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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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Leong SS, Korel F, King JH. Bacillus cereus: A review of "fried rice syndrome" causative agents. Microb Pathog 2023; 185:106418. [PMID: 37866551 DOI: 10.1016/j.micpath.2023.106418] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 10/19/2023] [Accepted: 10/19/2023] [Indexed: 10/24/2023]
Abstract
"Fried rice syndrome" originated from the first exposure to a fried rice dish contaminated with Bacillus cereus. This review compiles available data on the prevalence of B. cereus outbreak cases that occurred between 1984 and 2019. The outcome of B. cereus illness varies dramatically depending on the pathogenic strain encounter and the host's immune system. B. cereus causes a self-limiting, diarrheal illness caused by heat-resistant enterotoxin proteins, and an emetic illness caused by the deadly toxin named cereulide. The toxins together with their extrinsic factors are discussed. The possibility of more contamination of B. cereus in protein-rich food has also been shown. Therefore, the aim of this review is to summarize the available data, focusing mainly on B. cereus physiology as the causative agent for "fried rice syndrome." This review emphasizes the prevalence of B. cereus in starchy food contamination and outbreak cases reported, the virulence of both enterotoxins and emetic toxins produced, and the possibility of contaminated in protein-rich food. The impact of emetic or enterotoxin-producing B. cereus on public health cannot be neglected. Thus, it is essential to constantly monitor for B. cereus contamination during food handling and hygiene practices for food product preparation.
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Affiliation(s)
- Sui Sien Leong
- Department of Animal Sciences and Fishery, Faculty of Agricultural and Forestry Sciences, Universiti Putra Malaysia, Nyabau Road, Bintulu, 97008, Sarawak, Malaysia; Institute of Ecosystem Science Borneo, Universiti Putra Malaysia Bintulu Sarawak Campus, Nyabau Road, Bintulu, 97008, Sarawak, Malaysia.
| | - Figen Korel
- Food Engineering Department, Faculty of Engineering, Izmir Institute of Technology, Urla, 35430, İzmir, Turkey
| | - Jie Hung King
- Department of Crop Science, Faculty of Agricultural and Forestry Sciences, Universiti Putra Malaysia, Nyabau Road, Bintulu, 97008, Sarawak, Malaysia
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Deng F, Chen Y, Xiao H, Yao C, Chen J, Zhao Y, Jiang Y, Chen J, Deng Y, Wen J. Bacillus pfraonensis sp. nov., a new strain isolated from a probiotic feed additive with low cytotoxicity and antimicrobial activity. Res Microbiol 2023; 174:104090. [PMID: 37356781 DOI: 10.1016/j.resmic.2023.104090] [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: 10/21/2022] [Revised: 05/21/2023] [Accepted: 06/12/2023] [Indexed: 06/27/2023]
Abstract
Probiotic products containing living microorganisms are gaining popularity, increasing the importance of their taxonomic status. A Bacillus-like isolate, 70 b, cultured from a probiotic feed additive, was ambiguity in taxonomic assignment and could be a novel member of Bacillus cereus group. The results of colony and cellular morphology, physiological and biochemical analysis mainly including growth performance, carbon source utilization, and rMLST and MLST were not conclusive. Fatty acids profile and molecular genetic analysis especially ANI, DDH, and core genome SNPs-based phylogenetic tree confirmed 70 b as one novel species of B. cereus group and proposed as Bacillus pfraonensis sp. nov. Comparative genomic analysis revealed the genetic differences between 70 b and other species of B. cereus group. Pseudomycoicidin was identified in 70 b. 70 b was active against multidrug-resistant pathogenic strains MRSA. The findings support 70 b is a novel species with low cytotoxicity and antimicrobial activity, and provides a better understanding of its unique characteristics and probiotic potential, and exploration of bioactive potential.
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Affiliation(s)
- Fengru Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510642, Guangdong, PR China
| | - Yunsheng Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510642, Guangdong, PR China
| | - Huiying Xiao
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510642, Guangdong, PR China
| | - Chuying Yao
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510642, Guangdong, PR China
| | - Jiaqi Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510642, Guangdong, PR China
| | - Yuanting Zhao
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510642, Guangdong, PR China
| | - Yapei Jiang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510642, Guangdong, PR China
| | - Jiahang Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510642, Guangdong, PR China
| | - Yiqun Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510642, Guangdong, PR China.
| | - Jikai Wen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510642, Guangdong, PR China.
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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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Bacillus cereus Invasive Infections in Preterm Neonates: an Up-to-Date Review of the Literature. Clin Microbiol Rev 2022; 35:e0008821. [PMID: 35138121 PMCID: PMC8826972 DOI: 10.1128/cmr.00088-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus cereus group species are widespread, Gram-positive, spore-forming environmental bacteria. B. cereus sensu stricto is one of the major causes of food poisoning worldwide. In high-risk individuals, such as preterm neonates, B. cereus infections can cause fatal infections. It is important to note that the phenotypic identification methods commonly used in clinical microbiology laboratories make no distinction between B. cereus sensu stricto and the other members of the group (Bacillus anthracis excluded). As a result, all the invasive infections attributed to B. cereus are not necessarily due to B. cereus sensu stricto but likely to other closely related species of the B. cereus group. Next-generation sequencing (NGS) should be used to characterize the whole genome of the strains belonging to the B. cereus group. This could confirm whether the strains involved in previously reported B. cereus invasive infections preferentially belong to formerly known or emerging individual species. Moreover, infections related to B. cereus group species have probably been overlooked, since their isolation in human bacteriological samples has for a long time been regarded as an environmental contaminant of the cultures. Recent studies have questioned the emergence or reemergence of B. cereus invasive infections in preterm infants. This review reports our current understanding of B. cereus infections in neonates, including taxonomical updates, microbiological characteristics, bacterial identification, clinical features, host-pathogen interactions, environmental sources of contamination, and antimicrobial resistance.
