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Maktabdar M, Truelstrup Hansen L, Wemmenhove E, Gkogka E, Dalgaard P. Prevalence, characteristics, and selection of Bacillus cereus sub-groups from dairy products for challenge testing and predictive model development. J Food Prot 2024:100367. [PMID: 39357564 DOI: 10.1016/j.jfp.2024.100367] [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: 07/24/2024] [Revised: 09/24/2024] [Accepted: 09/26/2024] [Indexed: 10/04/2024]
Abstract
Prevalence, toxin gene profiles, lactose fermentation, and growth responses of B. cereus sensu lato sub-groups in various dairy and dairy alternative products and ingredients were studied to identify relevant isolates for challenge testing and model development to predict and manage growth responses. Out of 71 examined products or ingredients, 51 B. cereus s.l. isolates were obtained from 35 positive samples (49% prevalence). These 51 isolates along with 18 additional dairy isolates and 12 B. cereus s.l. reference strains were identified using MALDI-TOF. The 81 isolates were further characterized by panC sequencing, testing for cold shock and toxin genes (cspA; hbl, nhe, CytK and ces), lactose fermentation, and study of growth rates (µmax) under various conditions (45°C, 10°C, 6% NaCl, pH 5.1), resulting in 298 µmax-values. These conditions were selected to differentiate mesophilic and psychrotolerant strains and to identify tolerant isolates. Dairy powders (83%), pasteurized upconcentrated cheese whey (43%), and cheeses (42%) had the highest prevalences of B. cereus s.l. and the highest concentrations in positive samples (5-100 CFU/g or ml). The panC groups II, III, IV, VI, and VIII were detected among the dairy isolates, with 97% harbouring one or more toxin genes. Lactose fermentation was observed in 42% of isolates, with lactose-fermenting B. cereus s.l. isolates of panC groups III and IV dominant in dairy powders. Growth rates of B. cereus s.l. varied considerably, among and within panC groups of the dairy isolates. Based on the highest growth rates at 45°C, 10°C, 6 % NaCl, pH 5.1, panC group membership, toxin genes profiles, and lactose fermentation ability, two cocktails of "mesophilic" or "psychrotolerant" isolates were selected. These strain cocktails can be used in future challenge testing and predictive food microbiology studies to evaluate and manage growth of B. cereus s.l. in dairy products and ingredients.
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Affiliation(s)
- Maryam Maktabdar
- Food Microbiology and Hygiene, National Food Institute (DTU Food), Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Lisbeth Truelstrup Hansen
- Food Microbiology and Hygiene, National Food Institute (DTU Food), Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Ellen Wemmenhove
- Arla Foods Ingredients Innovation Center, Arla Foods Ingredients, Nr. Vium, Denmark
| | | | - Paw Dalgaard
- Food Microbiology and Hygiene, National Food Institute (DTU Food), Technical University of Denmark, Kgs. Lyngby, Denmark
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2
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Du Y, Qian C, Li X, Zheng X, Huang S, Yin Z, Chen T, Pan L. Unveiling intraspecific diversity and evolutionary dynamics of the foodborne pathogen Bacillus paranthracis through high-quality pan-genome analysis. Curr Res Food Sci 2024; 9:100867. [PMID: 39376581 PMCID: PMC11456886 DOI: 10.1016/j.crfs.2024.100867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2024] [Revised: 09/20/2024] [Accepted: 09/20/2024] [Indexed: 10/09/2024] Open
Abstract
Understanding the evolutionary dynamics of foodborne pathogens throughout host-associated habitats is of utmost importance. Bacterial pan-genomes, as dynamic entities, are strongly influenced by ecological lifestyles. As a phenotypically diverse species in the Bacillus cereus group, Bacillus paranthracis is recognized as an emerging foodborne pathogen and a probiotic simultaneously. This poorly understood species is a suitable study model for adaptive pan-genome evolution. In this study, we determined the biogeographic distribution, abundance, genetic diversity, and genotypic profiles of key genetic elements of B. paranthracis. Metagenomic read recruitment analyses demonstrated that B. paranthracis members are globally distributed and abundant in host-associated habitats. A high-quality pan-genome of B. paranthracis was subsequently constructed to analyze the evolutionary dynamics involved in ecological adaptation comprehensively. The open pan-genome indicated a flexible gene repertoire with extensive genetic diversity. Significant divergences in the phylogenetic relationships, functional enrichment, and degree of selective pressure between the different components demonstrated different evolutionary dynamics between the core and accessory genomes driven by ecological forces. Purifying selection and gene loss are the main signatures of evolutionary dynamics in B. paranthracis pan-genome. The plasticity of the accessory genome is characterized by horizontal gene transfer (HGT), massive gene losses, and weak purifying or positive selection, which might contribute to niche-specific adaptation. In contrast, although the core genome dominantly undergoes purifying selection, its association with HGT and positively selected mutations indicates its potential role in ecological diversification. Furthermore, host fitness-related dynamics are characterized by the loss of secondary metabolite biosynthesis gene clusters (BGCs) and CAZyme-encoding genes and the acquisition of antimicrobial resistance (AMR) and virulence genes via HGT. This study offers a case study of pan-genome evolution to investigate the ecological adaptations reflected by biogeographical characteristics, thereby advancing the understanding of intraspecific diversity and evolutionary dynamics of foodborne pathogens.
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Affiliation(s)
- Yuhui Du
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological slaEngineering, South China University of Technology, Guangzhou, 510006, Guangdong, PR China
| | - Chengqian Qian
- School of Biology and Biological Engineering, Guangzhou Higher Education Mega Centre, South China University of Technology, Guangzhou, 510006, Guangdong, PR China
- Foshan Branch of Tianyan (Tianjin) High-tech Co., Ltd, Foshan, 528000, Guangdong, PR China
| | - Xianxin Li
- Foshan Branch of Tianyan (Tianjin) High-tech Co., Ltd, Foshan, 528000, Guangdong, PR China
| | - Xinqian Zheng
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological slaEngineering, South China University of Technology, Guangzhou, 510006, Guangdong, PR China
| | - Shoucong Huang
- Foshan Haitian (Gaoming) Flavouring Food Co., Ltd, Foshan, 52a8000, Guangdong, PR China
| | - Zhiqiu Yin
- Department of Clinical Laboratory, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510700, Guangdong, PR China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological slaEngineering, South China University of Technology, Guangzhou, 510006, Guangdong, PR China
| | - Li Pan
- School of Biology and Biological Engineering, Guangzhou Higher Education Mega Centre, South China University of Technology, Guangzhou, 510006, Guangdong, PR China
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Farina D, Bianco A, Manzulli V, Castellana S, Parisi A, Caruso M, Fraccalvieri R, Serrecchia L, Rondinone V, Pace L, Fasanella A, Vetritto V, Difato LM, Cipolletta D, Iatarola M, Galante D. Antimicrobial and Phylogenomic Characterization of Bacillus cereus Group Strains Isolated from Different Food Sources in Italy. Antibiotics (Basel) 2024; 13:898. [PMID: 39335071 PMCID: PMC11444136 DOI: 10.3390/antibiotics13090898] [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: 06/25/2024] [Revised: 08/08/2024] [Accepted: 08/19/2024] [Indexed: 09/30/2024] Open
Abstract
Background:Bacillus cereus is a widespread environmental Gram-positive bacterium which is especially common in soil and dust. It produces two types of toxins that cause vomiting and diarrhea. At present, foodborne outbreaks due to Bacillus cereus group bacteria (especially Bacillus cereus sensu stricto) are rising, representing a serious problem in the agri-food supply chain. Methods: In this work, we analyzed 118 strains belonging to the Bacillus cereus group, isolated from several food sources, for which in vitro and in silico antibiotic resistance assessments were performed. Results: Many strains showed intermediate susceptibility to clindamycin, erythromycin, and tetracycline, suggesting an evolving acquisition of resistance against these antibiotics. Moreover, one strain showed intermediate resistance to meropenem, an antibiotic currently used to treat infections caused by Bacillus cereus. In addition to the phenotypic antimicrobial resistance profile, all strains were screened for the presence/absence of antimicrobial genes via whole-genome sequencing. There was inconsistency between the in vitro and in silico analyses, such as in the case of vancomycin, for which different isolates harbored resistance genes but, phenotypically, the same strains were sensitive. Conclusions: This would suggest that antibiotic resistance is a complex phenomenon due to a variety of genetic, epigenetic, and biochemical mechanisms.
