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Graham KA, Gomez J, Primm TP, Houston R. Comparison of nine extraction methods for bacterial identification using the ONT MinION sequencer. Int J Legal Med 2024; 138:351-360. [PMID: 37775594 DOI: 10.1007/s00414-023-03092-0] [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: 05/19/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023]
Abstract
The Anthrax mailings bioterrorism attack in 2001 revealed the need for universal and rapid microbial forensic analyses on unknown biological evidence. However, the gold standard for bacterial identification includes culturing isolates, which is laborious. Molecular approaches for bacterial identification revolve around 16S ribosomal gene sequencing using Sanger or next generation sequencing (NGS) platforms, but these techniques are laboratory-based and can also be time-consuming. The Oxford Nanopore Technologies (ONT) MinION sequencer can generate long read lengths that span the entire bacterial 16S rRNA gene and accurately identify the species level. This platform can be used in the field, allowing on-site evidence analysis. However, it requires higher quantities of pure DNA compared to other sequencing platforms; thus, the extraction method for bacterial DNA is critical for downstream analysis, which to date are tailored toward a priori knowledge of the species' taxonomic grouping. During an attack, the investigative team may not know what species they are handling; therefore, identifying an extraction method that can handle all bacterial groups and generate clean DNA for the MinION is useful for microbial forensic analysis. The purpose of this study was to identify a "universal" extraction method that can be coupled with ONT MinION sequencing for use in forensic situations for rapid identification. It also evaluated the cloud-based data analysis software provided by ONT, EPI2ME. No "universal" extraction method was identified as optimal for downstream MinION sequencing. However, the DNeasy PowerSoil Kit and Noda et al. Chelex-100 method gave comparable sequencing results and could be used as rapid extraction techniques. This study showed that the ONT 16S Barcoding Kit 1-24 coupled with the 16S FASTQ workflow might not be the best for use in forensic situations where species-level identification needs to be obtained, as most alignments were approximately 89% accurate. In all seven test organisms and nine extraction methods, accurate species identification was only obtained in 63% of the cases.
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Affiliation(s)
- Kari A Graham
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340-2525, USA
| | - Javier Gomez
- Department of Biological Sciences, College of Science and Engineering Technology, Sam Houston State University, 2000 Ave I, Huntsville, TX, 77341, USA
| | - Todd P Primm
- Department of Biological Sciences, College of Science and Engineering Technology, Sam Houston State University, 2000 Ave I, Huntsville, TX, 77341, USA
| | - Rachel Houston
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340-2525, USA.
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Abdelli M, Falaise C, Morineaux-Hilaire V, Cumont A, Taysse L, Raynaud F, Ramisse V. Get to Know Your Neighbors: Characterization of Close Bacillus anthracis Isolates and Toxin Profile Diversity in the Bacillus cereus Group. Microorganisms 2023; 11:2721. [PMID: 38004733 PMCID: PMC10673079 DOI: 10.3390/microorganisms11112721] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Unexpected atypical isolates of Bacillus cereus s.l. occasionally challenge conventional microbiology and even the most advanced techniques for anthrax detection. For anticipating and gaining trust, 65 isolates of Bacillus cereus s.l. of diverse origin were sequenced and characterized. The BTyper3 tool was used for assignation to genomospecies B. mosaicus (34), B. cereus s.s (29) and B. toyonensis (2), as well as virulence factors and toxin profiling. None of them carried any capsule or anthrax-toxin genes. All harbored the non-hemolytic toxin nheABC and sphygomyelinase spH genes, whereas 41 (63%), 30 (46%), 11 (17%) and 6 (9%) isolates harbored cytK-2, hblABCD, cesABCD and at least one insecticidal toxin gene, respectively. Matrix-assisted laser desorption ionization-time of flight mass spectrometry confirmed the production of cereulide (ces genes). Phylogeny inferred from single-nucleotide polymorphisms positioned isolates relative to the B. anthracis lineage. One isolate (BC38B) was of particular interest as it appeared to be the closest B. anthracis neighbor described so far. It harbored a large plasmid similar to other previously described B. cereus s.l. megaplasmids and at a lower extent to pXO1. Whereas bacterial collection is enriched, these high-quality public genetic data offer additional knowledge for better risk assessment using future NGS-based technologies of detection.
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Affiliation(s)
- Mehdi Abdelli
- DGA CBRN Defence Center, Biology Division, French Ministry of the Armed Forces, 91710 Vert-le-Petit, France; (M.A.); (V.M.-H.); (A.C.); (L.T.); (F.R.)