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7
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Jovanovic J, Tretiak S, Begyn K, Rajkovic A. Detection of Enterotoxigenic Psychrotrophic Presumptive Bacillus cereus and Cereulide Producers in Food Products and Ingredients. Toxins (Basel) 2022; 14:toxins14040289. [PMID: 35448897 PMCID: PMC9030337 DOI: 10.3390/toxins14040289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/07/2022] [Accepted: 04/13/2022] [Indexed: 02/04/2023] Open
Abstract
In the last decade, foodborne outbreaks and individual cases caused by bacterial toxins showed an increasing trend. The major contributors are enterotoxins and cereulide produced by Bacillus cereus, which can cause a diarrheal and emetic form of the disease, respectively. These diseases usually induce relatively mild symptoms; however, fatal cases have been reported. With the aim to detected potential toxin producers that are able to grow at refrigerator temperatures and subsequently produce cereulide, we screened the prevalence of enterotoxin and cereulide toxin gene carriers and the psychrotrophic capacity of presumptive B. cereus obtained from 250 food products (cereal products, including rice and seeds/pulses, dairy-based products, dried vegetables, mixed food, herbs, and spices). Of tested food products, 226/250 (90.4%) contained presumptive B. cereus, which communities were further tested for the presence of nheA, hblA, cytK-1, and ces genes. Food products were mainly contaminated with the nheA B. cereus carriers (77.9%), followed by hblA (64.8%), ces (23.2%), and cytK-1 (4.4%). Toxigenic B. cereus communities were further subjected to refrigerated (4 and 7 °C) and mild abuse temperatures (10 °C). Overall, 77% (94/121), 86% (104/121), and 100% (121/121) were able to grow at 4, 7, and 10 °C, respectively. Enterotoxin and cereulide potential producers were detected in 81% of psychrotrophic presumptive B. cereus. Toxin encoding genes nheA, hblA, and ces gene were found in 77.2, 55, and 11.7% of tested samples, respectively. None of the psychrotrophic presumptive B. cereus were carriers of the cytotoxin K-1 encoding gene (cytK-1). Nearly half of emetic psychrotrophic B. cereus were able to produce cereulide in optimal conditions. At 4 °C none of the examined psychrotrophs produced cereulide. The results of this research highlight the high prevalence of B. cereus and the omnipresence of toxin gene harboring presumptive B. cereus that can grow at refrigerator temperatures, with a focus on cereulide producers.
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Affiliation(s)
- Jelena Jovanovic
- Department of Food Technology, Safety, and Health, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (J.J.); (K.B.)
| | - Svitlana Tretiak
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, Salisburylaan 133, D5 Ingang 78, 9820 Merelbeke, Belgium;
- Impextraco nv, Wiekevorstsesteenweg 38, 2220 Heist-op-den-Berg, Belgium
| | - Katrien Begyn
- Department of Food Technology, Safety, and Health, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (J.J.); (K.B.)
| | - Andreja Rajkovic
- Department of Food Technology, Safety, and Health, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (J.J.); (K.B.)
- Correspondence:
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Fayad N, Koné KM, Gillis A, Mahillon J. Bacillus cytotoxicus Genomics: Chromosomal Diversity and Plasmidome Versatility. Front Microbiol 2021; 12:789929. [PMID: 34992589 PMCID: PMC8725734 DOI: 10.3389/fmicb.2021.789929] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022] Open
Abstract
Bacillus cytotoxicus is the thermotolerant representative of the Bacillus cereus group. This group, also known as B. cereus sensu lato, comprises both beneficial and pathogenic members and includes psychrotolerant and thermotolerant species. Bacillus cytotoxicus was originally recovered from a fatal outbreak in France in 1998. This species forms a remote cluster from the B. cereus group members and reliably contains the cytk-1 gene, coding for a cytotoxic variant of cytotoxin K. Although this species was originally thought to be homogenous, intra-species diversity has been recently described with four clades, six random amplified polymorphic DNA (RAPD) patterns, and 11 plasmids profiles. This study aimed to get new insights into the genomic diversity of B. cytotoxicus and to decipher the underlying chromosomal and plasmidial variations among six representative isolates through whole genome sequencing (WGS). Among the six sequenced strains, four fitted the previously described genomic clades A and D, while the remaining two constituted new distinct branches. As for the plasmid content of these strains, three large plasmids were putatively conjugative and three small ones potentially mobilizable, harboring coding genes for putative leaderless bacteriocins. Mobile genetic elements, such as prophages, Insertion Sequences (IS), and Bacillus cereus repeats (bcr) greatly contributed to the B. cytotoxicus diversity. As for IS elements and bcr, IS3 and bcr1 were the most abundant elements and, along with the group II intron B.c.I8, were found in all analyzed B. cytotoxicus strains. When compared to other B. cytotoxicus strains, the type-strain NVH 391-98 displayed a relatively low number of IS. Our results shed new light on the contribution of mobile genetic elements to the genome plasticity of B. cytotoxicus and their potential role in horizontal gene transfer.
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Affiliation(s)
- Nancy Fayad
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Louvain-la-Neuve, Belgium
- School of Pharmacy, Lebanese American University, Byblos, Lebanon
| | - Klèma Marcel Koné
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Louvain-la-Neuve, Belgium
| | - Annika Gillis
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Louvain-la-Neuve, Belgium
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Louvain-la-Neuve, Belgium
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Gamage NW, Bamforth J, Ashfaq T, Bernard K, Gräfenhan T, Walkowiak S. Profiling of Bacillus cereus on Canadian grain. PLoS One 2021; 16:e0259209. [PMID: 34735500 PMCID: PMC8568128 DOI: 10.1371/journal.pone.0259209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/14/2021] [Indexed: 11/18/2022] Open
Abstract
Microorganisms that cause foodborne illnesses challenge the food industry; however, environmental studies of these microorganisms on raw grain, prior to food processing, are uncommon. Bacillus cereus sensu lato is a diverse group of bacteria that is common in our everyday environment and occupy a wide array of niches. While some of these bacteria are beneficial to agriculture due to their entomopathogenic properties, others can cause foodborne illness; therefore, characterization of these bacteria is important from both agricultural and food safety standpoints. We performed a survey of wheat and flax grain samples in 2018 (n = 508) and 2017 (n = 636) and discovered that B. cereus was present in the majority of grain samples, as 56.3% and 85.2%, in two years respectively. Whole genome sequencing and comparative genomics of 109 presumptive B. cereus isolates indicates that most of the isolates were closely related and formed two genetically distinct groups. Comparisons to the available genomes of reference strains suggested that the members of these two groups are not closely related to strains previously reported to cause foodborne illness. From the same data set, another, genetically more diverse group of B. cereus was inferred, which had varying levels of similarity to previously reported strains that caused disease. Genomic analysis and PCR amplification of genes linked to toxin production indicated that most of the isolates carry the genes nheA and hbID, while other toxin genes and gene clusters, such as ces, were infrequent. This report of B. cereus on grain from Canada is the first of its kind and demonstrates the value of surveillance of bacteria naturally associated with raw agricultural commodities such as cereal grain and oilseeds.
