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Meng JN, Xu ZK, Li PR, Zeng X, Liu Y, Xu ZL, Wang J, Ding Y, Shen X. Universal and Naked-Eye Diagnostic Platform for Emetic Bacillus cereus Based on RPA-Assisted CRISPR/Cas12a. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8823-8830. [PMID: 38578074 DOI: 10.1021/acs.jafc.3c06744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Emetic Bacillus cereus (B. cereus), which can cause emetic food poisoning and in some cases even fulminant liver failure and death, has aroused widespread concern. Herein, a universal and naked-eye diagnostic platform for emetic B. cereus based on recombinase polymerase amplification (RPA)-assisted CRISPR/Cas12a was developed by targeting the cereulide synthetase biosynthetic gene (cesB). The diagnostic platform enabled one-pot detection by adding components at the bottom and cap of the tube separately. The visual limit of detection of RPA-CRISPR/Cas12a for gDNA and cells of emetic B. cereus was 10-2 ng μL-1 and 102 CFU mL-1, respectively. Meanwhile, it maintained the same sensitivity in the rice, milk, and cooked meat samples even if the gDNA was extracted by simple boiling. The whole detection process can be finished within 40 min, and the single cell of emetic B. cereus was able to be recognized through enrichment for 2-5 h. The good specificity, high sensitivity, rapidity, and simplicity of the RPA-assisted CRISPR/Cas12a diagnostic platform made it serve as a potential tool for the on-site detection of emetic B. cereus in food matrices. In addition, the RPA-assisted CRISPR/Cas12a assay is the first application in emetic B. cereus detection.
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Affiliation(s)
- Jing-Nan Meng
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
- College of Food Engineering, Anhui Science and Technology University, Chuzhou 233100, China
- Key Laboratory for Biobased Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Ze-Ke Xu
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Peng-Ru Li
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Xi Zeng
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
- Guangzhou Institute of Food Inspection, Guangzhou 510410, China
| | - Yingju Liu
- Key Laboratory for Biobased Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Zhen-Lin Xu
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Juan Wang
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Yu Ding
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Xing Shen
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
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Uvarova YE, Demenkov PS, Kuzmicheva IN, Venzel AS, Mischenko EL, Ivanisenko TV, Efimov VM, Bannikova SV, Vasilieva AR, Ivanisenko VA, Peltek SE. Accurate noise-robust classification of Bacillus species from MALDI-TOF MS spectra using a denoising autoencoder. J Integr Bioinform 2023; 20:jib-2023-0017. [PMID: 37978847 PMCID: PMC10757077 DOI: 10.1515/jib-2023-0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/10/2023] [Indexed: 11/19/2023] Open
Abstract
Bacillus strains are ubiquitous in the environment and are widely used in the microbiological industry as valuable enzyme sources, as well as in agriculture to stimulate plant growth. The Bacillus genus comprises several closely related groups of species. The rapid classification of these remains challenging using existing methods. Techniques based on MALDI-TOF MS data analysis hold significant promise for fast and precise microbial strains classification at both the genus and species levels. In previous work, we proposed a geometric approach to Bacillus strain classification based on mass spectra analysis via the centroid method (CM). One limitation of such methods is the noise in MS spectra. In this study, we used a denoising autoencoder (DAE) to improve bacteria classification accuracy under noisy MS spectra conditions. We employed a denoising autoencoder approach to convert noisy MS spectra into latent variables representing molecular patterns in the original MS data, and the Random Forest method to classify bacterial strains by latent variables. Comparison of the DAE-RF with the CM method using the artificially noisy test samples showed that DAE-RF offers higher noise robustness. Hence, the DAE-RF method could be utilized for noise-robust, fast, and neat classification of Bacillus species according to MALDI-TOF MS data.