- Institute for Integrative Biology of the Cell (I2BC), CNRS, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Charlotte Falaise
- DGA CBRN Defence Center, Biology Division, French Ministry of the Armed Forces, 91710 Vert-le-Petit, France; (M.A.); (V.M.-H.); (A.C.); (L.T.); (F.R.)
| | - Valérie Morineaux-Hilaire
- DGA CBRN Defence Center, Biology Division, French Ministry of the Armed Forces, 91710 Vert-le-Petit, France; (M.A.); (V.M.-H.); (A.C.); (L.T.); (F.R.)
| | - Amélie Cumont
- DGA CBRN Defence Center, Biology Division, French Ministry of the Armed Forces, 91710 Vert-le-Petit, France; (M.A.); (V.M.-H.); (A.C.); (L.T.); (F.R.)
| | - Laurent Taysse
- DGA CBRN Defence Center, Biology Division, French Ministry of the Armed Forces, 91710 Vert-le-Petit, France; (M.A.); (V.M.-H.); (A.C.); (L.T.); (F.R.)
| | - Françoise Raynaud
- DGA CBRN Defence Center, Biology Division, French Ministry of the Armed Forces, 91710 Vert-le-Petit, France; (M.A.); (V.M.-H.); (A.C.); (L.T.); (F.R.)
| | - Vincent Ramisse
- DGA CBRN Defence Center, Biology Division, French Ministry of the Armed Forces, 91710 Vert-le-Petit, France; (M.A.); (V.M.-H.); (A.C.); (L.T.); (F.R.)
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3
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Kim E, Yang SM, Jung DH, Kim HY. Differentiation between Weissella cibaria and Weissella confusa Using Machine-Learning-Combined MALDI-TOF MS. Int J Mol Sci 2023; 24:11009. [PMID: 37446188 DOI: 10.3390/ijms241311009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Although Weissella cibaria and W. confusa are essential food-fermenting bacteria, they are also opportunistic pathogens. Despite these species being commercially crucial, their taxonomy is still based on inaccurate identification methods. In this study, we present a novel approach for identifying two important Weissella species, W. cibaria and W. confusa, by combining matrix-assisted laser desorption/ionization and time-of-flight mass spectrometer (MALDI-TOF MS) data using machine-learning techniques. After on- and off-plate protein extraction, we observed that the BioTyper database misidentified or could not differentiate Weissella species. Although Weissella species exhibited very similar protein profiles, these species can be differentiated on the basis of the results of a statistical analysis. To classify W. cibaria, W. confusa, and non-target Weissella species, machine learning was used for 167 spectra, which led to the listing of potential species-specific mass-to-charge (m/z) loci. Machine-learning techniques including artificial neural networks, principal component analysis combined with the K-nearest neighbor, support vector machine (SVM), and random forest were used. The model that applied the Radial Basis Function kernel algorithm in SVM achieved classification accuracy of 1.0 for training and test sets. The combination of MALDI-TOF MS and machine learning can efficiently classify closely-related species, enabling accurate microbial identification.
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Affiliation(s)
- Eiseul Kim
- Institute of Life Sciences and Resources, Yongin 17104, Republic of Korea
- Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Seung-Min Yang
- Institute of Life Sciences and Resources, Yongin 17104, Republic of Korea
- Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Dae-Hyun Jung
- Institute of Life Sciences and Resources, Yongin 17104, Republic of Korea
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences and Resources, Yongin 17104, Republic of Korea
- Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
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Rhoades J, Fotiadou S, Paschalidou G, Papadimitriou T, Ordóñez AÁ, Kormas K, Vardaka E, Likotrafiti E. Microbiota and Cyanotoxin Content of Retail Spirulina Supplements and Spirulina Supplemented Foods. Microorganisms 2023; 11:1175. [PMID: 37317149 DOI: 10.3390/microorganisms11051175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/20/2023] [Accepted: 04/27/2023] [Indexed: 06/16/2023] Open
Abstract
Cyanobacterial biomass such as spirulina (Arthrospira spp.) is widely available as a food supplement and can also be added to foods as a nutritionally beneficial ingredient. Spirulina is often produced in open ponds, which are vulnerable to contamination by various microorganisms, including some toxin-producing cyanobacteria. This study examined the microbial population of commercially available spirulina products including for the presence of cyanobacterial toxins. Five products (two supplements, three foods) were examined. The microbial populations were determined by culture methods, followed by identification of isolates using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF), and by 16S rRNA amplicon sequencing of the products themselves and of the total growth on the enumeration plates. Toxin analysis was carried out by enzyme-linked immunosorbent assay (ELISA). Several potentially pathogenic bacteria were detected in the products, including Bacillus cereus and Klebsiella pneumoniae. Microcystin toxins were detected in all the products at levels that could lead to consumers exceeding their recommended daily limits. Substantial differences were observed in the identifications obtained using amplicon sequencing and MALDI-TOF, particularly between closely related Bacillus spp. The study showed that there are microbiological safety issues associated with commercial spirulina products that should be addressed, and these are most likely associated with the normal means of production in open ponds.