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Affiliation(s)
| | - Janice Bamforth
- Canadian Grain Commission, Government of Canada, Winnipeg, Canada
| | - Tehreem Ashfaq
- Canadian Grain Commission, Government of Canada, Winnipeg, Canada
| | - Kathryn Bernard
- Public Health Agency of Canada, National Microbiology Laboratory, Government of Canada, Winnipeg, Canada
| | - Tom Gräfenhan
- Canadian Grain Commission, Government of Canada, Winnipeg, Canada
- Public Health Agency of Canada, National Microbiology Laboratory, Government of Canada, Winnipeg, Canada
- * E-mail: (TG); (SW)
| | - Sean Walkowiak
- Canadian Grain Commission, Government of Canada, Winnipeg, Canada
- * E-mail: (TG); (SW)
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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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The Food Poisoning Toxins of Bacillus cereus. Toxins (Basel) 2021; 13:toxins13020098. [PMID: 33525722 PMCID: PMC7911051 DOI: 10.3390/toxins13020098] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/14/2021] [Accepted: 01/25/2021] [Indexed: 12/13/2022] Open
Abstract
Bacillus cereus is a ubiquitous soil bacterium responsible for two types of food-associated gastrointestinal diseases. While the emetic type, a food intoxication, manifests in nausea and vomiting, food infections with enteropathogenic strains cause diarrhea and abdominal pain. Causative toxins are the cyclic dodecadepsipeptide cereulide, and the proteinaceous enterotoxins hemolysin BL (Hbl), nonhemolytic enterotoxin (Nhe) and cytotoxin K (CytK), respectively. This review covers the current knowledge on distribution and genetic organization of the toxin genes, as well as mechanisms of enterotoxin gene regulation and toxin secretion. In this context, the exceptionally high variability of toxin production between single strains is highlighted. In addition, the mode of action of the pore-forming enterotoxins and their effect on target cells is described in detail. The main focus of this review are the two tripartite enterotoxin complexes Hbl and Nhe, but the latest findings on cereulide and CytK are also presented, as well as methods for toxin detection, and the contribution of further putative virulence factors to the diarrheal disease.
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12
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Torres Manno MA, Repizo GD, Magni C, Dunlap CA, Espariz M. The assessment of leading traits in the taxonomy of the Bacillus cereus group. Antonie van Leeuwenhoek 2020; 113:2223-2242. [PMID: 33179199 DOI: 10.1007/s10482-020-01494-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 10/23/2020] [Indexed: 12/18/2022]
Abstract
Bacillus cereus sensu lato strains (B. cereus group) are widely distributed in nature and have received interest for decades due to their importance in insect pest management, food production and their positive and negative repercussions in human health. Consideration of practical uses such as virulence, physiology, morphology, or ill-defined features have been applied to describe and classify species of the group. However, current comparative studies have exposed inconsistencies between evolutionary relatedness and biological significance among genomospecies of the B. cereus group. Here, the combined analyses of core-based phylogeny and all versus all Average Nucleotide Identity values based on 2116 strains were conducted to update the genomospecies circumscriptions within B. cereus group. These analyses suggested the existence of 57 genomospecies, 37 of which are novel, thus indicating that the taxonomic identities of more than 39% of the analyzed strains should be revised or updated. In addition, we found that whole-genome in silico analyses were suitable to differentiate genomospecies such as B. anthracis, B. cereus and B. thuringiensis. The prevalence of toxin and virulence factors coding genes in each of the genomospecies of the B. cereus group was also examined, using phylogeny-aware methods at wide-genome scale. Remarkably, Cry and emetic toxins, commonly assumed to be associated with B. thuringiensis and emetic B. paranthracis, respectively, did not show a positive correlation with those genomospecies. On the other hand, anthrax-like toxin and capsule-biosynthesis coding genes were positively correlated with B. anthracis genomospecies, despite not being present in all strains, and with presumably non-pathogenic genomospecies. Hence, despite these features have been so far considered relevant for industrial or medical classification of related species of the B. cereus group, they were inappropriate for their circumscription. In this study, genomospecies of the group were accurately affiliated and representative strains defined, generating a rational framework that will allow comparative analysis in epidemiological or ecological studies. Based on this classification the role of specific markers such as Type VII secretion system, cytolysin, bacillolysin, and siderophores such as petrobactin were pointed out for further analysis.
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Affiliation(s)
- Mariano A Torres Manno
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Municipalidad de Granadero Baigorria, Sede Suipacha 590, Rosario, Santa Fe, Argentina
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR - CONICET), sede FCByF - UNR, Rosario, Santa Fe, Argentina
- Área Estadística y Procesamiento de Datos, Departamento de Matemática y Estadística, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Guillermo D Repizo
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Rosario, Argentina
- Laboratorio de Resistencia bacteriana a antimicrobianos, Instituto de Biología Molecular y Celular de Rosario (IBR), sede FCByF - UNR, Rosario, Santa Fe, Argentina
| | - Christian Magni
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Municipalidad de Granadero Baigorria, Sede Suipacha 590, Rosario, Santa Fe, Argentina
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR - CONICET), sede FCByF - UNR, Rosario, Santa Fe, Argentina
| | - Christopher A Dunlap
- United States Department of Agriculture, Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, 1815 North University Street, Peoria, IL, 61604, USA
| | - Martín Espariz
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Municipalidad de Granadero Baigorria, Sede Suipacha 590, Rosario, Santa Fe, Argentina.
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR - CONICET), sede FCByF - UNR, Rosario, Santa Fe, Argentina.
- Área Estadística y Procesamiento de Datos, Departamento de Matemática y Estadística, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
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Jessberger N, Dietrich R, Granum PE, Märtlbauer E. The Bacillus cereus Food Infection as Multifactorial Process. Toxins (Basel) 2020; 12:E701. [PMID: 33167492 PMCID: PMC7694497 DOI: 10.3390/toxins12110701] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 02/06/2023] Open
Abstract
The ubiquitous soil bacterium Bacillus cereus presents major challenges to food safety. It is responsible for two types of food poisoning, the emetic form due to food intoxication and the diarrheal form emerging from food infections with enteropathogenic strains, also known as toxico-infections, which are the subject of this review. The diarrheal type of food poisoning emerges after production of enterotoxins by viable bacteria in the human intestine. Basically, the manifestation of the disease is, however, the result of a multifactorial process, including B. cereus prevalence and survival in different foods, survival of the stomach passage, spore germination, motility, adhesion, and finally enterotoxin production in the intestine. Moreover, all of these processes are influenced by the consumed foodstuffs as well as the intestinal microbiota which have, therefore, to be considered for a reliable prediction of the hazardous potential of contaminated foods. Current knowledge regarding these single aspects is summarized in this review aiming for risk-oriented diagnostics for enteropathogenic B. cereus.