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Affiliation(s)
- Yulia E. Uvarova
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
| | - Pavel S. Demenkov
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
- Kurchatov Center for Genome Research, Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
- Novosibirsk State University, 630090Novosibirsk, Russia
| | | | - Artur S. Venzel
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
- Novosibirsk State University, 630090Novosibirsk, Russia
| | - Elena L. Mischenko
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
| | - Timofey V. Ivanisenko
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
- Kurchatov Center for Genome Research, Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
| | - Vadim M. Efimov
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
| | - Svetlana V. Bannikova
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
| | - Asya R. Vasilieva
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
| | - Vladimir A. Ivanisenko
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
- Kurchatov Center for Genome Research, Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
- Novosibirsk State University, 630090Novosibirsk, Russia
| | - Sergey E. Peltek
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
- Kurchatov Center for Genome Research, Institute of Cytology and Genetics SB RAS, 630090Novosibirsk, Russia
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3
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Detection of emetic Bacillus cereus and the emetic toxin cereulide in food matrices: Progress and perspectives. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.03.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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4
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Differentiation of Bacillus cereus and Bacillus thuringiensis Using Genome-Guided MALDI-TOF MS Based on Variations in Ribosomal Proteins. Microorganisms 2022; 10:microorganisms10050918. [PMID: 35630362 PMCID: PMC9146703 DOI: 10.3390/microorganisms10050918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 12/10/2022] Open
Abstract
Bacillus cereus and B. thuringiensis are closely related species that are relevant to foodborne diseases and biopesticides, respectively. Unambiguous differentiation of these two species is crucial for bacterial taxonomy. As genome analysis offers an objective but time-consuming classification of B. cereus and B. thuringiensis, in the present study, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was used to accelerate this process. By combining in silico genome analysis and MALDI-TOF MS measurements, four species-specific peaks of B. cereus and B. thuringiensis were screened and identified. The species-specific peaks of B. cereus were m/z 3211, 6427, 9188, and 9214, and the species-specific peaks of B. thuringiensis were m/z 3218, 6441, 9160, and 9229. All the above peaks represent ribosomal proteins, which are conserved and consistent with the phylogenetic relationship between B. cereus and B. thuringiensis. The specificity of the peaks was robustly verified using common foodborne pathogens. Thus, we concluded that genome-guided MALDI-TOF MS allows high-throughput differentiation of B. cereus and B. thuringiensis and provides a framework for differentiating other closely related species.
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Carroll LM, Cheng RA, Wiedmann M, Kovac J. Keeping up with the Bacillus cereus group: taxonomy through the genomics era and beyond. Crit Rev Food Sci Nutr 2021; 62:7677-7702. [PMID: 33939559 DOI: 10.1080/10408398.2021.1916735] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The Bacillus cereus group, also known as B. cereus sensu lato (s.l.), is a species complex that contains numerous closely related lineages, which vary in their ability to cause illness in humans and animals. The classification of B. cereus s.l. isolates into species-level taxonomic units is thus essential for informing public health and food safety efforts. However, taxonomic classification of these organisms is challenging. Numerous-often conflicting-taxonomic changes to the group have been proposed over the past two decades, making it difficult to remain up to date. In this review, we discuss the major nomenclatural changes that have accumulated in the B. cereus s.l. taxonomic space prior to 2020, particularly in the genomic sequencing era, and outline the resulting problems. We discuss several contemporary taxonomic frameworks as applied to B. cereus s.l., including (i) phenotypic, (ii) genomic, and (iii) hybrid nomenclatural frameworks, and we discuss the advantages and disadvantages of each. We offer suggestions as to how readers can avoid B. cereus s.l. taxonomic ambiguities, regardless of the nomenclatural framework(s) they choose to employ. Finally, we discuss future directions and open problems in the B. cereus s.l. taxonomic realm, including those that cannot be solved by genomic approaches alone.
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Affiliation(s)
- Laura M Carroll
- Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Rachel A Cheng
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
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6
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The Food Poisoning Toxins of Bacillus cereus. Toxins (Basel) 2021; 13:toxins13020098. [PMID: 33525722 PMCID: PMC7911051 DOI: 10.3390/toxins13020098] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/14/2021] [Accepted: 01/25/2021] [Indexed: 12/13/2022] Open
Abstract
Bacillus cereus is a ubiquitous soil bacterium responsible for two types of food-associated gastrointestinal diseases. While the emetic type, a food intoxication, manifests in nausea and vomiting, food infections with enteropathogenic strains cause diarrhea and abdominal pain. Causative toxins are the cyclic dodecadepsipeptide cereulide, and the proteinaceous enterotoxins hemolysin BL (Hbl), nonhemolytic enterotoxin (Nhe) and cytotoxin K (CytK), respectively. This review covers the current knowledge on distribution and genetic organization of the toxin genes, as well as mechanisms of enterotoxin gene regulation and toxin secretion. In this context, the exceptionally high variability of toxin production between single strains is highlighted. In addition, the mode of action of the pore-forming enterotoxins and their effect on target cells is described in detail. The main focus of this review are the two tripartite enterotoxin complexes Hbl and Nhe, but the latest findings on cereulide and CytK are also presented, as well as methods for toxin detection, and the contribution of further putative virulence factors to the diarrheal disease.