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Affiliation(s)
- Jonathan Rhoades
- Laboratory of Food Microbiology, Department of Food Science and Technology, International Hellenic University, 57400 Thessaloniki, Greece
| | - Stamatia Fotiadou
- Laboratory of Food Microbiology, Department of Food Science and Technology, International Hellenic University, 57400 Thessaloniki, Greece
| | - Georgia Paschalidou
- Laboratory of Food Microbiology, Department of Food Science and Technology, International Hellenic University, 57400 Thessaloniki, Greece
| | - Theodoti Papadimitriou
- Department of Ichthyology and Aquatic Environment, University of Thessaly, 38446 Volos, Greece
| | | | - Konstantinos Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, 38446 Volos, Greece
- Agricultural Development Institiute, University Research and Innovation Centre "IASON", Argonafton & Filellinon, 38221 Volos, Greece
| | - Elisabeth Vardaka
- Department of Nutritional Sciences and Dietetics, International Hellenic University, 57400 Thessaloniki, Greece
| | - Eleni Likotrafiti
- Laboratory of Food Microbiology, Department of Food Science and Technology, International Hellenic University, 57400 Thessaloniki, Greece
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Doganay M, Dinc G, Kutmanova A, Baillie L. Human Anthrax: Update of the Diagnosis and Treatment. Diagnostics (Basel) 2023; 13:diagnostics13061056. [PMID: 36980364 PMCID: PMC10046981 DOI: 10.3390/diagnostics13061056] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
Anthrax is one of the most important zoonotic diseases which primarily infects herbivores and occasionally humans. The etiological agent is Bacillus anthracis which is a Gram-positive, aerobic, spore-forming, nonmotile, rod-shaped bacillus. The spores are resistant to environmental conditions and remain viable for a long time in contaminated soil, which is the main reservoir for wild and domestic mammals. Infections still occur in low-income countries where they cause suffering and economic hardship. Humans are infected by contact with ill or dead animals, contaminated animal products, directly exposed to the spores in the environment or spores released as a consequence of a bioterrorist event. Three classical clinical forms of the disease, cutaneous, gastrointestinal and inhalation, are seen, all of which can potentially lead to sepsis or meningitis. A new clinical form in drug users has been described recently and named “injectional anthrax” with high mortality (>33%). The symptoms of anthrax in the early stage mimics many diseases and as a consequence it is important to confirm the diagnosis using a bacterial culture or a molecular test. With regards to treatment, human isolates are generally susceptible to most antibiotics with penicillin G and amoxicillin as the first choice, and ciprofloxacin and doxycycline serving as alternatives. A combination of one or more antibiotics is suggested in systemic anthrax. Controlling anthrax in humans depends primarily on effective control of the disease in animals. Spore vaccines are used in veterinary service, and an acellular vaccine is available for humans but its use is limited.
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Affiliation(s)
- Mehmet Doganay
- Department of Infectious Diseases, Faculty of Medicine, Lokman Hekim University, 06510 Ankara, Turkey
- Correspondence:
| | - Gokcen Dinc
- Department of Medical Microbiology, Faculty of Medicine, Erciyes University, 38039 Kayseri, Turkey;
- Department of Molecular Microbiology, Genome and Stem Cell Center, Erciyes University, 38280 Kayseri, Turkey
| | - Ainura Kutmanova
- Department of Infectious Diseases, International Higher School of Medicine, Bishkek 720010, Kyrgyzstan;
| | - Les Baillie
- School of Pharmacy and Pharmaceutical Science, College of Biomedical and Life Sciences, Cardiff University, Cardiff CF10 3NB, UK;
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Muigg V, Cuénod A, Purushothaman S, Siegemund M, Wittwer M, Pflüger V, Schmidt KM, Weisser M, Ritz N, Widmer A, Goldenberger D, Hinic V, Roloff T, Søgaard KK, Egli A, Seth-Smith HM. Diagnostic challenges within the Bacillus cereus-group: finding the beast without teeth. New Microbes New Infect 2022; 49-50:101040. [DOI: 10.1016/j.nmni.2022.101040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
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7
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Kim E, Yang SM, Cho EJ, Kim HY. Evaluation of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the discrimination of Lacticaseibacillus species. Food Microbiol 2022; 107:104094. [DOI: 10.1016/j.fm.2022.104094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 07/09/2022] [Accepted: 07/12/2022] [Indexed: 11/16/2022]
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8
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Machine Learning Algorithms for Classification of MALDI-TOF MS Spectra from Phylogenetically Closely Related Species Brucella melitensis, Brucella abortus and Brucella suis. Microorganisms 2022; 10:microorganisms10081658. [PMID: 36014076 PMCID: PMC9416640 DOI: 10.3390/microorganisms10081658] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/29/2022] [Accepted: 08/08/2022] [Indexed: 11/25/2022] Open
Abstract
(1) Background: MALDI-TOF mass spectrometry (MS) is the gold standard for microbial fingerprinting, however, for phylogenetically closely related species, the resolution power drops down to the genus level. In this study, we analyzed MALDI-TOF spectra from 44 strains of B. melitensis, B. suis and B. abortus to identify the optimal classification method within popular supervised and unsupervised machine learning (ML) algorithms. (2) Methods: A consensus feature selection strategy was applied to pinpoint from among the 500 MS features those that yielded the best ML model and that may play a role in species differentiation. Unsupervised k-means and hierarchical agglomerative clustering were evaluated using the silhouette coefficient, while the supervised classifiers Random Forest, Support Vector Machine, Neural Network, and Multinomial Logistic Regression were explored in a fine-tuning manner using nested k-fold cross validation (CV) with a feature reduction step between the two CV loops. (3) Results: Sixteen differentially expressed peaks were identified and used to feed ML classifiers. Unsupervised and optimized supervised models displayed excellent predictive performances with 100% accuracy. The suitability of the consensus feature selection strategy for learning system accuracy was shown. (4) Conclusion: A meaningful ML approach is here introduced, to enhance Brucella spp. classification using MALDI-TOF MS data.