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Affiliation(s)
- Nadja Jessberger
- Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Schönleutnerstr. 8, 85764 Oberschleißheim, Germany; (R.D.); (E.M.)
| | - Richard Dietrich
- Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Schönleutnerstr. 8, 85764 Oberschleißheim, Germany; (R.D.); (E.M.)
| | - Per Einar Granum
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003 NMBU, 1432 Ås, Norway;
| | - Erwin Märtlbauer
- Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Schönleutnerstr. 8, 85764 Oberschleißheim, Germany; (R.D.); (E.M.)
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Novel Effective Bacillus cereus Group Species " Bacillus clarus" Is Represented by Antibiotic-Producing Strain ATCC 21929 Isolated from Soil. mSphere 2020; 5:5/6/e00882-20. [PMID: 33148822 PMCID: PMC7643830 DOI: 10.1128/msphere.00882-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The B. cereus group comprises numerous closely related lineages with various degrees of pathogenic potential and industrial relevance. Species-level taxonomic classification of B. cereus group strains is important for risk evaluation and communication but remains challenging. Biochemical and phenotypic assays are often used to assign B. cereus group strains to species but are insufficient for accurate taxonomic classification on a genomic scale. Here, we show that antibiotic-producing ATCC 21929 represents a novel lineage within the B. cereus group that, by all metrics used to delineate prokaryotic species, exemplifies a novel effective species. Furthermore, we show that ATCC 21929 is incapable of producing enterotoxins Hbl and Nhe or exhibiting cytotoxic effects on HeLa cells at human body temperature in vitro. These results provide greater insight into the genomic and phenotypic diversity of the B. cereus group and may be leveraged to inform future public health and food safety efforts. Gram-positive, spore-forming members of the Bacillus cereus group species complex are widespread in natural environments and display various degrees of pathogenicity. Recently, B. cereus group strain Bacillus mycoides Flugge ATCC 21929 was found to represent a novel lineage within the species complex, sharing a relatively low degree of genomic similarity with all B. cereus group genomes (average nucleotide identity [ANI] < 88). ATCC 21929 has been previously associated with the production of a patented antibiotic, antibiotic 60-6 (i.e., cerexin A); however, the virulence potential and growth characteristics of this lineage have never been assessed. Here, we provide an extensive genomic and phenotypic characterization of ATCC 21929, and we assess its pathogenic potential in vitro. ATCC 21929 most closely resembles Bacillus paramycoides NH24A2T (ANI and in silico DNA-DNA hybridization values of 86.70 and 34.10%, respectively). Phenotypically, ATCC 21929 does not possess cytochrome c oxidase activity and is able to grow at a range of temperatures between 15 and 43°C and a range of pH between 6 and 9. At 32°C, ATCC 21929 shows weak production of diarrheal enterotoxin hemolysin BL (Hbl) but no production of nonhemolytic enterotoxin (Nhe); at 37°C, neither Hbl nor Nhe is produced. Additionally, at 37°C, ATCC 21929 does not exhibit cytotoxic effects toward HeLa cells. With regard to fatty acid composition, ATCC 21929 has iso-C17:0 present in highest abundance. Based on the characterization provided here, ATCC 21929T (= PS00077AT = PS00077BT = PSU-0922T = BHPT) represents a novel effective B. cereus group species, which we propose as effective species “Bacillus clarus.” IMPORTANCE The B. cereus group comprises numerous closely related lineages with various degrees of pathogenic potential and industrial relevance. Species-level taxonomic classification of B. cereus group strains is important for risk evaluation and communication but remains challenging. Biochemical and phenotypic assays are often used to assign B. cereus group strains to species but are insufficient for accurate taxonomic classification on a genomic scale. Here, we show that antibiotic-producing ATCC 21929 represents a novel lineage within the B. cereus group that, by all metrics used to delineate prokaryotic species, exemplifies a novel effective species. Furthermore, we show that ATCC 21929 is incapable of producing enterotoxins Hbl and Nhe or exhibiting cytotoxic effects on HeLa cells at human body temperature in vitro. These results provide greater insight into the genomic and phenotypic diversity of the B. cereus group and may be leveraged to inform future public health and food safety efforts.
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15
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Bacillus cereus: Epidemiology, Virulence Factors, and Host-Pathogen Interactions. Trends Microbiol 2020; 29:458-471. [PMID: 33004259 DOI: 10.1016/j.tim.2020.09.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 12/30/2022]
Abstract
The toxin-producing bacterium Bacillus cereus is an important and neglected human pathogen and a common cause of food poisoning. Several toxins have been implicated in disease, including the pore-forming toxins hemolysin BL (HBL) and nonhemolytic enterotoxin (NHE). Recent work revealed that HBL binds to the mammalian surface receptors LITAF and CDIP1 and that both HBL and NHE induce potassium efflux and activate the NLRP3 inflammasome, leading to pyroptosis. These mammalian receptors, in part, contribute to inflammation and pathology. Other putative virulence factors of B. cereus include cytotoxin K, cereulide, metalloproteases, sphingomyelinase, and phospholipases. In this review, we highlight the latest progress in our understanding of B. cereus biology, epidemiology, and pathogenesis, and discuss potential new directions for research in this field.
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Carroll LM, Cheng RA, Kovac J. No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods. Front Microbiol 2020; 11:580691. [PMID: 33072050 PMCID: PMC7536271 DOI: 10.3389/fmicb.2020.580691] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/25/2020] [Indexed: 12/19/2022] Open
Abstract
The Bacillus cereus group, also known as B. cereus sensu lato (s.l.), is a species complex comprising 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 essential for facilitating communication between and among microbiologists, clinicians, public health officials, and industry professionals, but is not always straightforward. A recently proposed genomospecies-subspecies-biovar taxonomic framework aims to provide a standardized nomenclature for this species complex but relies heavily on whole-genome sequencing (WGS). It thus is unclear whether popular, low-cost typing methods (e.g., single- and multi-locus sequence typing) remain congruent with the proposed taxonomy. Here, we characterize 2,231 B. cereus s.l. genomes using a combination of in silico (i) average-nucleotide identity (ANI)-based genomospecies assignment, (ii) ANI-based subspecies assignment, (iii) seven-gene multi-locus sequence typing (MLST), (iv) single-locus panC group assignment, (v) rpoB allelic typing, and (vi) virulence factor detection. We show that sequence types (STs) assigned using MLST can be used for genomospecies assignment, and we provide a comprehensive list of ST/genomospecies associations. For panC group assignment, we show that an adjusted, eight-group framework is largely, albeit not perfectly, congruent with the proposed eight-genomospecies taxonomy, as panC alone may not distinguish (i) B. luti from Group II B. mosaicus and (ii) B. paramycoides from Group VI B. mycoides. We additionally provide a list of loci that capture the topology of the whole-genome B. cereus s.l. phylogeny that may be used in future sequence typing efforts. For researchers with access to WGS, MLST, and/or panC data, we showcase how our recently released software, BTyper3 (https://github.com/lmc297/BTyper3), can be used to assign B. cereus s.l. isolates to taxonomic units within this proposed framework with little-to-no user intervention or domain-specific knowledge of B. cereus s.l. taxonomy. We additionally outline a novel method for assigning B. cereus s.l. genomes to pseudo-gene flow units within proposed genomospecies. The results presented here highlight the backward-compatibility and accessibility of the recently proposed genomospecies-subspecies-biovar taxonomic framework and illustrate that WGS is not a necessity for microbiologists who want to use the proposed nomenclature effectively.