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Affiliation(s)
- Donatella Farina
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Angelica Bianco
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Viviana Manzulli
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Stefano Castellana
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Marta Caruso
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Rosa Fraccalvieri
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Luigina Serrecchia
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Valeria Rondinone
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Lorenzo Pace
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Antonio Fasanella
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Valerio Vetritto
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Laura Maria Difato
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Dora Cipolletta
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Michela Iatarola
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Domenico Galante
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
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Kain T, Albahri M, Plötz M, Jessberger N. Growth, persistence and toxin production of pathogenic bacteria in plant-based drinking milk alternatives. J Food Sci 2024; 89:5799-5811. [PMID: 39169550 DOI: 10.1111/1750-3841.17309] [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: 06/07/2024] [Revised: 07/23/2024] [Accepted: 07/28/2024] [Indexed: 08/23/2024]
Abstract
The present study investigated the microbiological safety of the increasingly popular plant-based milk alternatives. No (10/27) or only very low microbial counts (17/27) were detected in the tested products. These were mainly identified as spore formers via MALDI-ToF-MS. Three products contained Bacillus cereus group isolates, which were able to form considerable amounts of enterotoxins and exhibited cytotoxicity towards CaCo-2 cells. Preliminary tests showed good growth of B. cereus, Listeria monocytogenes, and Salmonella enterica in all tested products (maximum bacterial counts: 5 × 1012 cfu/mL). These experiments also revealed strain-, time-, and temperature-, but especially product-specific enterotoxin production of B. cereus. In propagation and persistence tests according to DIN EN ISO 20976-1:2019-09, rapid bacterial proliferation was also detected in all products. B. cereus generally showed lower bacterial counts (106-107 cfu/mL) compared to L. monocytogenes and S. enterica (108-109 cfu/mL), but was detectable in a larger number of products over the test period of 6 weeks. pH values decreased (20/27) over time and visual and/or olfactory alterations (24/27) were observed. The present study provides information on the occurrence, growth and persistence of pathogenic bacteria in plant-based drinking milk alternatives. It also points out that the accompanying changes in pH, odor, and appearance are not necessarily recognizable to the consumer. PRACTICAL APPLICATION: The present study contributes to the understanding of the microbial risk related to plant-based drinking milk alternatives. It is crucial that the manufacturer ensures that particularly spore formers have been effectively eliminated from the products. Among them, especially toxin-producing bacteria can pose a risk to the consumer, as these products promote proliferation and persistence of the bacteria.
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Affiliation(s)
- Theresa Kain
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Manar Albahri
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Madeleine Plötz
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Nadja Jessberger
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hanover, Germany
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5
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Su J, Chandross-Cohen T, Qian C, Carroll L, Kimble K, Yount M, Wiedmann M, Kovac J. Assessment of the exposure to cytotoxic Bacillus cereus group genotypes through HTST milk consumption. J Dairy Sci 2024:S0022-0302(24)00896-8. [PMID: 38851576 DOI: 10.3168/jds.2024-24703] [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: 01/22/2024] [Accepted: 05/02/2024] [Indexed: 06/10/2024]
Abstract
This study addresses the limited tools available for assessing food safety risks from cytotoxic Bacillus cereus group strains in contaminated food. We quantified the growth, in skim milk broth, of 17 cytotoxic B. cereus strains across 6 phylogenetic groups with various virulence gene profiles. The strains did not grow in HTST milk at 4 or 6°C. At 10°C, 15 strains exhibited growth; at 8°C, one strain grew; and all strains grew at temperatures ≥ 14°C. Using growth data from 16 strains, we developed linear secondary growth models and an exposure assessment model. This model, simulating a 5-stage HTST milk supply chain and up to 35 d of consumer storage with an initial contamination of 100 cfu/mL, estimated that 2.81 ± 0.66% and 4.13 ± 2.53% of milk containers would surpass 105 cfu/mL of B. cereus by d 21 and 35, respectively. A sensitivity analysis identified the initial physiological state of cells (Q0) as the most influential variable affecting predictions for specific isolates. What-if scenarios indicated that increases in mean and variability of consumer storage temperatures significantly affected the predicted B. cereus concentrations in milk. This model serves as an initial tool for risk-based food safety decision making regarding low-level B. cereus contamination.
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Affiliation(s)
- Jun Su
- Department of Food Science, Cornell University, Ithaca, NY 14850
| | - Tyler Chandross-Cohen
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802
| | - Chenhao Qian
- Department of Food Science, Cornell University, Ithaca, NY 14850
| | - Laura Carroll
- Department of Clinical Microbiology, SciLifeLab, Umeå University, Umeå, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden; Integrated Science Lab (IceLab), Umeå University, Umeå, Sweden
| | - Kayla Kimble
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802
| | - Mackenna Yount
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY 14850
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802
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6
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Pal A, Mann A, den Bakker HC. Analysis of Microbial Composition of Edible Insect Products Available for Human Consumption within the United States Using Traditional Microbiological Methods and Whole Genome Sequencing. J Food Prot 2024; 87:100277. [PMID: 38615992 DOI: 10.1016/j.jfp.2024.100277] [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: 09/25/2023] [Revised: 04/03/2024] [Accepted: 04/09/2024] [Indexed: 04/16/2024]
Abstract
Edible insects offer a promising protein source for humans, but their food safety risks have not been previously investigated within the United States. Therefore, the aim of this study was to investigate the microbial content of processed edible insect products. A total of eight different types of edible insect products, including diving beetles, silkworms, grasshoppers, Jamaican crickets, mealworms, mole crickets, whole roasted crickets, and 100% pure cricket powder, were purchased from a large online retailer for the analysis. All the products were purchased in August 2022 and examined between August 2022 and November 2022. Traditional microbiological methods were employed to determine microbial counts for each product type using three replicates (total number of samples = 24). This included assessing aerobic bacterial spore, lactic acid bacteria, Enterobacteriaceae, total viable counts, and the presence of Salmonella. Additionally, whole genome sequencing was employed to further characterize selected colonies (n = 96). Microbial counts data were statistically analyzed using one-way ANOVA, while sequence data were taxonomically classified using Sepia.Bacilluscereusgroup isolates underwent additional characterization with Btyper3. Product type significantly influenced total viable counts, bacterial spore counts, and lactic acid bacteria counts (P = 0.00391, P = 0.0065, and P < 0.001, respectively), with counts ranging from < 1.70 to 6.01 Log10 CFU/g, <1.70 to 5.25 Log10 CFU/g, and < 1.70 to 4.86 Log10 CFU/g, respectively. Enterobacteriaceae were only detected in mole crickets (<2.30 Log10 CFU/g) and house cricket powder (<2.15 Log10 CFU/g). All samples were negative for Salmonella. Whole genome sequencing revealed the presence of 12 different bacterial genera among the analyzed isolates, with a majority belonging to the Bacillus genus. Some of the isolates of Bacillus cereus group were identified as biovar Emeticus. Overall, although edible insects offer a promising food alternative, the presence of Bacillus cereus group in some products could raise concerns regarding food safety.