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Carroll LM, Wiedmann M. Cereulide Synthetase Acquisition and Loss Events within the Evolutionary History of Group III Bacillus cereus Sensu Lato Facilitate the Transition between Emetic and Diarrheal Foodborne Pathogens. mBio 2020; 11:e01263-20. [PMID: 32843545 PMCID: PMC7448271 DOI: 10.1128/mbio.01263-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/17/2020] [Indexed: 11/20/2022] Open
Abstract
Cereulide-producing members of Bacillus cereussensu lato group III (also known as emetic B. cereus) possess cereulide synthetase, a plasmid-encoded, nonribosomal peptide synthetase encoded by the ces gene cluster. Despite the documented risks that cereulide-producing strains pose to public health, the level of genomic diversity encompassed by emetic B. cereus has never been evaluated at a whole-genome scale. Here, we employ a phylogenomic approach to characterize group III B. cereussensu lato genomes which possess ces (ces positive) alongside their closely related, ces-negative counterparts (i) to assess the genomic diversity encompassed by emetic B. cereus and (ii) to identify potential ces loss and/or gain events within the evolutionary history of the high-risk and medically relevant sequence type (ST) 26 lineage often associated with emetic foodborne illness. Using all publicly available ces-positive group III B. cereussensu lato genomes and the ces-negative genomes interspersed among them (n = 159), we show that emetic B. cereus is not clonal; rather, multiple lineages within group III harbor cereulide-producing strains, all of which share an ancestor incapable of producing cereulide (posterior probability = 0.86 to 0.89). Members of ST 26 share an ancestor that existed circa 1748 (95% highest posterior density [HPD] interval = 1246.89 to 1915.64) and first acquired the ability to produce cereulide before 1876 (95% HPD = 1641.43 to 1946.70). Within ST 26 alone, two subsequent ces gain events were observed, as well as three ces loss events, including among isolates responsible for B. cereussensu lato toxicoinfection (i.e., "diarrheal" illness).IMPORTANCEB. cereus is responsible for thousands of cases of foodborne disease each year worldwide, causing two distinct forms of illness: (i) intoxication via cereulide (i.e., emetic syndrome) or (ii) toxicoinfection via multiple enterotoxins (i.e., diarrheal syndrome). Here, we show that emetic B. cereus is not a clonal, homogenous unit that resulted from a single cereulide synthetase gain event followed by subsequent proliferation; rather, cereulide synthetase acquisition and loss is a dynamic, ongoing process that occurs across lineages, allowing some group III B. cereussensu lato populations to oscillate between diarrheal and emetic foodborne pathogens over the course of their evolutionary histories. We also highlight the care that must be taken when selecting a reference genome for whole-genome sequencing-based investigation of emetic B. cereussensu lato outbreaks, since some reference genome selections can lead to a confounding loss of resolution and potentially hinder epidemiological investigations.
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Affiliation(s)
- Laura M Carroll
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA
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8
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Ducrest PJ, Pfammatter S, Stephan D, Vogel G, Thibault P, Schnyder B. Rapid detection of Bacillus ionophore cereulide in food products. Sci Rep 2019; 9:5814. [PMID: 30967595 PMCID: PMC6456620 DOI: 10.1038/s41598-019-42167-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 03/22/2019] [Indexed: 12/17/2022] Open
Abstract
Cereulide is a toxic cyclic depsipeptide produced by certain strains of Bacillus cereus found in soil and food products. While some harmless strains of Bacillus are used as probiotic, others can cause nausea and vomiting, and represent an important food safety concern. Current detection methods are time consuming and do not necessarily detect toxic cereulide. Here, we developed a rapid protocol using Matrix Assisted Laser Desorption/Ionization-Time of Flight (MALDI-TOF) mass spectrometry that detects the toxin originating from a colony smear of B. cereus. The distinct molecular feature of the toxin peak at m/z 1,191 was clearly identified from bacterial extracts with a limit of detection (LOD) of 30 ng/mL. Final optimisation of the sample preparation was based on cereulide chelating cations to produce the alkali adduct [M + K]+ without the use of a MALDI matrix, and provided a 1,000-fold improvement of LOD with 30 pg/mL of cereulide. We evaluated the application of this method for the detection of cereulide in rice, milk, and different ready-to-eat meals. The proposed protocol is quick, easy and provides an improvement over conventional methods for the detection of B. cereus toxin.