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9
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Wang X, Chen C, Yang Y, Wang L, Li M, Zhang P, Deng S, Liang S. Proteome-Based Serotyping of the Food-Borne Pathogens Salmonella Enterica by Label-Free Mass Spectrometry. Molecules 2022; 27:molecules27144334. [PMID: 35889206 PMCID: PMC9321705 DOI: 10.3390/molecules27144334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/27/2022] [Accepted: 07/01/2022] [Indexed: 11/16/2022] Open
Abstract
Food-borne diseases caused by Salmonella enterica of 2500 serovars represent a serious public health problem worldwide. A quick identification for the pathogen serovars is critical for controlling food pollution and disease spreading. Here, we applied a mass spectrum-based proteomic profiling for identifying five epidemiologically important Salmonella enterica subsp. enterica serovars (Enteritidis, Typhimurium, London, Rissen and Derby) in China. By label-free analysis, the 53 most variable serovar-related peptides, which were almost all enzymes related to nucleoside phosphate and energy metabolism, were screened as potential peptide biomarkers, and based on which a C5.0 predicted model for Salmonella enterica serotyping with four predictor peptides was generated with the accuracy of 94.12%. In comparison to the classic gene patterns by PFGE analysis, the high-throughput proteomic fingerprints were also effective to determine the genotypic similarity among Salmonella enteric isolates according to each strain of proteome profiling, which is indicative of the potential breakout of food contamination. Generally, the proteomic dissection on Salmonella enteric serovars provides a novel insight and real-time monitoring of food-borne pathogens.
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Affiliation(s)
- Xixi Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and National Collaborative Innovation Center for Biotherapy, Chengdu 610041, China;
- Chengdu Center for Disease Control and Prevention, Chengdu 610041, China; (Y.Y.); (L.W.); (M.L.)
| | - Chen Chen
- Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu 610041, China;
| | - Yang Yang
- Chengdu Center for Disease Control and Prevention, Chengdu 610041, China; (Y.Y.); (L.W.); (M.L.)
| | - Lian Wang
- Chengdu Center for Disease Control and Prevention, Chengdu 610041, China; (Y.Y.); (L.W.); (M.L.)
| | - Ming Li
- Chengdu Center for Disease Control and Prevention, Chengdu 610041, China; (Y.Y.); (L.W.); (M.L.)
| | - Peng Zhang
- Department of Urinary Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China; (P.Z.); (S.D.)
| | - Shi Deng
- Department of Urinary Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China; (P.Z.); (S.D.)
| | - Shufang Liang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and National Collaborative Innovation Center for Biotherapy, Chengdu 610041, China;
- Correspondence:
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Bacillus cereus Invasive Infections in Preterm Neonates: an Up-to-Date Review of the Literature. Clin Microbiol Rev 2022; 35:e0008821. [PMID: 35138121 PMCID: PMC8826972 DOI: 10.1128/cmr.00088-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus cereus group species are widespread, Gram-positive, spore-forming environmental bacteria. B. cereus sensu stricto is one of the major causes of food poisoning worldwide. In high-risk individuals, such as preterm neonates, B. cereus infections can cause fatal infections. It is important to note that the phenotypic identification methods commonly used in clinical microbiology laboratories make no distinction between B. cereus sensu stricto and the other members of the group (Bacillus anthracis excluded). As a result, all the invasive infections attributed to B. cereus are not necessarily due to B. cereus sensu stricto but likely to other closely related species of the B. cereus group. Next-generation sequencing (NGS) should be used to characterize the whole genome of the strains belonging to the B. cereus group. This could confirm whether the strains involved in previously reported B. cereus invasive infections preferentially belong to formerly known or emerging individual species. Moreover, infections related to B. cereus group species have probably been overlooked, since their isolation in human bacteriological samples has for a long time been regarded as an environmental contaminant of the cultures. Recent studies have questioned the emergence or reemergence of B. cereus invasive infections in preterm infants. This review reports our current understanding of B. cereus infections in neonates, including taxonomical updates, microbiological characteristics, bacterial identification, clinical features, host-pathogen interactions, environmental sources of contamination, and antimicrobial resistance.