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Affiliation(s)
- Amrit Pal
- Center for Food Safety, Department of Food Science and Technology, College of Agriculture and Environmental Sciences, University of Georgia, Griffin, GA, USA
| | - Amy Mann
- Center for Food Safety, Department of Food Science and Technology, College of Agriculture and Environmental Sciences, University of Georgia, Griffin, GA, USA
| | - Henk C den Bakker
- Center for Food Safety, Department of Food Science and Technology, College of Agriculture and Environmental Sciences, University of Georgia, Griffin, GA, USA.
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7
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Roch FF, Dzieciol M, Quijada NM, Alteio LV, Mester PJ, Selberherr E. Microbial community structure of plant-based meat alternatives. NPJ Sci Food 2024; 8:27. [PMID: 38740858 DOI: 10.1038/s41538-024-00269-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
A reduction in animal-based diets has driven market demand for alternative meat products, currently raising a new generation of plant-based meat alternatives (PBMAs). It remains unclear whether these substitutes are a short-lived trend or become established in the long term. Over the last few years, the trend of increasing sales and diversifying product range has continued, but publication activities in this field are currently limited mainly to market research and food technology topics. As their popularity increases, questions emerge about the safety and nutritional risks of these novel products. Even though all the examined products must be heated before consumption, consumers lack experience with this type of product and thus further research into product safety, is desirable. To consider these issues, we examined 32 PBMAs from Austrian supermarkets. Based on 16S rRNA gene amplicon sequencing, the majority of the products were dominated by lactic acid bacteria (either Leuconostoc or Latilactobacillus), and generally had low alpha diversity. Pseudomonadota (like Pseudomonas and Shewanella) dominated the other part of the products. In addition to LABs, a high diversity of different Bacillus, but also some Enterobacteriaceae and potentially pathogenic species were isolated with the culturing approach. We assume that especially the dominance of heterofermentative LABs has high relevance for the product stability and quality with the potential to increase shelf life of the products. The number of isolated Enterobacteriaceae and potential pathogens were low, but they still demonstrated that these products are suitable for their presence.
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Affiliation(s)
- Franz-Ferdinand Roch
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Monika Dzieciol
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Narciso M Quijada
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185, Villamayor (Salamanca), Spain
| | - Lauren V Alteio
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, 3430, Tulln, Austria
| | - Patrick-Julian Mester
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Evelyne Selberherr
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria.
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Chung T, Salazar A, Harm G, Johler S, Carroll LM, Kovac J. Comparison of the performance of multiple whole-genome sequence-based tools for the identification of Bacillus cereus sensu stricto biovar Thuringiensis. Appl Environ Microbiol 2024; 90:e0177823. [PMID: 38470126 PMCID: PMC11026089 DOI: 10.1128/aem.01778-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/19/2024] [Indexed: 03/13/2024] Open
Abstract
The Bacillus cereus sensu stricto (s.s.) species comprises strains of biovar Thuringiensis (Bt) known for their bioinsecticidal activity, as well as strains with foodborne pathogenic potential. Bt strains are identified (i) based on the production of insecticidal crystal proteins, also known as Bt toxins, or (ii) based on the presence of cry, cyt, and vip genes, which encode Bt toxins. Multiple bioinformatics tools have been developed for the detection of crystal protein-encoding genes based on whole-genome sequencing (WGS) data. However, the performance of these tools is yet to be evaluated using phenotypic data. Thus, the goal of this study was to assess the performance of four bioinformatics tools for the detection of crystal protein-encoding genes. The accuracy of sequence-based identification of Bt was determined in reference to phenotypic microscope-based screening for the production of crystal proteins. A total of 58 diverse B. cereus sensu lato strains isolated from clinical, food, environmental, and commercial biopesticide products underwent WGS. Isolates were examined for crystal protein production using phase contrast microscopy. Crystal protein-encoding genes were detected using BtToxin_Digger, BTyper3, IDOPS (identification of pesticidal sequences), and Cry_processor. Out of 58 isolates, the phenotypic production of crystal proteins was confirmed for 18 isolates. Specificity and sensitivity of Bt identification based on sequences were 0.85 and 0.94 for BtToxin_Digger, 0.97 and 0.89 for BTyper3, 0.95 and 0.94 for IDOPS, and 0.88 and 1.00 for Cry_processor, respectively. Cry_processor predicted crystal protein production with the highest specificity, and BtToxin_Digger and IDOPS predicted crystal protein production with the highest sensitivity. Three out of four tested bioinformatics tools performed well overall, with IDOPS achieving high sensitivity and specificity (>0.90).IMPORTANCEStrains of Bacillus cereus sensu stricto (s.s.) biovar Thuringiensis (Bt) are used as organic biopesticides. Bt is differentiated from the foodborne pathogen Bacillus cereus s.s. by the production of insecticidal crystal proteins. Thus, reliable genomic identification of biovar Thuringiensis is necessary to ensure food safety and facilitate risk assessment. This study assessed the accuracy of whole-genome sequencing (WGS)-based identification of Bt compared to phenotypic microscopy-based screening for crystal protein production. Multiple bioinformatics tools were compared to assess their performance in predicting crystal protein production. Among them, identification of pesticidal sequences performed best overall at WGS-based Bt identification.
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Affiliation(s)
- Taejung Chung
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Abimel Salazar
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Grant Harm
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Sophia Johler
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Laura M. Carroll
- Department of Clinical Microbiology, SciLifeLab, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
- Integrated Science Lab (IceLab), Umeå University, Umeå, Sweden
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
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9
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Zheng Z, Ye L, Xiong W, Hu Q, Chen K, Sun R, Chen S. Prevalence and genomic characterization of the Bacillus cereus group strains contamination in food products in Southern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 921:170903. [PMID: 38354793 DOI: 10.1016/j.scitotenv.2024.170903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/16/2024]
Abstract
The Bacillus cereus group, as one of the important opportunistic foodborne pathogens, is considered a risk to public health due to foodborne diseases and an important cause of economic losses to food industries. This study aimed to gain essential information on the prevalence, phenotype, and genotype of B. cereus group strains isolated from various food products in China. A total of 890 strains of B. cereus group bacteria from 1181 food samples from 2020 to 2023 were identified using the standardized detection method. These strains were found to be prevalent in various food types, with the highest contamination rates observed in cereal flour (55.8 %) and wheat/rice noodles (45.7 %). The tested strains exhibited high resistance rates against penicillin (98.5 %) and ampicillin (98.9 %). Strains isolated from cereal flour had the highest rate of meropenem resistance (7.8 %), while strains from sausages were most resistant to vancomycin (16.8 %). A total of 234 out of the 891 B. cereus group strains were randomly selected for WGS analysis, 18.4 % of which displayed multidrug resistance. The species identification by WGS analysis revealed the presence of 10 distinct species within the B. cereus group, with B. cereus species being the most prevalent. The highest level of species diversity was observed in sausages. Notably, B. anthracis strains lacking the anthrax toxin genes were detected in flour-based food products and sausages. A total of 20 antibiotic resistance genes have been identified, with β-lactam resistance genes (bla1, bla2, BcI, BcII, and blaTEM-116) being the most common. The B. tropicus strains exhibit the highest average number of virulence genes (23.4). The diarrheal virulence genes nheABC, hblACD, and cytK were found in numerous strains. Only 4 of the 234 (1.7 %) sequenced strains contain the ces gene cluster linked to emetic symptoms. These data offer valuable insights for public health policymakers on addressing foodborne B. cereus group infections and ensuring food safety.