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Affiliation(s)
- Laura M. Carroll
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rachel A. Cheng
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
| | - Jasna Kovac
- Department of Food Science, College of Agricultural Sciences, The Pennsylvania State University, University Park, PA, United States
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17
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Baldwin VM. You Can't B. cereus - A Review of Bacillus cereus Strains That Cause Anthrax-Like Disease. Front Microbiol 2020; 11:1731. [PMID: 32973690 PMCID: PMC7468541 DOI: 10.3389/fmicb.2020.01731] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022] Open
Abstract
Emerging strains of Bacillus cereus, traditionally considered a self-limiting foodborne pathogen, have been associated with anthrax-like disease in mammals, including humans. The strains have emerged by divergent evolution and, as exchange of genetic material in the Bacillus genus occurs naturally, it is possible that further isolates will be identified in the future. The strains vary in their genotypes and phenotypes, combining traits of both B. cereus and B. anthracis species. Cases of anthrax-like disease associated with these strains result in similar symptoms and mortality rates as those caused by B. anthracis. The strains are susceptible to frontline antibiotics used in the treatment of anthrax and existing vaccines provide protection in animal models. The emergence of these strains has reignited the debate surrounding classification of the B. cereus sensu lato group and serves as a reminder that the field of medical microbiology is constantly changing and remains an important and ongoing area of research.
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18
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Drewnowska JM, Stefanska N, Czerniecka M, Zambrowski G, Swiecicka I. Potential Enterotoxicity of Phylogenetically Diverse Bacillus cereus Sensu Lato Soil Isolates from Different Geographical Locations. Appl Environ Microbiol 2020; 86:e03032-19. [PMID: 32220844 PMCID: PMC7237779 DOI: 10.1128/aem.03032-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 03/20/2020] [Indexed: 02/06/2023] Open
Abstract
Bacillus cereus sensu lato comprises Gram-positive spore-forming bacteria producing toxins associated with foodborne diseases. Three pore-forming enterotoxins, nonhemolytic enterotoxin (Nhe), hemolysin BL (Hbl), and cytotoxin K (CytK), are considered the primary factors in B. cereus sensu lato diarrhea. The aim of this study was to determine the potential risk of enterotoxicity among soil B. cereus sensu lato isolates representing diverse phylogroups and originated from different geographic locations with various climates (Burkina Faso, Kenya, Argentina, Kazakhstan, and Poland). While nheA- and hblA-positive isolates were present among all B. cereus sensu lato populations and distributed across all phylogenetic groups, cytK-2-positive strains predominated in geographic regions with an arid hot climate (Africa) and clustered together on a phylogenetic tree mainly within mesophilic groups III and IV. The highest in vitro cytotoxicity to Caco-2 and HeLa cells was demonstrated by the strains clustered within phylogroups II and IV. Overall, our results suggest that B. cereus sensu lato pathogenicity is a comprehensive process conditioned by many intracellular factors and diverse environmental conditions.IMPORTANCE This research offers a new route for a wider understanding of the dependency between pathogenicity and phylogeny of a natural bacterial population, specifically within Bacillus cereus sensu lato, that is widely distributed around the world and easily transferred into food products. Our study indicates differences in the phylogenetic and geographical distributions of potential enterotoxigenic B. cereus sensu lato strains. Hence, these bacilli possess a risk for human health, and rapid testing methods for their identification are greatly needed. In particular, the detection of the CytK enterotoxin should be a supporting strategy for the identification of pathogenic B. cereus sensu lato.
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Affiliation(s)
| | - Natalia Stefanska
- Department of Microbiology, Faculty of Biology, University of Bialystok, Bialystok, Poland
| | - Magdalena Czerniecka
- Department of Cytobiochemistry, Faculty of Biology, University of Bialystok, Bialystok, Poland
- Laboratory of Tissue Culture, Faculty of Biology, University of Bialystok, Bialystok, Poland
| | - Grzegorz Zambrowski
- Laboratory of Applied Microbiology, University of Bialystok, Bialystok, Poland
| | - Izabela Swiecicka
- Department of Microbiology, Faculty of Biology, University of Bialystok, Bialystok, Poland
- Laboratory of Applied Microbiology, University of Bialystok, Bialystok, Poland
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Carroll LM, Wiedmann M, Kovac J. Proposal of a Taxonomic Nomenclature for the Bacillus cereus Group Which Reconciles Genomic Definitions of Bacterial Species with Clinical and Industrial Phenotypes. mBio 2020; 11:e00034-20. [PMID: 32098810 PMCID: PMC7042689 DOI: 10.1128/mbio.00034-20] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 01/15/2020] [Indexed: 02/07/2023] Open
Abstract
The Bacillus cereus group comprises numerous closely related species, including bioterrorism agent B. anthracis, foodborne pathogen B. cereus, and biopesticide B. thuringiensis Differentiating organisms capable of causing illness or death from those used in industry is essential for risk assessment and outbreak preparedness. However, current species definitions facilitate species-phenotype incongruences, particularly when horizontally acquired genes are responsible for a phenotype. Using all publicly available B. cereus group genomes (n = 2,231), we show that current species definitions lead to overlapping genomospecies clusters, in which 66.2% of genomes belong to multiple genomospecies at a conventional 95 average nucleotide identity (ANI) genomospecies threshold. A genomospecies threshold of ≈92.5 ANI is shown to reflect a natural gap in genome similarity for the B. cereus group, and medoid genomes identified at this threshold are shown to yield resolvable genomospecies clusters with minimal overlap (six of 2,231 genomes assigned to multiple genomospecies; 0.269%). We thus propose a nomenclatural framework for the B. cereus group which accounts for (i) genomospecies using resolvable genomospecies clusters obtained at ≈92.5 ANI, (ii) established lineages of medical importance using a formal collection of subspecies names, and (iii) heterogeneity of clinically and industrially important phenotypes using a formalized and extended collection of biovar terms. We anticipate that the proposed nomenclature will remain interpretable to clinicians, without sacrificing genomic species definitions, which can in turn aid in pathogen surveillance; early detection of emerging, high-risk genotypes; and outbreak preparedness.IMPORTANCE Historical species definitions for many prokaryotes, including pathogens, have relied on phenotypic characteristics that are inconsistent with genome evolution. This scenario forces microbiologists and clinicians to face a tradeoff between taxonomic rigor and clinical interpretability. Using the Bacillus cereus group as a model, a conceptual framework for the taxonomic delineation of prokaryotes which reconciles genomic definitions of species with clinically and industrially relevant phenotypes is presented. The nomenclatural framework outlined here serves as a model for genomics-based bacterial taxonomy that moves beyond arbitrarily set genomospecies thresholds while maintaining congruence with phenotypes and historically important species names.