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Accurate classification of Listeria species by MALDI-TOF mass spectrometry incorporating denoising autoencoder and machine learning. J Microbiol Methods 2021; 192:106378. [PMID: 34818574 DOI: 10.1016/j.mimet.2021.106378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/06/2021] [Accepted: 11/16/2021] [Indexed: 11/21/2022]
Abstract
Listeria monocytogenes belongs to the category of facultative anaerobic bacteria, and is the pathogen of listeriosis, potentially lethal disease for humans. There are many similarities between L. monocytogenes and other non-pathogenic Listeria species, which causes great difficulties for their correct identification. The level of L. monocytogenes contamination in food remains high according to statistics from the Food and Drug Administration. This situation leads to food recall and destruction, which has caused huge economic losses to the food industry. Therefore, the identification of Listeria species is very important for clinical treatment and food safety. This work aims to explore an efficient classification algorithm which could easily and reliably distinguish Listeria species. We attempted to classify Listeria species by incorporating denoising autoencoder (DAE) and machine learning algorithms in matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). In addition, convolutional neural networks were used to map the high dimensional original mass spectrometry data to low dimensional core features. By analyzing MALDI-TOF MS data via incorporating DAE and support vector machine (SVM), the identification accuracy of Listeria species was 100%. The proposed classification algorithm is fast (range of seconds), easy to handle, and, more importantly, this method also allows for extending the identification scope of bacteria. The DAE model used in our research is an effective tool for the extraction of MALDI-TOF mass spectrometry features. Despite the fact that the MALDI-TOF MS dataset examined in our research had high dimensionality, the DAE + SVM algorithm was still able to exploit the hidden information embedded in the original MALDI-TOF mass spectra. The experimental results in our work demonstrated that MALDI-TOF mass spectrum combined with DAE + SVM could easily and reliably distinguish Listeria species.
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12
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Braun P, Rupprich N, Neif D, Grass G. Enzyme-Linked Phage Receptor Binding Protein Assays (ELPRA) Enable Identification of Bacillus anthracis Colonies. Viruses 2021; 13:1462. [PMID: 34452328 PMCID: PMC8402711 DOI: 10.3390/v13081462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/19/2021] [Accepted: 07/24/2021] [Indexed: 01/04/2023] Open
Abstract
Bacteriophage receptor binding proteins (RBPs) are employed by viruses to recognize specific surface structures on bacterial host cells. Recombinant RBPs have been utilized for detection of several pathogens, typically as fusions with reporter enzymes or fluorescent proteins. Identification of Bacillus anthracis, the etiological agent of anthrax, can be difficult because of the bacterium's close relationship with other species of the Bacillus cereussensu lato group. Here, we facilitated the identification of B. anthracis using two implementations of enzyme-linked phage receptor binding protein assays (ELPRA). We developed a single-tube centrifugation assay simplifying the rapid analysis of suspect colonies. A second assay enables identification of suspect colonies from mixed overgrown solid (agar) media derived from the complex matrix soil. Thus, these tests identified vegetative cells of B. anthracis with little processing time and may support or confirm pathogen detection by molecular methods such as polymerase chain reaction.
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Affiliation(s)
| | | | | | - Gregor Grass
- Department of Bacteriology and Toxinology, Bundeswehr Institute of Microbiology (IMB), 80937 Munich, Germany; (P.B.); (N.R.); (D.N.)
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Performance of MALDI-TOF Mass Spectrometry in the Philippines. Trop Med Infect Dis 2021; 6:tropicalmed6030112. [PMID: 34206828 PMCID: PMC8293455 DOI: 10.3390/tropicalmed6030112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/20/2021] [Accepted: 06/23/2021] [Indexed: 11/23/2022] Open
Abstract
Identification of the causative pathogen in infectious diseases is important for surveillance and to guide treatment. In low- and middle-income countries (LMIC), conventional culture and identification methods, including biochemical methods, are reference-standard. Biochemical methods can lack sensitivity and specificity and have slow turnaround times, causing delays in definitive therapy. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI–TOF MS) is a rapid and accurate diagnostic method. Most studies comparing MALDI–TOF MS and biochemical methods are from high-income countries, with few reports from LMIC with tropical climates. The aim of this study was to assess the performance of MALDI–TOF MS compared to conventional methods in the Philippines. Clinical bacterial or fungal isolates were identified by both MALDI–TOF MS and automated (VITEK2) or manual biochemical methods in the San Lazaro Hospital, Metro Manila, the Philippines. The concordance between MALDI–TOF MS and automated (VITEK2) or manual biochemical methods was analyzed at the species and genus levels. In total, 3530 bacterial or fungal isolates were analyzed. The concordance rate between MALDI–TOF MS and biochemical methods was 96.2% at the species level and 99.9% at the genus level. Twenty-three isolates could not be identified by MALDI–TOF MS. In this setting, MALDI–TOF MS was accurate compared with biochemical methods, at both the genus and the species level. Additionally, MALDI–TOF MS improved the turnaround time for results. These advantages could lead to improved infection management and infection control in low- and middle-income countries, even though the initial cost is high.
