tartu, Estonia
| | - Lauris Kaplinski
- Department of Bioinformatics, University of Tartu, Tartu, Estonia
| | - Märt Möls
- Department of Bioinformatics, University of Tartu, Tartu, Estonia.,Institute of Mathematical Statistics, University of Tartu, Tartu, Estonia
| | - Reidar Andreson
- Department of Bioinformatics, University of Tartu, Tartu, Estonia
| | - Maarja Lepamets
- Department of Bioinformatics, University of Tartu, Tartu, Estonia
| | - Triinu Kõressaar
- Department of Bioinformatics, University of Tartu, Tartu, Estonia
| | - Paul Naaber
- Synlab Eesti, Tallinn, Estonia.,Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Siiri Kõljalg
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.,United Laboratories, Tartu University Clinics, Tartu, Estonia
| | - Maido Remm
- Department of Bioinformatics, University of Tartu, Tartu, Estonia
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Zhao YQ, Song J, Wang HL, Xu B, Liu F, He K, Wang N. Rapid Detection of Ricin in Serum Based on Cu-Chelated Magnetic Beads Using Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:748-751. [PMID: 26873724 DOI: 10.1007/s13361-016-1340-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 01/02/2016] [Accepted: 01/09/2016] [Indexed: 06/05/2023]
Abstract
The protein toxin ricin obtained from castor bean plant (Ricinus communis) seeds is a potent biological warfare agent due to its ease of availability and acute toxicity. In this study, we demonstrated a rapid and simple method to detect ricin in serum in vitro. The ricin was mixed with serum and digested by trypsin, then all the peptides were efficiently extracted using Cu-chelated magnetic beads and were detected with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The specific ricin peptides were identified by Nanoscale Ultra Performance liquid chromatography coupled to tandem mass spectrometry according to their sequences. The assay required 2.5 hours, and a characteristic peptide could be detected down to 4 ng/μl and used as a biomarker to detect ricin in serum. The high sensitivity and simplicity of the procedure makes it valuable in clinical practice. Graphical Abstract ᅟ.
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Affiliation(s)
- Yong-Qiang Zhao
- The Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing, China, 100850
| | - Jian Song
- The School of Pharmacy, Jilin University, Changchun, China, 130021
| | - Hong-Li Wang
- The Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing, China, 100850
| | - Bin Xu
- The Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing, China, 100850
| | - Feng Liu
- The Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing, China, 100850
| | - Kun He
- The Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing, China, 100850.
| | - Na Wang
- The Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing, China, 100850.
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8
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Diversity of O Antigens within the Genus Cronobacter: from Disorder to Order. Appl Environ Microbiol 2015; 81:5574-82. [PMID: 26070668 DOI: 10.1128/aem.00277-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 06/01/2015] [Indexed: 11/20/2022] Open
Abstract
Cronobacter species are Gram-negative opportunistic pathogens that can cause serious infections in neonates. The lipopolysaccharides (LPSs) that form part of the outer membrane of such bacteria are possibly related to the virulence of particular bacterial strains. However, currently there is no clear overview of O-antigen diversity within the various Cronobacter strains and links with virulence. In this study, we tested a total of 82 strains, covering each of the Cronobacter species. The nucleotide variability of the O-antigen gene cluster was determined by restriction fragment length polymorphism (RFLP) analysis. As a result, the 82 strains were distributed into 11 previously published serotypes and 6 new serotypes, each defined by its characteristic restriction profile. These new serotypes were confirmed using genomic analysis of strains available in public databases: GenBank and PubMLST Cronobacter. Laboratory strains were then tested using the current serotype-specific PCR probes. The results show that the current PCR probes did not always correspond to genomic O-antigen gene cluster variation. In addition, we analyzed the LPS phenotype of the reference strains of all distinguishable serotypes. The identified serotypes were compared with data from the literature and the MLST database (www.pubmlst.org/cronobacter/). Based on the findings, we systematically classified a total of 24 serotypes for the Cronobacter genus. Moreover, we evaluated the clinical history of these strains and show that Cronobacter sakazakii O2, O1, and O4, C. turicensis O1, and C. malonaticus O2 serotypes are particularly predominant in clinical cases.
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Lindsay D, Hill B, Venter P. Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry as a confirmation procedure in internationally recognised standard test methods for Cronobacter sakazakii. Int Dairy J 2014. [DOI: 10.1016/j.idairyj.2014.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Krásný L, Rohlová E, Růžičková H, Šantrůček J, Hynek R, Hochel I. Differentiation of Cronobacter spp. by tryptic digestion of the cell suspension followed by MALDI-TOF MS analysis. J Microbiol Methods 2014; 98:105-13. [DOI: 10.1016/j.mimet.2014.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 01/14/2014] [Accepted: 01/15/2014] [Indexed: 11/27/2022]
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11
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Lu Y, Chen Y, Lu X, Lv J, Man C, Chai Y, Jiang Y. Comparison of methods for the microbiological identification and typing of Cronobacter species in infant formula. J Dairy Sci 2014; 97:632-41. [DOI: 10.3168/jds.2013-7147] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 10/06/2013] [Indexed: 11/19/2022]
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12
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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: 514] [Impact Index Per Article: 51.4] [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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Joseph S, Hariri S, Forsythe SJ. Lack of continuity between Cronobacter biotypes and species as determined using multilocus sequence typing. Mol Cell Probes 2013; 27:137-9. [PMID: 23474194 DOI: 10.1016/j.mcp.2013.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 02/09/2013] [Accepted: 02/19/2013] [Indexed: 10/27/2022]
Abstract
The accuracy of the Cronobacter biotyping scheme was compared with the 7-loci multilocus sequence typing scheme. Biotyping did not reliably assign species level identification, as only half (17/31) of the biotype variants were unique to any of the seven Cronobacter species and the remaining biotypes were shared across the genus.
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Affiliation(s)
- Susan Joseph
- Pathogen Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
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