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Affiliation(s)
- Zhiwei Zheng
- State Key Lab of Chemical Biology and Drug Discovery, Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong; Shenzhen Key Lab for Biological Safety Control, The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China
| | - Lianwei Ye
- State Key Lab of Chemical Biology and Drug Discovery, Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong; Shenzhen Key Lab for Biological Safety Control, The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China; Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Wenguang Xiong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Qiao Hu
- State Key Lab of Chemical Biology and Drug Discovery, Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong; Shenzhen Key Lab for Biological Safety Control, The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China; Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Kaichao Chen
- State Key Lab of Chemical Biology and Drug Discovery, Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong; Shenzhen Key Lab for Biological Safety Control, The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China
| | - Ruanyang Sun
- State Key Lab of Chemical Biology and Drug Discovery, Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong; Shenzhen Key Lab for Biological Safety Control, The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China
| | - Sheng Chen
- State Key Lab of Chemical Biology and Drug Discovery, Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong; Shenzhen Key Lab for Biological Safety Control, The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China.
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10
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Sornchuer P, Saninjuk K, Amonyingcharoen S, Ruangtong J, Thongsepee N, Martviset P, Chantree P, Sangpairoj K. Whole Genome Sequencing Reveals Antimicrobial Resistance and Virulence Genes of Both Pathogenic and Non-Pathogenic B. cereus Group Isolates from Foodstuffs in Thailand. Antibiotics (Basel) 2024; 13:245. [PMID: 38534680 DOI: 10.3390/antibiotics13030245] [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: 01/20/2024] [Revised: 03/01/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024] Open
Abstract
Members of the Bacillus cereus group are spore-forming Gram-positive bacilli that are commonly associated with diarrheal or emetic food poisoning. They are widespread in nature and frequently present in both raw and processed food products. Here, we genetically characterized 24 B. cereus group isolates from foodstuffs. Whole-genome sequencing (WGS) revealed that most of the isolates were closely related to B. cereus sensu stricto (12 isolates), followed by B. pacificus (5 isolates), B. paranthracis (5 isolates), B. tropicus (1 isolate), and "B. bingmayongensis" (1 isolate). The most detected virulence genes were BAS_RS06430, followed by bacillibactin biosynthesis genes (dhbA, dhbB, dhbC, dhbE, and dhbF), genes encoding the three-component non-hemolytic enterotoxin (nheA, nheB, and nheC), a gene encoding an iron-regulated leucine-rich surface protein (ilsA), and a gene encoding a metalloprotease (inhA). Various biofilm-associated genes were found, with high prevalences of tasA and sipW genes (matrix protein-encoding genes); purA, purC, and purL genes (eDNA synthesis genes); lytR and ugd genes (matrix polysaccharide synthesis genes); and abrB, codY, nprR, plcR, sinR, and spo0A genes (biofilm transcription regulator genes). Genes related to fosfomycin and beta-lactam resistance were identified in most of the isolates. We therefore demonstrated that WGS analysis represents a useful tool for rapidly identifying and characterizing B. cereus group strains. Determining the genetic epidemiology, the presence of virulence and antimicrobial resistance genes, and the pathogenic potential of each strain is crucial for improving the risk assessment of foodborne B. cereus group strains.
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Affiliation(s)
- Phornphan Sornchuer
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
- Thammasat University Research Unit in Nutraceuticals and Food Safety, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
| | | | - Sumet Amonyingcharoen
- Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Jittiporn Ruangtong
- Thammasat University Research Unit in Nutraceuticals and Food Safety, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
| | - Nattaya Thongsepee
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
- Thammasat University Research Unit in Nutraceuticals and Food Safety, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
| | - Pongsakorn Martviset
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
- Thammasat University Research Unit in Nutraceuticals and Food Safety, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
| | - Pathanin Chantree
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
- Thammasat University Research Unit in Nutraceuticals and Food Safety, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
| | - Kant Sangpairoj
- Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
- Thammasat University Research Unit in Nutraceuticals and Food Safety, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
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11
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Etter D, Biggel M, Greutmann M, Cernela N, Johler S. New insights into Bacillus cytotoxicus sources, screening, toxicity, and persistence in food production facilities. Food Microbiol 2024; 117:104399. [PMID: 37919007 DOI: 10.1016/j.fm.2023.104399] [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: 05/26/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 11/04/2023]
Abstract
Bacillus cytotoxicus is a thermotolerant member of the Bacillus cereus group. It has been linked to rare, but at times fatal cases of diarrheal disease and might be missed at routine diagnostic screening temperatures commonly used for the B. cereus group. The pathogen is mostly found on dehydrated foods containing potato starch or insects. How it enters the food chain or whether it persists in food producing environments is largely unknown. Increased consumption of insects and convenience foods in Europe and the lack of information on the persistence of B. cytotoxicus in food environments and its virulence demand for further characterization. In this study, we aimed to obtain a better understanding of i) the food sources of B. cytotoxicus, ii) screening temperatures needed for its isolation from food matrices, iii) cytotoxicity of the organism, and iv) its ecological niche and potential epidemiological links. To this end, 112 food samples were collected, with a focus on foods exhibiting low water activity. The samples were screened for B. cytotoxicus at 42 °C and at 50 °C. Presumptive isolates were characterized by cytK-1 toxin gene PCR for differentiation of B. cytotoxicus from other B. cereus group members. Vero cell cytotoxicity assays were performed, and selected isolates were sequenced. Our results show that screening at 42 °C might be insufficient for detecting B. cytotoxicus in foods that harbor other less thermophilic Bacillus species. When screening at 50 °C, B. cytotoxicus was detected in 23% of the food samples (n = 26 isolates). The highest prevalence was detected in mashed potato products (82%) and potato flakes (67%). In contrast, a wide range of products not containing any potato ingredients did not yield B. cytotoxicus isolates. All B. cytotoxicus isolates exhibited either low or no detectable cytotoxicity. WGS analysis revealed that a highly toxic isolate is closely related to the French outbreak strain NVH 391-98. In addition, we could show that two isolates sampled 5 years apart from the same production facility only differed by seven SNPs, making it likely that B. cytotoxicus is able to persist in production facilities over a long time. Interestingly, the reoccurring strain possessed an additional plasmid and did not show cytotoxic potential when re-isolated after 5 years.
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Affiliation(s)
- Danai Etter
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Michael Biggel
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Mariella Greutmann
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Nicole Cernela
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Sophia Johler
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland.
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12
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Tönnies H, Heep A, Herrmann J, Lange M, Mellmann A, Hamprecht A. Investigating environmental transmission to resolve a Bacillus cereus group outbreak in a neonatal intensive care unit using core genome multilocus sequence typing. Antimicrob Resist Infect Control 2024; 13:1. [PMID: 38184647 PMCID: PMC10771705 DOI: 10.1186/s13756-023-01359-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/21/2023] [Indexed: 01/08/2024] Open
Abstract
BACKGROUND We analyzed an outbreak of Bacillus cereus group (Bcg) at a single-center neonatal intensive care unit level IV by conducting comprehensive sampling of both patients and the environment. METHODS Between 06/2020 and 10/2021, all Bcg isolates identified by both regular colonization screening and additional sampling of the environment were subjected to whole-genome sequencing, followed by in vitro extraction of MLST ST, resistance genes and virulence factors. Using publicly available genome sequences, we defined an ad hoc core genome multilocus sequence typing (cgMLST) scheme comprising 2759 target genes for Bcg typing, which we applied to the detected isolates. We have compared the results with a stable cgMLST that was published in the meantime and completed the investigation with a SNP analysis. RESULTS We analyzed 28 Bcg isolates from patient and environmental samples using MLST and cgMLST. This revealed multiple sequence types, with ST127 being the most common (n = 13). Both cgMLST schemes grouped ten of the 13 ST127 isolates into a cluster, including two invasive isolates from two different patients and several environmental samples. SNP analysis postulated a screen from a ventilation machine as a possible reservoir. CONCLUSION In sensitive settings such as neonatal intensive care units, considering the environment in outbreak analyses is crucial, especially when investigating potential transmission routes through shared devices. When dealing with widespread bacteria such as Bcg, high-resolution typing techniques are necessary. In this study, we successfully resolved an outbreak of Bcg infections using a custom cgMLST scheme combined with a SNP analysis.