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Manzulli V, Rondinone V, Buchicchio A, Serrecchia L, Cipolletta D, Fasanella A, Parisi A, Difato L, Iatarola M, Aceti A, Poppa E, Tolve F, Pace L, Petruzzi F, Rovere ID, Raele DA, Del Sambro L, Giangrossi L, Galante D. Discrimination of Bacillus cereus Group Members by MALDI-TOF Mass Spectrometry. Microorganisms 2021; 9:microorganisms9061202. [PMID: 34199368 PMCID: PMC8228078 DOI: 10.3390/microorganisms9061202] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/29/2021] [Accepted: 05/30/2021] [Indexed: 11/16/2022] Open
Abstract
Matrix-Assisted Laser Desorption/Ionization Time Of Flight Mass Spectrometry (MALDI-TOF MS) technology is currently increasingly used in diagnostic laboratories as a cost effective, rapid and reliable routine technique for the identification and typing of microorganisms. In this study, we used MALDI-TOF MS to analyze a collection of 160 strains belonging to the Bacillus cereus group (57 B. anthracis, 49 B. cereus, 1 B. mycoides, 18 B. wiedmannii, 27 B. thuringiensis, 7 B. toyonensis and 1 B. weihenstephanensis) and to detect specific biomarkers which would allow an unequivocal identification. The Main Spectra Profiles (MSPs) were added to an in-house reference library, expanding the current commercial library which does not include B. toyonensis and B. wiedmannii mass spectra. The obtained mass spectra were statistically compared by Principal Component Analysis (PCA) that revealed seven different clusters. Moreover, for the identification purpose, were generated dedicate algorithms for a rapid and automatic detection of characteristic ion peaks after the mass spectra acquisition. The presence of specific biomarkers can be used to differentiate strains within the B. cereus group and to make a reliable identification of Bacillus anthracis, etiologic agent of anthrax, which is the most pathogenic and feared bacterium of the group. This could offer a critical time advantage for the diagnosis and for the clinical management of human anthrax even in case of bioterror attacks.
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Affiliation(s)
- Viviana Manzulli
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Valeria Rondinone
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
- Correspondence: ; Tel.: +39-0881-786330
| | - Alessandro Buchicchio
- Bruker Italia s.r.l., Daltonics Division, Strada Cluentina, 26/R, 62100 Macerata, Italy;
| | - Luigina Serrecchia
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Dora Cipolletta
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Antonio Fasanella
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Laura Difato
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Michela Iatarola
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Angela Aceti
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Elena Poppa
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Francesco Tolve
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Lorenzo Pace
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Fiorenza Petruzzi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Ines Della Rovere
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Donato Antonio Raele
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Laura Del Sambro
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Luigi Giangrossi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
| | - Domenico Galante
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (V.M.); (L.S.); (D.C.); (A.F.); (A.P.); (L.D.); (M.I.); (A.A.); (E.P.); (F.T.); (L.P.); (F.P.); (I.D.R.); (D.A.R.); (L.D.S.); (L.G.); (D.G.)
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Novel Strategy for Rapidly and Safely Distinguishing Bacillus anthracis and Bacillus cereus by Use of Peptide Mass Fingerprints Based on Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. J Clin Microbiol 2020; 59:JCM.02358-20. [PMID: 33115846 DOI: 10.1128/jcm.02358-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 10/19/2020] [Indexed: 12/28/2022] Open
Abstract
The objective of this study was to construct a rapid, high-throughput, and biosafety-compatible screening method for Bacillus anthracis and Bacillus cereus based on matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). MALDI-TOF MS coupled to ClinProTools was used to discover MALDI-TOF MS biomarker peaks and generate a classification model based on a genetic algorithm (GA) to differentiate between different Bacillus anthracis and Bacillus cereus isolates. Thirty Bacillus anthracis and 19 Bacillus cereus strains were used to construct and analyze the model, and 40 Bacillus strains were used for validation. For the GA screening model, the cross-validation values, which reflect the ability of the model to handle variability among the test spectra, and the recognition capability values, which reflect the model's ability to correctly identify its component spectra, were all 100%. This model contained 10 biomarker peaks (m/z 3,339.9, 3,396.3, 3,682.4, 5,476.7, 6,610.6, 6,680.1, 7,365.3, 7,792.4, 9,475.8, and 10,934.1) used to correctly identify 28 Bacillus anthracis and 12 Bacillus cereus isolates from 40 Bacillus isolates, with a sensitivity and specificity of 100%. With the obvious advantages of being rapid, highly accurate, and highly sensitive and having a low cost and high throughput, MALDI-TOF MS ClinProTools is a powerful and reliable tool for screening Bacillus anthracis and Bacillus cereus strains.