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Affiliation(s)
- P J Ducrest
- University of Applied Sciences, HES-SO Valais//Wallis, Institute of Life Technologies, Sion, Switzerland
| | - S Pfammatter
- University of Montreal, Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
| | - D Stephan
- University of Applied Sciences, HES-SO Valais//Wallis, Institute of Life Technologies, Sion, Switzerland
| | - G Vogel
- Mabritec AG, Riehen, Switzerland
| | - P Thibault
- University of Montreal, Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
| | - B Schnyder
- University of Applied Sciences, HES-SO Valais//Wallis, Institute of Life Technologies, Sion, Switzerland.
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9
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Chelliah R, Wei S, Park BJ, Rubab M, Banan-Mwine Dalirii E, Barathikannan K, Jin YG, Oh DH. Whole genome sequence of Bacillus thuringiensis ATCC 10792 and improved discrimination of Bacillus thuringiensis from Bacillus cereus group based on novel biomarkers. Microb Pathog 2019; 129:284-297. [DOI: 10.1016/j.micpath.2019.02.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 02/08/2019] [Accepted: 02/08/2019] [Indexed: 11/17/2022]
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10
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Ulrich S, Gottschalk C, Dietrich R, Märtlbauer E, Gareis M. Identification of cereulide producing Bacillus cereus by MALDI-TOF MS. Food Microbiol 2019; 82:75-81. [PMID: 31027822 DOI: 10.1016/j.fm.2019.01.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 01/11/2019] [Accepted: 01/21/2019] [Indexed: 12/23/2022]
Abstract
The Bacillus (B.) cereus group consists of nine recognized species which are present worldwide. B. cereus play an important role in food-borne diseases by producing different toxins. Yet, only a small percentage of B. cereus strains are able to produce the heat stable cereulide, the causative agent of emetic food poisoning. To minimize the entry of emetic B. cereus into the food chain, food business operators are dependent on efficient and reliable methods enabling the differentiation between emetic and non-emetic strains. Currently, only time-consuming cell bioassays, molecular methods and tandem mass spectrometry are available for this purpose. Thus, the aim of the present study was to establish a fast and reliable method for the differentiation between emetic/non-emetic strains by MALDI-TOF MS. Selected strains/isolates of the B. cereus group as well as other Bacillus spp. (total n = 121) were cultured on sheep blood agar for 48 h before analysis. Subsequently, the cultures were directly analyzed by MALDI-TOF MS without prior extraction steps. The samples were measured in the mass range of m/z 800-1800 Da. Using ClinProTools 3.0 statistical software and Flex analysis software (Bruker Daltonics GmbH, Bremen, Germany), a differentiation between emetic/non-emetic isolates was possible with a rate of correct identification of 99.1% by means of the evaluation of two specific biomarkers (m/z 1171 and 1187 Da).
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Affiliation(s)
- Sebastian Ulrich
- Food Safety, Veterinary Faculty, Ludwig-Maximilians-University Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany.