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Affiliation(s)
- Laura M Carroll
- Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - 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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20
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Koné KM, Douamba Z, Halleux MD, Bougoudogo F, Mahillon J. Prevalence and Diversity of the Thermotolerant Bacterium Bacillus cytotoxicus among Dried Food Products. J Food Prot 2019; 82:1210-1216. [PMID: 31233363 DOI: 10.4315/0362-028x.jfp-19-006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
HIGHLIGHTS Bacillus cytotoxicus was found in all tested potato flakes but at loads lower than 102 CFU/g. B. cytotoxicus was observed in other potato-containing products and in millet flour. B. cytotoxicus isolates (n = 57) fell into six RAPD patterns and 11 plasmid profiles. A large proportion of B. cytotoxicus isolates contained small and/or large plasmids.
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Affiliation(s)
- Klèma Marcel Koné
- 1 Laboratory of Food and Environmental Microbiology, Earth and Life Institute, UCLouvain, Croix du Sud 2/L7.05.12 1348, Louvain-la-Neuve, Belgium
| | - Zoénabo Douamba
- 1 Laboratory of Food and Environmental Microbiology, Earth and Life Institute, UCLouvain, Croix du Sud 2/L7.05.12 1348, Louvain-la-Neuve, Belgium
| | - Maëlle de Halleux
- 1 Laboratory of Food and Environmental Microbiology, Earth and Life Institute, UCLouvain, Croix du Sud 2/L7.05.12 1348, Louvain-la-Neuve, Belgium
| | - Flabou Bougoudogo
- 2 Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako, BP:1805, Bamako, Mali
| | - Jacques Mahillon
- 1 Laboratory of Food and Environmental Microbiology, Earth and Life Institute, UCLouvain, Croix du Sud 2/L7.05.12 1348, Louvain-la-Neuve, Belgium
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21
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Liu B, Liu GH, Wang XY, Wang JP, Chen Z, Chen MC, Zhang HF, Singonca C. Bacillus urbisdiaboli sp. nov., isolated from soil sampled in Xinjiang. Int J Syst Evol Microbiol 2019; 69:1591-1596. [DOI: 10.1099/ijsem.0.003363] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Bo Liu
- 1Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Guo-Hong Liu
- 1Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Xiao-Ying Wang
- 1Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Jie-Ping Wang
- 1Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Zheng Chen
- 1Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Mei-Chun Chen
- 1Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Hai-Feng Zhang
- 1Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Cetin Singonca
- 2Institute of Crop Sciences and Resource Conservation (INRES), University of Bonn, Meckenheimer Allee 166A D-53115 Bonn, Germany
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22
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Fayad N, Kallassy Awad M, Mahillon J. Diversity of Bacillus cereus sensu lato mobilome. BMC Genomics 2019; 20:436. [PMID: 31142281 PMCID: PMC6542083 DOI: 10.1186/s12864-019-5764-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 05/03/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Bacillus cereus sensu lato s.l.) is a group of bacteria displaying close phylogenetic relationships but a high ecological diversity. The three most studied species are Bacillus anthracis, Bacillus cereus sensu stricto and Bacillus thuringiensis. While some species are pathogenic to mammals or associated with food poisoning, Bacillus thuringiensis is a well-known entomopathogenic bacterium used as biopesticide worldwide. B. cereus s.l. also contains a large variety of mobile genetic elements (MGEs). RESULTS In this study, we detail the occurrence and plasmid vs. chromosome distribution of several MGEs in 102 complete and annotated genomes of B. cereus s.l. These MGEs include 16 Insertion Sequence (IS) families, the Tn3 family, 18 different Bacillus cereus repeats (BCRs) and 30 known group II introns. CONCLUSIONS Our analysis not only shows the diversity of these MGEs among strains of the same species and between different species within the B. cereus s.l. group, but also highlights the potential impact of these elements on the plasticity of the plasmid pool, and the TEs (Transposable Elements) - species relationship within B. cereus s.l.
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Affiliation(s)
- Nancy Fayad
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, UCLouvain, Croix du Sud, 2 - L7.05.12, B-1348, Louvain-la-Neuve, Belgium
- Laboratory of Biodiversity and Functional Genomics, Faculty of Science, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
| | - Mireille Kallassy Awad
- Laboratory of Biodiversity and Functional Genomics, Faculty of Science, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, UCLouvain, Croix du Sud, 2 - L7.05.12, B-1348, Louvain-la-Neuve, Belgium.
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Tamindžija D, Chromikova Z, Spaić A, Barak I, Bernier-Latmani R, Radnović D. Chromate tolerance and removal of bacterial strains isolated from uncontaminated and chromium-polluted environments. World J Microbiol Biotechnol 2019; 35:56. [PMID: 30900044 DOI: 10.1007/s11274-019-2638-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 03/14/2019] [Indexed: 10/27/2022]
Abstract
Investigation of bacterial chromate tolerance has mostly focused on strains originating from polluted sites. In the present study, we isolated 33 chromate tolerant strains from diverse environments harbouring varying concentrations of chromium (Cr). All of these strains were able to grow on minimal media with at least 2 mM hexavalent chromium (Cr(VI)) and their classification revealed that they belonged to 12 different species and 8 genera, with a majority (n = 20) being affiliated to the Bacillus cereus group. Selected B. cereus group strains were further characterised for their chromate tolerance level and the ability to remove toxic Cr(VI) from solution. A similar level of chromate tolerance was observed in isolates originating from environments harbouring high or low Cr. Reference B. cereus strains exhibited the same Cr(VI) tolerance which indicates that a high chromate tolerance could be an intrinsic group characteristic. Cr(VI) removal varied from 22.9% (strain PCr2a) to 98.5% (strain NCr4). Strains NCr1a and PCr12 exhibited the ability to grow to the greatest extent in Cr(VI) containing media (maximum growth of 65.3% and 64.9% relative to that in the absence of Cr(VI), respectively) accompanied with high chromate removal activity (73.7% and 74.4%, respectively), making them prime candidates for the investigation of chromate tolerance mechanisms in Gram-positive bacteria and Cr(VI) bioremediation applications.