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Affiliation(s)
- Hauke Tönnies
- Institute of Hygiene, University Hospital Münster, Münster, Germany.
| | - Axel Heep
- Department of Pediatrics, Elisabeth Children's Hospital, University of Oldenburg, Oldenburg, Germany
| | - Jörg Herrmann
- Institute of Hygiene, University Hospital Oldenburg, Oldenburg, Germany
| | - Matthias Lange
- Department of Pediatrics, Elisabeth Children's Hospital, University of Oldenburg, Oldenburg, Germany
| | | | - Axel Hamprecht
- Institute of Medical Microbiology and Virology, University Hospital Oldenburg, Oldenburg, Germany
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13
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Vanhee C, Jacobs B, Kamugisha A, Canfyn M, Van Der Meersch H, Ceyssens B, Deconinck E, Van Hoorde K, Willocx M. Substandard and falsified ivermectin tablets obtained for self-medication during the COVID-19 pandemic as a source of potential harm. Drug Test Anal 2023. [PMID: 38043940 DOI: 10.1002/dta.3618] [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: 10/11/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 12/05/2023]
Abstract
In 2019, a global viral pandemic, due to the SARS-CoV-2 virus, broke out. Soon after, the search for a vaccine and/or antiviral medicine began. One of the candidate antiviral medicines tested was ivermectin. Although several health authorities warned the public against the use of this medicine outside clinical trials, the drug was widely used at the end of 2020 and in 2021. Simultaneously, several reports started to emerge demonstrating serious adverse effects after self-medicating with ivermectin. It stands to reason that the self-administration of substandard or falsified (SF) medicines bearing harmful quality deficiencies have contributed to this phenomenon. In order to have a better view on the nature of these harmful quality deficiencies, SF ivermectin samples, intercepted in large quantities by the Belgian regulatory agencies during the period 2021-2022, were analyzed in our official medicines control laboratory. None of the samples (n = 19) were compliant to the quality criteria applicable to medicinal products. These SF products either suffered from a systematic underdosing of the active pharmaceutical ingredient or were severely contaminated with bacteria, two of which were contaminated with known pathogens that cause gastrointestinal illness upon oral intake. In addition to the direct risks of self-medicating with such a product, the improper usage and dosage of ivermectin medication might also facilitate ivermectin tolerance or resistance in parasites. This may have detrimental consequences on a global scale, certainly as the number of newly developed active pharmaceutical ingredients that can safely be used to combat parasites is rather scarce.
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Affiliation(s)
- Celine Vanhee
- Service Medicines and Health Products, Scientific Direction of Chemical and Physical Health Risks, Sciensano, Brussels, Belgium
| | - Bram Jacobs
- Service of Foodborne Pathogen, Scientific Direction of Infectious Diseases in Humans, Sciensano, Brussels, Belgium
| | - Angélique Kamugisha
- Service Medicines and Health Products, Scientific Direction of Chemical and Physical Health Risks, Sciensano, Brussels, Belgium
| | - Michael Canfyn
- Service Medicines and Health Products, Scientific Direction of Chemical and Physical Health Risks, Sciensano, Brussels, Belgium
| | | | - Bart Ceyssens
- Federal Agency for Medicine and Health Care Products, Brussels, Belgium
| | - Eric Deconinck
- Service Medicines and Health Products, Scientific Direction of Chemical and Physical Health Risks, Sciensano, Brussels, Belgium
| | - Koenraad Van Hoorde
- Service of Foodborne Pathogen, Scientific Direction of Infectious Diseases in Humans, Sciensano, Brussels, Belgium
| | - Marie Willocx
- Service Medicines and Health Products, Scientific Direction of Chemical and Physical Health Risks, Sciensano, Brussels, Belgium
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14
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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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15
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Wang K, Shu C, Bravo A, Soberón M, Zhang H, Crickmore N, Zhang J. Development of an Online Genome Sequence Comparison Resource for Bacillus cereus sensu lato Strains Using the Efficient Composition Vector Method. Toxins (Basel) 2023; 15:393. [PMID: 37368694 DOI: 10.3390/toxins15060393] [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: 03/23/2023] [Revised: 05/21/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
An automated method was developed for differentiating closely related B. cereus sensu lato (s.l.) species, especially biopesticide Bacillus thuringiensis, from other human pathogens, B. anthracis and B. cereus sensu stricto (s.s.). In the current research, four typing methods were initially compared, including multi-locus sequence typing (MLST), single-copy core genes phylogenetic analysis (SCCGPA), dispensable genes content pattern analysis (DGCPA) and composition vector tree (CVTree), to analyze the genomic variability of 23 B. thuringiensis strains from aizawai, kurstaki, israelensis, thuringiensis and morrisoni serovars. The CVTree method was the best option to be used for typing B. thuringiensis strains since it proved to be the fastest method, whilst giving high-resolution data about the strains. In addition, CVTree agrees well with ANI-based method, revealing the relationship between B. thuringiensis and other B. cereus s.l. species. Based on these data, an online genome sequence comparison resource was built for Bacillus strains called the Bacillus Typing Bioinformatics Database to facilitate strain identification and characterization.
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Affiliation(s)
- Kui Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Changlong Shu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Alejandra Bravo
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62250, Mexico
| | - Mario Soberón
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62250, Mexico
| | - Hongjun Zhang
- Institute for the Control of Agrochemicals, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Neil Crickmore
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
| | - Jie Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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16
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Xiao D, Tong C, Yang T, Huo Z, Li Y, Zeng Z, Xiong W. First insights into antimicrobial resistance, toxigenic profiles, and genetic diversity in Bacillus cereus isolated from Chinese sausages. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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17
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Schäfer L, Volk F, Kleespies RG, Jehle JA, Wennmann JT. Elucidating the genomic history of commercially used Bacillus thuringiensis subsp. tenebrionis strain NB176. Front Cell Infect Microbiol 2023; 13:1129177. [PMID: 37021121 PMCID: PMC10067926 DOI: 10.3389/fcimb.2023.1129177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/17/2023] [Indexed: 04/07/2023] Open
Abstract
Bacillus thuringiensis subsp. tenebrionis (Btt) produces a coleopteran-specific crystal protoxin protein (Cry3Aa δ-endotoxin). After its discovery in 1982, the strain NB125 (DSM 5526) was eventually registered in 1990 to control the Colorado potato beetle (Leptinotarsa decemlineata). Gamma-irradiation of NB125 resulted in strain NB176-1 (DSM 5480) that exhibited higher cry3Aa production and became the active ingredient of the plant protection product Novodor® FC. Here, we report a comparative genome analysis of the parental strain NB125, its derivative NB176-1 and the current commercial production strain NB176. The entire genome sequences of the parental and derivative strains were deciphered by a hybrid de novo approach using short (Illumina) and long (Nanopore) read sequencing techniques. Genome assembly revealed a chromosome of 5.4 to 5.6 Mbp and six plasmids with a size range from 14.9 to 250.5 kbp for each strain. The major differences among the original NB125 and the derivative strains NB176-1 and NB176 were an additional copy of the cry3Aa gene, which translocated to another plasmid as well as a chromosomal deletion (~ 178 kbp) in NB176. The assembled genome sequences were further analyzed in silico for the presence of virulence and antimicrobial resistance (AMR) genes.