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16
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Kim E, Yang SM, Kim HB, Kim HY. Novel specific peaks for differentiating the Lactobacillus plantarum group using matrix-assisted laser desorption ionization time-of-flight mass spectrometry. J Microbiol Methods 2020; 178:106064. [PMID: 32961241 DOI: 10.1016/j.mimet.2020.106064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/12/2020] [Accepted: 09/18/2020] [Indexed: 11/30/2022]
Abstract
Identifying the Lactobacillus plantarum group using conventional taxonomic methods such as biochemical analysis and 16S rRNA gene sequencing is inaccurate, expensive, and time-consuming. In this study, for the first time, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was used to identify the L. plantarum group and develop a classification method for species level differentiation with specific peaks based on mass spectra. Furthermore, from the mass spectra of 131 isolates aligned with the biotyper database, 131 isolates (100%) were correctly identified at the species level with a mean score of 2.316. However, commercial databases could not accurately differentiate some isolates of L. plantarum group species because the same colony was identified as different species with similar score values. Moreover, these two species showed a similar mass pattern in the main spectrum profiles-dendrogram and Principal component analysis clustering generated by the mass peak of the reference strains and isolates. Specific peaks to each species were investigated from the analyzed mass peak, and they clearly showed that three species could be differentiated. These peaks were verified by re-identifying 131 isolates, and it demonstrated 100% specificity and accuracy. Also, using a specific peak, isolates that were undifferentiated from the biotyper database were clearly identified as one species, similar to species-specific polymerase chain reaction. Our data demonstrate that the specific peaks accurately differentiate the L. plantarum group and enable high-resolution identification at the species level; this methodology can be used to rapidly and easily identify them and determine their nomenclature.
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Affiliation(s)
- Eiseul Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Seung-Min Yang
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Hyeon-Be Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea.
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17
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Rapid Microscopic Detection of Bacillus anthracis by Fluorescent Receptor Binding Proteins of Bacteriophages. Microorganisms 2020; 8:microorganisms8060934. [PMID: 32575866 PMCID: PMC7356292 DOI: 10.3390/microorganisms8060934] [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: 05/29/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 12/19/2022] Open
Abstract
Bacillus anthracis, the etiological agent of anthrax disease, is typically diagnosed by immunological and molecular methods such as polymerase chain reaction (PCR). Alternatively, mass spectrometry techniques may aid in confirming the presence of the pathogen or its toxins. However, because of the close genetic relationship between B. anthracis and other members of the Bacillus cereus sensu lato group (such as Bacillus cereus or Bacillus thuringiensis) mis- or questionable identification occurs frequently. Also, bacteriophages such as phage gamma (which is highly specific for B. anthracis) have been in use for anthrax diagnostics for many decades. Here we employed host cell-specific receptor binding proteins (RBP) of (pro)-phages, also known as tail or head fibers, to develop a microscopy-based approach for the facile, rapid and unambiguous detection of B. anthracis cells. For this, the genes of (putative) RBP from Bacillus phages gamma, Wip1, AP50c and from lambdoid prophage 03 located on the chromosome of B. anthracis were selected. Respective phage genes were heterologously expressed in Escherichia coli and purified as fusions with fluorescent proteins. B. anthracis cells incubated with either of the reporter fusion proteins were successfully surface-labeled. Binding specificity was confirmed as RBP fusion proteins did not bind to most isolates of a panel of other B. cereus s.l. species or to more distantly related bacteria. Remarkably, RBP fusions detected encapsulated B. anthracis cells, thus RBP were able to penetrate the poly-γ-d-glutamate capsule of B. anthracis. From these results we anticipate this RBP-reporter assay may be useful for rapid confirmative identification of B. anthracis.
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18
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Bacillus paranthracis Isolate from Blood of Fatal Ebola Virus Disease Case. Pathogens 2020; 9:pathogens9060475. [PMID: 32560095 PMCID: PMC7350349 DOI: 10.3390/pathogens9060475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/12/2020] [Accepted: 06/14/2020] [Indexed: 11/20/2022] Open
Abstract
A Bacillus paranthracis isolate was cultured from the blood of a fatal Ebola virus disease (EVD) case in Liberia and was identified by whole genome sequencing. Although B. paranthracis has only recently been described and is poorly characterized, this case may represent the bacterial co-infection of an EVD patient.
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19
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Cen YK, Lin JG, Wang YL, Wang JY, Liu ZQ, Zheng YG. The Gibberellin Producer Fusarium fujikuroi: Methods and Technologies in the Current Toolkit. Front Bioeng Biotechnol 2020; 8:232. [PMID: 32292777 PMCID: PMC7118215 DOI: 10.3389/fbioe.2020.00232] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 03/06/2020] [Indexed: 12/18/2022] Open
Abstract
In recent years, there has been a noticeable increase in research interests on the Fusarium species, which includes prevalent plant pathogens and human pathogens, common microbial food contaminants and industrial microbes. Taken the advantage of gibberellin synthesis, Fusarium fujikuroi succeed in being a prevalent plant pathogen. At the meanwhile, F. fujikuroi was utilized for industrial production of gibberellins, a group of extensively applied phytohormone. F. fujikuroi has been known for its outstanding performance in gibberellin production for almost 100 years. Research activities relate to this species has lasted for a very long period. The slow development in biological investigation of F. fujikuroi is largely due to the lack of efficient research technologies and molecular tools. During the past decade, technologies to analyze the molecular basis of host-pathogen interactions and metabolic regulations have been developed rapidly, especially on the aspects of genetic manipulation. At the meanwhile, the industrial fermentation technologies kept sustained development. In this article, we reviewed the currently available research tools/methods for F. fujikuroi research, focusing on the topics about genetic engineering and gibberellin production.