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Affiliation(s)
- Dragana Tamindžija
- Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, University of Novi Sad, Trg Dositeja Obradovića 3, Novi Sad, 21000, Serbia
| | - Zuzana Chromikova
- Department of Microbial Genetics, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, Bratislava, 845 51, Slovakia
| | - Andrea Spaić
- Faculty of Sciences, Department of Biology and Ecology, University of Novi Sad, Trg Dositeja Obradovića 2, Novi Sad, 21000, Serbia
| | - Imrich Barak
- Department of Microbial Genetics, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, Bratislava, 845 51, Slovakia
| | - Rizlan Bernier-Latmani
- Environmental Microbiology Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Dragan Radnović
- Faculty of Sciences, Department of Biology and Ecology, University of Novi Sad, Trg Dositeja Obradovića 2, Novi Sad, 21000, Serbia.
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Whole-genome-based phylogeny of Bacillus cytotoxicus reveals different clades within the species and provides clues on ecology and evolution. Sci Rep 2019; 9:1984. [PMID: 30760727 PMCID: PMC6374410 DOI: 10.1038/s41598-018-36254-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/16/2018] [Indexed: 12/19/2022] Open
Abstract
Bacillus cytotoxicus is a member of the Bacillus cereus group linked to fatal cases of diarrheal disease. Information on B. cytotoxicus is very limited; in particular comprehensive genomic data is lacking. Thus, we applied a genomic approach to characterize B. cytotoxicus and decipher its population structure. To this end, complete genomes of ten B. cytotoxicus were sequenced and compared to the four publicly available full B. cytotoxicus genomes and genomes of other B. cereus group members. Average nucleotide identity, core genome, and pan genome clustering resulted in clear distinction of B. cytotoxicus strains from other strains of the B. cereus group. Genomic content analyses showed that a hydroxyphenylalanine operon is present in B. cytotoxicus, but absent in all other members of the B. cereus group. It enables degradation of aromatic compounds to succinate and pyruvate and was likely acquired from another Bacillus species. It allows for utilization of tyrosine and might have given a B. cytotoxicus ancestor an evolutionary advantage resulting in species differentiation. Plasmid content showed that B. cytotoxicus is flexible in exchanging genes, allowing for quick adaptation to the environment. Genome-based phylogenetic analyses divided the B. cytotoxicus strains into four clades that also differed in virulence gene content.
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Rossi GAM, Aguilar CEG, Silva HO, Vidal AMC. Bacillus cereus group: genetic aspects related to food safety and dairy processing. ARQUIVOS DO INSTITUTO BIOLÓGICO 2018. [DOI: 10.1590/1808-1657000232017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
ABSTRACT: Bacillus cereus group includes not pathogenic and high pathogenic species. They are considered as a risk to public health due to foodborne diseases and as an important cause of economic losses to industries due to production of spoilage enzymes. Some researches have been performed in order to assess the possible factors that contribute to put public health into risk because of consumption of food contaminated with viable cells or toxins which have complex mechanisms of production. The control of these bacteria in food is difficult because they are resistant to several processes used in industries. Thus, in this way, this review focused on highlighting the risk due to toxins production by bacteria from B. cereus group in food and the consequences for food safety and dairy industries.
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Genes under positive selection in the core genome of pathogenic Bacillus cereus group members. INFECTION GENETICS AND EVOLUTION 2018; 65:55-64. [PMID: 30006047 DOI: 10.1016/j.meegid.2018.07.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/06/2018] [Accepted: 07/07/2018] [Indexed: 11/24/2022]
Abstract
In this comparative genomics study our aim was to unravel genes under positive selection in the core genome of the Bacillus cereus group. Indeed, the members of this group share close genetic relationships but display a rather large phenotypic and ecological diversity, providing a unique opportunity for studying how genomic changes reflect ecological adaptation during the divergence of a bacterial group. For this purpose, we screened ten completely sequenced genomes of four pathogenic Bacillus species, finding that 254 out of 3093 genes have codon sites with dN/dS (ω) values above one. These results remained unchanged after having disentangled the confounding effects of recombination and selection signature in a Bayesian framework. The presumably adaptive nucleotide polymorphisms are distributed over a wide range of biological functions, such as antibiotic resistance, DNA repair, nutrient uptake, metabolism, cell wall assembly and spore structure. Our results indicate that adaptation to animal hosts, whether as pathogens, saprophytes or symbionts, is the major driving force in the evolution of the Bacillus cereus group. Future work should seek to understand the evolutionary dynamics of both core and accessory genes in an integrative framework to ultimately unravel the key networks involved in host adaptation.
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Porcellato D, Aspholm M, Skeie SB, Mellegård H. Application of a novel amplicon-based sequencing approach reveals the diversity of the Bacillus cereus group in stored raw and pasteurized milk. Food Microbiol 2018; 81:32-39. [PMID: 30910086 DOI: 10.1016/j.fm.2018.01.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/20/2017] [Accepted: 01/15/2018] [Indexed: 12/16/2022]
Abstract
Members of the Bacillus cereus sensu lato (B. cereus group) are spore-forming organisms commonly associated with spoilage of milk and dairy products. Previous studies have shown, by using 16S marker gene sequencing, that the genus Bacillus is part of the core microbiota of raw bovine milk and that some members of this genus are able to grow during sub-optimal storage (8 °C) of pasteurized consumption milk. Here, the composition of this genus in pasteurized consumption milk samples, collected from two dairies, over a one-year period and stored at 4 or 8 °C up to the end of shelf life is uncovered. Our results show that the B. cereus group is the dominant Bacillus group in stored consumption milk. By applying a new marker gene sequencing approach, several dominating phylogenetic clusters were identified within the B. cereus group populations from the milk samples. There was a higher phylogenetic diversity among bacteria from milk stored at 8 °C compared to milk stored at 4 °C. Sampling period and the dairy the samples were collected from, also significantly influenced the diversity, which shows that the B. cereus group population in consumption milk is heterogeneous and subjected to temporal and spatial changes. The new approach applied in this study will facilitate the identification of isolates within the B. cereus group, of which some are potential spoilage bacteria and pathogenic contaminants of milk and dairy products.