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Affiliation(s)
- Lea Schäfer
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Dossenheim, Germany
| | | | - Regina G. Kleespies
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Dossenheim, Germany
| | - Johannes A. Jehle
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Dossenheim, Germany
| | - Jörg T. Wennmann
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Dossenheim, Germany
- *Correspondence: Jörg T. Wennmann,
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18
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Fraccalvieri R, Bianco A, Difato LM, Capozzi L, Del Sambro L, Simone D, Catanzariti R, Caruso M, Galante D, Normanno G, Palazzo L, Tempesta M, Parisi A. Toxigenic Genes, Pathogenic Potential and Antimicrobial Resistance of Bacillus cereus Group Isolated from Ice Cream and Characterized by Whole Genome Sequencing. Foods 2022; 11:foods11162480. [PMID: 36010481 PMCID: PMC9407285 DOI: 10.3390/foods11162480] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/22/2022] Open
Abstract
Bacillus cereus is isolated from a variety of foods where it may cause food spoilage and/or food poisoning due to its toxigenic and pathogenic nature. In this study, we identified members of B. cereus groups in 65% of the ice cream samples analyzed, which were characterized based on multi locus variable number tandem repeats analysis (MLVA) and whole genome sequencing (WGS). The MLVA revealed that 36 strains showed different allelic profiles. Analyses of WGS data enabled the identification of three members of the B. cereus group: B. cereus sensu stricto, B. mosaicus and B. thuringiensis. Based on the multi locus sequence typing (MLST) scheme, the strains were classified in 27 sequence types (STs), including ST26 that causes food poisoning. Toxin genes’ detection revealed the presence of the genes encoding nonhemolytic enterotoxin (NHE), hemolysin BL (HBL), cytotoxin K (cytK) and cereulide (ces) in 100%, 44%, 42% and 8% of the strains, respectively. The identification of eleven antimicrobial resistance (AMR) genes predicted the resistance to five different antimicrobials, and the resistance to beta-lactam antibiotics was confirmed with a phenotypic antimicrobial test. Taken together, the results showed that the B. cereus strains isolated from ice cream were a potential hazard for consumer safety.
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Affiliation(s)
- Rosa Fraccalvieri
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Angelica Bianco
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
- Experimental Zooprophylactic Institute of Apulia and Basilicata, 71121 Foggia, Italy
- Correspondence: ; Tel.: +39-080-4057858; Fax: +39-080-4057753
| | - Laura Maria Difato
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Loredana Capozzi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Laura Del Sambro
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Domenico Simone
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Roberta Catanzariti
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Marta Caruso
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Domenico Galante
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Giovanni Normanno
- Department of Science of Agriculture, Food and the Environment (SAFE), University of Foggia, 71121 Foggia, Italy
| | - Lucia Palazzo
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
| | - Maria Tempesta
- Department of Veterinary Medicine, University Aldo Moro of Bari, Strada per Casamassima Km 3, 70010 Valenzano, Italy
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZS PB), Via Manfredonia 20, 71121 Foggia, Italy
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Biggel M, Jessberger N, Kovac J, Johler S. Recent paradigm shifts in the perception of the role of Bacillus thuringiensis in foodborne disease. Food Microbiol 2022; 105:104025. [DOI: 10.1016/j.fm.2022.104025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 12/16/2022]
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Strains Associated with Two 2020 Welder Anthrax Cases in the United States Belong to Separate Lineages within Bacillus cereus sensu lato. Pathogens 2022; 11:pathogens11080856. [PMID: 36014977 PMCID: PMC9413466 DOI: 10.3390/pathogens11080856] [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: 06/20/2022] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 12/04/2022] Open
Abstract
Anthrax-causing members of Bacillus cereus sensu lato (s.l.) pose a serious threat to public health. While most anthrax-causing strains resemble B. anthracis phenotypically, rare cases of anthrax-like illness caused by strains resembling “B. cereus” have been reported. Here, whole-genome sequencing was used to characterize three B. cereus s.l. isolates associated with two 2020 welder anthrax cases in the United States, which resembled “B. cereus” phenotypically. Comparison of the three genomes sequenced here to all publicly available, high-quality B. cereus s.l. genomes (n = 2890 total genomes) demonstrated that genomes associated with each case effectively belonged to separate species at the conventional 95% average nucleotide identity prokaryotic species threshold. Two PubMLST sequence type 78 (ST78) genomes affiliated with a case in Louisiana were most closely related to B. tropicus and possessed genes encoding the Bps exopolysaccharide capsule, as well as hemolysin BL (Hbl) and cytotoxin K (CytK). Comparatively, a ST108 genome associated with a case in Texas was most closely related to B. anthracis; however, like other anthrax-causing strains most closely related to B. anthracis, this genome did not possess Bps-, Hbl-, or CytK-encoding genes. Overall, results presented here provide insights into the evolution of anthrax-causing B. cereus s.l.
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Regulation of Enterotoxins Associated with Bacillus cereus Sensu Lato Toxicoinfection. Appl Environ Microbiol 2022; 88:e0040522. [PMID: 35730937 PMCID: PMC9275247 DOI: 10.1128/aem.00405-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bacillus cereus sensu lato (s.l.) includes foodborne pathogens, as well as beneficial microorganisms, such as bioinsecticides. Some of the beneficial and commercially used B. cereus s.l. strains have been shown to carry enterotoxin genes, the products of which can cause toxicoinfection in humans. Furthermore, recent epidemiological reports indicated that some bioinsecticidal strains have been linked with foodborne illness outbreaks. This demonstrates the need for improved surveillance of B. cereus s.l., which includes characterization of isolates' virulence capacity. However, the prediction of virulence capacity of B. cereus s.l. strains is challenging. Genetic screening for enterotoxin gene presence has proven to be insufficient for accurate discrimination between virulent and avirulent strains, given that nearly all B. cereus s.l. strains carry at least one enterotoxin gene. Furthermore, complex regulatory networks governing the expression of enterotoxins, and potential synergistic interactions between enterotoxins and other virulence factors make the prediction of toxicoinfection based on isolates' genome sequences challenging. In this review, we summarize and synthesize the current understanding of the regulation of enterotoxins associated with the B. cereus s.l. toxicoinfection and identify gaps in the knowledge that need to be addressed to facilitate identification of genetic markers predictive of cytotoxicity and toxicoinfection.
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Carroll LM, Pierneef R, Mathole A, Atanda A, Matle I. Genomic Sequencing of Bacillus cereus Sensu Lato Strains Isolated from Meat and Poultry Products in South Africa Enables Inter- and Intranational Surveillance and Source Tracking. Microbiol Spectr 2022; 10:e0070022. [PMID: 35475639 PMCID: PMC9241823 DOI: 10.1128/spectrum.00700-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/06/2022] [Indexed: 12/22/2022] Open
Abstract
Members of the Bacillus cereus sensu lato species complex, also known as the B. cereus group, vary in their ability to cause illness but are frequently isolated from foods, including meat products; however, food safety surveillance efforts that use whole-genome sequencing (WGS) often neglect these potential pathogens. Here, we evaluate the surveillance and source tracking potential of WGS as applied to B. cereus sensu lato by (i) using WGS to characterize B. cereus sensu lato strains isolated during routine surveillance of meat products across South Africa (n = 25) and (ii) comparing the genomes sequenced here to all publicly available, high-quality B. cereus sensu lato genomes (n = 2,887 total genomes). Strains sequenced here were collected from meat products obtained from (i) retail outlets, processing plants, and butcheries across six South African provinces (n = 23) and (ii) imports held at port of entry (n = 2). The 25 strains sequenced here were partitioned into 15 lineages via in silico seven-gene multilocus sequence typing (MLST). While none of the South African B. cereus sensu lato strains sequenced here were identical to publicly available genomes, six MLST lineages contained multiple strains sequenced in this study, which were identical or nearly identical at the whole-genome scale (≤3 core single nucleotide polymorphisms). Five MLST lineages contained (nearly) identical genomes collected from two or three South African provinces; one MLST lineage contained nearly identical genomes from two countries (South Africa and the Netherlands), indicating that B. cereus sensu lato can spread intra- and internationally via foodstuffs. IMPORTANCE Nationwide foodborne pathogen surveillance programs that use high-resolution genomic methods have been shown to provide vast public health and economic benefits. However, Bacillus cereus sensu lato is often overlooked during large-scale routine WGS efforts. Thus, to our knowledge, no studies to date have evaluated the potential utility of WGS for B. cereus sensu lato surveillance and source tracking in foodstuffs. In this preliminary proof-of-concept study, we applied WGS to B. cereus sensu lato strains collected via South Africa's national surveillance program of domestic and imported meat products, and we provide strong evidence that B. cereus sensu lato can be disseminated intra- and internationally via the agro-food supply chain. Our results showcase that WGS has the potential to be used for source tracking of B. cereus sensu lato in foods, although future WGS and metadata collection efforts are needed to ensure that B. cereus sensu lato surveillance initiatives are on par with those of other foodborne pathogens.