| | - Christoph Gottschalk
- Food Safety, Veterinary Faculty, Ludwig-Maximilians-University Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany
| | - Richard Dietrich
- Hygiene and Technology of Milk, Veterinary Faculty, Ludwig-Maximilians-University Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany
| | - Erwin Märtlbauer
- Hygiene and Technology of Milk, Veterinary Faculty, Ludwig-Maximilians-University Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany
| | - Manfred Gareis
- Food Safety, Veterinary Faculty, Ludwig-Maximilians-University Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany
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11
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Giacometti F, Piva S, Vranckx K, De Bruyne K, Drigo I, Lucchi A, Manfreda G, Serraino A. Application of MALDI-TOF MS for the subtyping of Arcobacter butzleri strains and comparison with their MLST and PFGE types. Int J Food Microbiol 2018; 277:50-57. [PMID: 29684765 DOI: 10.1016/j.ijfoodmicro.2018.04.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 04/05/2018] [Accepted: 04/13/2018] [Indexed: 12/19/2022]
Abstract
For the first time, this study evaluated the use of MALDI-TOF as a typing tool for Arcobacter butzleri. A total of 104 A. butzleri strains isolated from different sources in an artisanal dairy plant in Italy were identified and typed using MALDI-TOF and compared with their multilocus sequence typing (MLST) and pulsed field gel electrophoresis (PFGE) profiles found in previous studies. MALDI-TOF correctly identified all the isolates to species level. No clearly delineated clusters appeared on dendrograms based on either the complete spectra or the significant peaks, but nine clusters were defined using the cophenetic correlation. Interestingly, MALDI-TOF proved able to discriminate A. butzleri strains below species level, confirming its potential use for epidemiological surveys. As expected, the comparative analysis with PFGE and MLST showed that the discriminatory index was lower for MALDI-TOF but roughly comparable to sequence types and pulsotypes. MALDI-TOF appears to be a relatively low cost answer to the urgent need for more rapid, less expensive typing tools suitable for source attribution studies, readily allowing multiple typing methods to be combined. This study provides insights into MALDI-TOF as potential epidemiological tool. Its application in healthcare surveillance systems awaits further exploration to encourage interaction and convergence studies between primary care in humans and animal and food veterinary authorities as part of the One Health concept.
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Affiliation(s)
- Federica Giacometti
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Italy.
| | - Silvia Piva
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Italy.
| | | | | | - Ilenia Drigo
- Istituto Zooprofilattico Sperimentale delle Venezie, Villorba, Treviso, Italy.
| | - Alex Lucchi
- Department of Agricultural and Food Sciences, University of Bologna, Ozzano dell'Emilia, Italy.
| | - Gerardo Manfreda
- Department of Agricultural and Food Sciences, University of Bologna, Ozzano dell'Emilia, Italy.
| | - Andrea Serraino
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Italy.
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12
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Fiedoruk K, Drewnowska JM, Daniluk T, Leszczynska K, Iwaniuk P, Swiecicka I. Ribosomal background of the Bacillus cereus group thermotypes. Sci Rep 2017; 7:46430. [PMID: 28406161 PMCID: PMC5390287 DOI: 10.1038/srep46430] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/08/2017] [Indexed: 11/09/2022] Open
Abstract
In this study we reconstructed the architecture of Bacillus cereus sensu lato population based on ribosomal proteins, and identified a link between the ribosomal proteins’ variants and thermal groups (thermotypes) of the bacilli. The in silico phyloproteomic analysis of 55 ribosomal proteins (34 large and 21 small subunit r-proteins) of 421 strains, representing 14 well-established or plausible B. cereus sensu lato species, revealed several ribosomal clusters (r-clusters), which in general were well correlated with the strains’ affiliation to phylogenetic/thermal groups I–VII. However, a conformity and possibly a thermal characteristic of certain phylogenetic groups, e.g. the group IV, were not supported by a distribution of the corresponding r-clusters, and consequently neither by the analysis of cold-shock proteins (CSPs) nor by a content of heat shock proteins (HSPs). Furthermore, a preference for isoleucine and serine over valine and alanine in r-proteins along with a lack of HSP16.4 were recognized in non-mesophilic thermotypes. In conclusion, we suggest that the observed divergence in ribosomal proteins may be connected with an adaptation of B. cereus sensu lato members to various thermal niches.
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Affiliation(s)
- Krzysztof Fiedoruk
- Department of Microbiology, Medical University of Bialystok, Bialystok, Poland
| | - Justyna M Drewnowska
- Department of Microbiology, Institute of Biology, University of Bialystok, Bialystok, Poland
| | - Tamara Daniluk
- Department of Microbiology, Medical University of Bialystok, Bialystok, Poland
| | | | - Piotr Iwaniuk
- Department of Microbiology, Institute of Biology, University of Bialystok, Bialystok, Poland
| | - Izabela Swiecicka
- Department of Microbiology, Institute of Biology, University of Bialystok, Bialystok, Poland.,Laboratory of Applied Microbiology, University of Bialystok, Bialystok, Poland
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