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Affiliation(s)
- Yu-Ke Cen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Jian-Guang Lin
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - You-Liang Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Jun-You Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
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20
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Zasada AA. Detection and Identification of Bacillus anthracis: From Conventional to Molecular Microbiology Methods. Microorganisms 2020; 8:E125. [PMID: 31963339 PMCID: PMC7023132 DOI: 10.3390/microorganisms8010125] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 02/06/2023] Open
Abstract
Rapid and reliable identification of Bacillus anthracis is of great importance, especially in the event of suspected deliberate release of anthrax spores. However, the identification of B. anthracis is challenging due to its high similarity to closely related species. Since Amerithrax in 2001, a lot of effort has been made to develop rapid methods for detection and identification of this microorganism with special focus on easy-to-perform rapid tests for first-line responders. This article presents an overview of the evolution of B. anthracis identification methods from the time of the first description of the microorganism until the present day.
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Affiliation(s)
- Aleksandra A Zasada
- Department of Sera and Vaccines Evaluation, National Institute of Public Health-National Institute of Hygiene, Chocimska 24, 00-791 Warsaw, Poland
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21
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Abdel Samad R, Al Disi Z, Mohammad Ashfaq MY, Wahib SM, Zouari N. The use of principle component analysis and MALDI-TOF MS for the differentiation of mineral forming Virgibacillus and Bacillus species isolated from sabkhas. RSC Adv 2020; 10:14606-14616. [PMID: 35497157 PMCID: PMC9051895 DOI: 10.1039/d0ra01229g] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 04/01/2020] [Indexed: 01/23/2023] Open
Abstract
Occurrence of mineral forming and other bacteria in mats is well demonstrated. However, their high diversity shown by ribotyping has not been explained, although it could explain the diversity of formed minerals. Common biomarkers as well as phylogenic relationships are useful tools for clustering the isolates and the prediction of their potential role in the natural niche. In this study, a combination of MALDI-TOF MS with PCA was shown to be a powerful tool to categorize 35 mineral forming bacterial isolates isolated from Dohat Faishakh sabkha, northwest of Qatar (23 from decaying mats and 12 from living ones). The 23 strains from decaying mats belong to the Virgibacillus genus as identified by ribotyping and are shown to be highly involved in the formation of protodolomite and a diversity of minerals. They were used as internal references for the categorization of sabkha bacteria. Combination of the isolation of bacteria on selective mineral forming media, their MALDI TOF MS protein profiling and PCA analysis established their relationship in a phylloproteomic dendrogram based on protein biomarkers including m/z 4905, 3265, 5240, 6430, 7765, and 9815. PCA analysis clustered the studied isolates into 3 major clusters, showing strong correspondence to the 3 phylloproteomic groups that were established by the dendrogram. Both clustering analysis means have evidently demonstrated a relationship between known Virgibacillus strains and other related bacteria based on profiling of their synthesized proteins. Thus, larger populations of bacteria in mats can be easily screened for their potential to exhibit certain activities, which is of ecological, environmental and biotechnological significance. Occurrence of mineral forming and other bacteria in mats is well demonstrated.![]()
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Affiliation(s)
- Rim Abdel Samad
- Department of Biological and Environmental Sciences
- College of Arts and Sciences
- Qatar University
- Doha
- Qatar
| | - Zulfa Al Disi
- Department of Biological and Environmental Sciences
- College of Arts and Sciences
- Qatar University
- Doha
- Qatar
| | | | - Sara Mohiddin Wahib
- Department of Biological and Environmental Sciences
- College of Arts and Sciences
- Qatar University
- Doha
- Qatar
| | - Nabil Zouari
- Department of Biological and Environmental Sciences
- College of Arts and Sciences
- Qatar University
- Doha
- Qatar
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Pereira JQ, Ritter AC, Cibulski S, Brandelli A. Functional genome annotation depicts probiotic properties of Bacillus velezensis FTC01. Gene 2019; 713:143971. [DOI: 10.1016/j.gene.2019.143971] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022]
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23
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Analysis of bacteria associated with honeys of different geographical and botanical origin using two different identification approaches: MALDI-TOF MS and 16S rDNA PCR technique. PLoS One 2019; 14:e0217078. [PMID: 31120945 PMCID: PMC6532876 DOI: 10.1371/journal.pone.0217078] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/05/2019] [Indexed: 12/14/2022] Open
Abstract
In the presented work identification of microorganisms isolated from various types of honeys was performed. Martix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rDNA sequencing were applied to study environmental bacteria strains.With both approches, problematic spore-forming Bacillus spp, but also Staphylococcus spp., Lysinibacillus spp., Micrococcus spp. and Brevibacillus spp were identified. However, application of spectrometric technique allows for an unambiguous distinction between species/species groups e.g.B. subtilis or B. cereus groups. MALDI TOF MS and 16S rDNA sequencing allow for construction of phyloproteomic and phylogenetic trees of identified bacterial species. Furthermore, the correlation beetween physicochemical properties, geographical and botanical origin and the presence bacterial species in honey samples were investigated.
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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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