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Affiliation(s)
- Laura M. Carroll
- Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Rian Pierneef
- Biotechnology Platform, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort, South Africa
| | - Aletta Mathole
- Bacteriology Division, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort, South Africa
| | - Abimbola Atanda
- Bacteriology Division, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort, South Africa
| | - Itumeleng Matle
- Bacteriology Division, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort, South Africa
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Comparative analysis of Bacillus cereus group isolates' resistance using disk diffusion and broth microdilution and the correlation between antimicrobial resistance phenotypes and genotypes. Appl Environ Microbiol 2022; 88:e0230221. [PMID: 35225691 PMCID: PMC8939351 DOI: 10.1128/aem.02302-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus cereus group isolates (n = 85) were screened for phenotypic resistance to 18 antibiotics using broth microdilution and CLSI M45 Bacillus spp. breakpoints. The susceptibility to 9 out of 18 antibiotics was tested also using disk diffusion method and M100 Staphylococcus spp. breakpoints. Overall, a high prevalence of susceptibility to clinically relevant antibiotics was identified using broth microdilution. For most tested antibiotics, a poor correlation was found between zones of inhibition and minimum inhibitory concentrations. Using the broth microdilution results as a reference for comparison, we identified high error rates and low categorical agreement between results produced using disk diffusion and broth microdilution for the seven tested antibiotics with defined breakpoints. This suggests that disk diffusion should be avoided for AST of B. cereus group isolates. Further, we detected antimicrobial resistance genes with ARIBA and ABRIcate to calculate the sensitivity and specificity for predicting phenotypic resistance determined using broth microdilution based on the presence of detected antimicrobial resistance genes (ARGs). ARGs with poor sensitivity and high specificity included rph (rifampicin, 0%, 93%), mph (erythromycin, 0%, 99%), bla1 (penicillin, 29%, 100), and blaZ (penicillin, 56%, 100%). Compared to penicillin, bla1 and blaZ had lower specificity for the prediction of ampicillin resistance. Overall, none of the ARGs had both high sensitivity and specificity, suggesting the need for further study of the mechanisms underlying phenotypic antimicrobial resistance in the B. cereus group. IMPORTANCE Bacillus cereus group includes human pathogens that can cause severe infections requiring antibiotic treatment. Screening of environmental and food isolates for antimicrobial resistance can provide insight into what antibiotics may be more effective therapeutic options based on the lower prevalence of resistance. Currently, the comparison of antimicrobial susceptibility testing results using the disk diffusion method is complicated by the fact that many previous studies have used Staphylococcus spp. breakpoints to interpret their results. In this study, we compared the results of disk diffusion interpreted using the Staphylococcus spp. breakpoints against the results of broth microdilution interpreted using Bacillus spp. breakpoints. We demonstrated that the disk diffusion method does not produce reliable results for B. cereus group isolates and should therefore be avoided. This study also provides new insight into poor associations between the presence of antimicrobial resistance genes and resistance phenotypes for the B. cereus group.
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Biggel M, Etter D, Corti S, Brodmann P, Stephan R, Ehling-Schulz M, Johler S. Whole Genome Sequencing Reveals Biopesticidal Origin of Bacillus thuringiensis in Foods. Front Microbiol 2022; 12:775669. [PMID: 35095794 PMCID: PMC8790155 DOI: 10.3389/fmicb.2021.775669] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/13/2021] [Indexed: 01/06/2023] Open
Abstract
Bacillus thuringiensis is a microbial insecticide widely used to control agricultural pests. Although generally regarded as safe, B. thuringiensis is phylogenetically intermingled with the foodborne pathogen B. cereus sensu stricto and has been linked to foodborne outbreaks. Limited data on the pathogenicity potential of B. thuringiensis and the occurrence of biopesticide residues in food compromise a robust consumer risk assessment. In this study, we analyzed whole-genome sequences of 33 B. thuringiensis isolates from biopesticides, food, and human fecal samples linked to outbreaks. All food and outbreak-associated isolates genomically matched (≤ 6 wgSNPs; ≤ 2 cgSNPs) with one of six biopesticide strains, suggesting biopesticide products as their source. Long-read sequencing revealed a more diverse virulence gene profile than previously assumed, including a transposase-mediated disruption of the promoter region of the non-hemolytic enterotoxin gene nhe and a bacteriophage-mediated disruption of the sphingomyelinase gene sph in some biopesticide strains. Furthermore, we provide high-quality genome assemblies of seven widely used B. thuringiensis biopesticide strains, which will facilitate improved microbial source tracking and risk assessment of B. thuringiensis-based biopesticides in the future.
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Affiliation(s)
- Michael Biggel
- Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Danai Etter
- Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Sabrina Corti
- Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | | | - Roger Stephan
- Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Monika Ehling-Schulz
- Department of Pathobiology, Functional Microbiology, Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Sophia Johler
- Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
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25
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Gaballa A, Cheng RA, Trmcic A, Kovac J, Kent DJ, Martin NH, Wiedmann M. Development of a database and standardized approach for rpoB sequence-based subtyping and identification of aerobic spore-forming Bacillales. J Microbiol Methods 2021; 191:106350. [PMID: 34710512 DOI: 10.1016/j.mimet.2021.106350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 10/20/2022]
Abstract
Aerobic spore-forming Bacillales are a highly diverse and ubiquitous group that includes organisms that cause foodborne illnesses and food spoilage. Classical microbiological and biochemical identification of members of the order Bacillales represents a challenge due to the diversity of organisms in this group as well as the fact that the phenotypic-based taxonomic assignment of some named species in this group is not consistent with their phylogenomic characteristics. DNA-sequencing-based tools, on the other hand, can be fast and cost-effective, and can provide for a more reliable identification and characterization of Bacillales isolates. In comparison to 16S rDNA, rpoB was shown to better discriminate between Bacillales isolates and to allow for improved taxonomic assignment to the species level. However, the lack of a publicly accessible rpoB database, as well as the lack of standardized protocols for rpoB-based typing and strain identification, is a major challenge. Here, we report (i) the curation of a DNA sequence database for rpoB-based subtype classification of Bacillales isolates; (ii) the development of standardized protocols for generating rpoB sequence data, and a scheme for rpoB-based initial taxonomic identification of Bacillales isolates at the species level; and (iii) the integration of the database in a publicly accessible online platform that allows for the analysis of rpoB sequence data from uncharacterized Bacillales isolates. Specifically, we curated a database of DNA sequences for a 632-nt internal variable region within the rpoB gene from representative Bacillales reference type strains and a large number of isolates that we have previously isolated and characterized through multiple projects. As of May 21, 2021, the rpoB database contained more than 8350 rpoB sequences representing 1902 distinct rpoB allelic types that can be classified into 160 different genera. The database also includes 1129 rpoB sequences for representative Bacillales reference type strains as available on May 21, 2021 in the NCBI database. The rpoB database is integrated into the online Food Microbe Tracker platform (www.foodmicrobetracker.com) and can be queried using the integrated BLAST tool to initially subtype and taxonomically identify aerobic and facultative anaerobic spore-formers. While whole-genome sequencing is increasingly used in bacterial taxonomy, the rpoB sequence-based identification scheme described here provides a valuable tool as it allows for rapid and cost-effective initial isolate characterization, which can help to identify and characterize foodborne pathogens and food spoilage bacteria. In addition, the database and primers described here can also be adopted for metagenomics approaches that include rpoB as a target, improving discriminatory power and identification over what can be achieved using 16S rDNA as a target.
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Affiliation(s)
- Ahmed Gaballa
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA.
| | - Rachel A Cheng
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Aljosa Trmcic
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Jasna Kovac
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA; Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - David J Kent
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Nicole H Martin
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
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26
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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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27
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Luo JC, Long H, Zhang J, Zhao Y, Sun L. Characterization of a Deep Sea Bacillus toyonensis Isolate: Genomic and Pathogenic Features. Front Cell Infect Microbiol 2021; 11:629116. [PMID: 33777842 PMCID: PMC7988205 DOI: 10.3389/fcimb.2021.629116] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/01/2021] [Indexed: 01/09/2023] Open
Abstract
Bacillus toyonensis is a group of Gram-positive bacteria belonging to the Bacillus cereus group and used in some cases as probiotics or biocontrol agents. To our knowledge, B. toyonensis from the deep sea (depth >1,000 m) has not been documented. Here, we report the isolation and characterization of a B. toyonensis strain, P18, from a deep sea hydrothermal field. P18 is aerobic, motile, and able to grow at low temperatures (4°C) and high concentrations of NaCl (8%). P18 possesses a circular chromosome of 5,250,895 bp and a plasmid of 536,892 bp, which encode 5,380 and 523 genes, respectively. Of these genes, 2,229 encode hypothetical proteins that could not be annotated based on the COG database. Comparative genomic analysis showed that P18 is most closely related to the type strain of B. toyonensis, BCT-7112T. Compared to BCT-7112T, P18 contains 1,401 unique genes, 441 of which were classified into 20 COG functional categories, and the remaining 960 genes could not be annotated. A total of 319 putative virulence genes were identified in P18, including toxin-related genes, and 24 of these genes are absent in BCT-7112T. P18 exerted strong cytopathic effects on fish and mammalian cells that led to rapid cell death. When inoculated via injection into fish and mice, P18 rapidly disseminated in host tissues and induced acute infection and mortality. Histopathology revealed varying degrees of tissue lesions in the infected animals. Furthermore, P18 could survive in fish and mouse sera and possessed hemolytic activity. Taken together, these results provide the first evidence that virulent B. toyonensis exists in deep sea environments.
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Affiliation(s)
- Jing-Chang Luo
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hao Long
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Jian Zhang
- School of Ocean, Yan Tai University, Yantai, China
| | - Yan Zhao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Li Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
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28
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Bonis M, Felten A, Pairaud S, Dijoux A, Maladen V, Mallet L, Radomski N, Duboisset A, Arar C, Sarda X, Vial G, Mistou MY, Firmesse O, Hennekinne JA, Herbin S. Comparative phenotypic, genotypic and genomic analyses of Bacillus thuringiensis associated with foodborne outbreaks in France. PLoS One 2021; 16:e0246885. [PMID: 33607651 PMCID: PMC7895547 DOI: 10.1371/journal.pone.0246885] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/28/2021] [Indexed: 11/18/2022] Open
Abstract
Bacillus thuringiensis (Bt) belongs to the Bacillus cereus (Bc) group, well known as an etiological agent of foodborne outbreaks (FBOs). Bt distinguishes itself from other Bc by its ability to synthesize insecticidal crystals. However, the search for these crystals is not routinely performed in food safety or clinical investigation, and the actual involvement of Bt in the occurrence of FBOs is not known. In the present study, we reveal that Bt was detected in the context of 49 FBOs declared in France between 2007 and 2017. In 19 of these FBOs, Bt was the only microorganism detected, making it the most likely causal agent. Searching for its putative origin of contamination, we noticed that more than 50% of Bt isolates were collected from dishes containing raw vegetables, in particular tomatoes (48%). Moreover, the genomic characterization of isolates showed that most FBO-associated Bt isolates exhibited a quantified genomic proximity to Bt strains, used as biopesticides, especially those from subspecies aizawai and kurstaki. Taken together, these results strengthen the hypothesis of an agricultural origin for the Bt contamination and call for further investigations on Bt pesticides.
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Affiliation(s)
- Mathilde Bonis
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, Maisons-Alfort, France
| | - Arnaud Felten
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, Maisons-Alfort, France
| | - Sylvie Pairaud
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, Maisons-Alfort, France
| | - Angélie Dijoux
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, Maisons-Alfort, France
| | - Véronique Maladen
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, Maisons-Alfort, France
| | - Ludovic Mallet
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, Maisons-Alfort, France
| | - Nicolas Radomski
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, Maisons-Alfort, France
| | - Arnaud Duboisset
- Regulated Products Assessment Department, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, Maisons-Alfort, France
| | - Chantal Arar
- Regulated Products Assessment Department, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, Maisons-Alfort, France
| | - Xavier Sarda
- Regulated Products Assessment Department, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, Maisons-Alfort, France
| | - Gaelle Vial
- Regulated Products Assessment Department, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, Maisons-Alfort, France
| | - Michel-Yves Mistou
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, Maisons-Alfort, France
| | - Olivier Firmesse
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, Maisons-Alfort, France
- * E-mail:
| | - Jacques-Antoine Hennekinne
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, Maisons-Alfort, France
| | - Sabine Herbin
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, Maisons-Alfort, France
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29
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Bianco A, Capozzi L, Monno MR, Del Sambro L, Manzulli V, Pesole G, Loconsole D, Parisi A. Characterization of Bacillus cereus Group Isolates From Human Bacteremia by Whole-Genome Sequencing. Front Microbiol 2021; 11:599524. [PMID: 33510722 PMCID: PMC7835510 DOI: 10.3389/fmicb.2020.599524] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/27/2020] [Indexed: 12/18/2022] Open
Abstract
Members of the Bacillus cereus group are spore-forming organisms commonly associated with food poisoning and intestinal infections. Moreover, some strains of the group (i.e., B. cereus sensu stricto and Bacillus thuringiensis) can cause bacteremia in humans, mainly in immunocompromised individuals. Here we performed the genetic characterization of 17 human clinical strains belonging to B. cereus group isolated from blood culture. The whole-genome sequencing (WGS) revealed that the isolates were closely related to B. cereus sensu stricto and B. thuringiensis-type strain. Multilocus sequence typing analysis performed on the draft genome revealed the genetic diversity of our isolates, which were assigned to different sequence types. Based on panC nucleotide sequence, the isolates were grouped in the phylogenetic groups III and IV. The NHE, cer, and inhA gene cluster, entA, entFM, plcA, and plcB, were the most commonly detected virulence genes. Although we did not assess the ability to generate biofilm by phenotypic tests, we verified the prevalence of biofilm associated genes using an in silico approach. A high prevalence of pur gene cluster, xerC, clpY, codY, tasA, sipW, sinI, and sigB genes, was found. Genes related to the resistance to penicillin, trimethoprim, and ceftriaxone were identified in most of the isolates. Intriguingly, the majority of these virulence and AMR genes appeared to be evenly distributed among B. cereus s.s. isolates, as well as closely related to B. thuringiensis isolates. We showed the WGS represents a good approach to rapidly characterize B. cereus group strains, being able to give useful information about genetic epidemiology, the presence of virulence and antimicrobial genes, and finally about the potential hazard related to this underestimated risk.
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Affiliation(s)
- Angelica Bianco
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Loredana Capozzi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Maria Rosa Monno
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", Bari, Italy
| | - Laura Del Sambro
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Viviana Manzulli
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Graziano Pesole
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari "A. Moro", Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council and Consorzio Interuniversitario Biotecnologie, Bari, Italy
| | - Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
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