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Affiliation(s)
- Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway.
| | - Marina Aspholm
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine, The Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway
| | - Siv Borghild Skeie
- Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway
| | - Hilde Mellegård
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine, The Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway
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Frentzel H, Kraushaar B, Krause G, Bodi D, Wichmann-Schauer H, Appel B, Mader A. Phylogenetic and toxinogenic characteristics of Bacillus cereus group members isolated from spices and herbs. Food Control 2018. [DOI: 10.1016/j.foodcont.2016.12.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Liu B, Liu GH, Wang XY, Wang JP, Zhu YJ, Zhang HF, Sengonca C. Bacillus populi sp. nov. isolated from Populus euphratica rhizosphere soil of the Taklamakan desert. Int J Syst Evol Microbiol 2018; 68:155-159. [DOI: 10.1099/ijsem.0.002476] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Bo Liu
- Agricultural Bio-resource Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Guo-Hong Liu
- Agricultural Bio-resource Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Xiao-Ying Wang
- Agricultural Bio-resource Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
- Fuzhou University, Fuzhou, Fujian 350108, PR China
| | - Jie-Ping Wang
- Agricultural Bio-resource Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Yu-Jing Zhu
- Agricultural Bio-resource Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Hai-Feng Zhang
- Agricultural Bio-resource Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Cetin Sengonca
- Institute of Crop Sciences and Resource Conservation (INRES), University of Bonn, Meckenheimer Allee 166A D-53115 Bonn, Germany
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30
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Bartoszewicz M, Marjańska PS. Milk-originated Bacillus cereus sensu lato strains harbouring Bacillus anthracis- like plasmids are genetically and phenotypically diverse. Food Microbiol 2017. [DOI: 10.1016/j.fm.2017.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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31
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Bartoszewicz M, Czyżewska U. Spores and vegetative cells of phenotypically and genetically diverse Bacillus cereus sensu lato are common bacteria in fresh water of northeastern Poland. Can J Microbiol 2017; 63:939-950. [PMID: 28930645 DOI: 10.1139/cjm-2017-0337] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Gram-positive rods Bacillus cereus sensu lato (sl) are common in natural habitats and food products. It is believed that they are restricted to spores; however, their ecology in aquatic habitats is still poorly investigated. Thus, the aim of the study was to assess the rain-dependent fluctuations in the concentration of B. cereus sl vegetative cells and spores, with evaluation of their phylogenetic and population structure in relation to the toxicity and psychrotolerance. We proved that vegetative cells of B. cereus sl are widely distributed in fresh water of rivers and lakes, being as common as spores. Moreover, heavy rain has a huge impact on their concentration in undisturbed environments. The diversity of B. cereus sl reflects the multiple sources of bacteria and the differences between their distinct environments. Next, their diverse genetic structure and phenotypes better fit their ecological properties than their taxonomic affiliation.
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Affiliation(s)
- Marek Bartoszewicz
- a Department of Microbiology, Institute of Biology, Faculty of Biology and Chemistry, University of Bialystok, 1J Ciolkowski Street, Bialystok 15-245, Poland
| | - Urszula Czyżewska
- b Department of Cytobiochemistry, Institute of Biology, Faculty of Biology and Chemistry, University of Bialystok, 1J Ciolkowski Street, Bialystok 15-245, Poland
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Hollensteiner J, Poehlein A, Spröer C, Bunk B, Sheppard AE, Rosentstiel P, Schulenburg H, Liesegang H. Complete Genome sequence of the nematicidal Bacillus thuringiensis MYBT18246. Stand Genomic Sci 2017; 12:48. [PMID: 28852435 PMCID: PMC5569534 DOI: 10.1186/s40793-017-0259-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 08/08/2017] [Indexed: 01/22/2023] Open
Abstract
10.1601/nm.5000 is a rod-shaped facultative anaerobic spore forming bacterium of the genus 10.1601/nm.4857. The defining feature of the species is the ability to produce parasporal crystal inclusion bodies, consisting of δ-endotoxins, encoded by cry-genes. Here we present the complete annotated genome sequence of the nematicidal 10.1601/nm.5000 strain MYBT18246. The genome comprises one 5,867,749 bp chromosome and 11 plasmids which vary in size from 6330 bp to 150,790 bp. The chromosome contains 6092 protein-coding and 150 RNA genes, including 36 rRNA genes. The plasmids encode 997 proteins and 4 t-RNA's. Analysis of the genome revealed a large number of mobile elements involved in genome plasticity including 11 plasmids and 16 chromosomal prophages. Three different nematicidal toxin genes were identified and classified according to the Cry toxin naming committee as cry13Aa2, cry13Ba1, and cry13Ab1. Strikingly, these genes are located on the chromosome in close proximity to three separate prophages. Moreover, four putative toxin genes of different toxin classes were identified on the plasmids p120510 (Vip-like toxin), p120416 (Cry-like toxin) and p109822 (two Bin-like toxins). A comparative genome analysis of 10.1601/nm.5000 MYBT18246 with three closely related 10.1601/nm.5000 strains enabled determination of the pan-genome of 10.1601/nm.5000 MYBT18246, revealing a large number of singletons, mostly represented by phage genes, morons and cryptic genes.
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Affiliation(s)
- Jacqueline Hollensteiner
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Anna E. Sheppard
- Present address: Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Philip Rosentstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Heiko Liesegang
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
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Liu Y, Du J, Lai Q, Zeng R, Ye D, Xu J, Shao Z. Proposal of nine novel species of the Bacillus cereus group. Int J Syst Evol Microbiol 2017; 67:2499-2508. [PMID: 28792367 DOI: 10.1099/ijsem.0.001821] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nine novel Gram-stain-positive bacteria were investigated by a polyphasic taxonomic approach. Based on the analysis of 16S rRNA gene sequences, these strains belonged to the Bacillus cereus group, sharing over 97 % similarity with the known species of this group, and less than 95 % similarity with other species of the genus Bacillus. Multilocus sequence typing analysis showed that they formed nine robust and well-separated branches from the known species. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the nine strains were, respectively, below the 70 and 96 % threshold values for species definition, and between each strain and the known type strains of this group were also below the two threshold values. On the basis of the phenotypic and phylogenetic data, along with low dDDH and ANI values among these strains, these bacteria are assigned to the following nine novel species of the B. cereus group: Bacillus paranthracis sp. nov., type strain Mn5T (=MCCC 1A00395T=KCTC 33714T=LMG 28873T); Bacillus pacificus sp. nov., type strain EB422T (=MCCC 1A06182T=KCTC 33858T); Bacillus tropicus sp. nov., type strain N24T (=MCCC 1A01406T=KCTC 33711T=LMG 28874T); Bacillus albus sp. nov., type strain N35-10-2T (=MCCC 1A02146T=KCTC 33710T=LMG 28875T); Bacillus mobilis sp. nov., type strain 0711P9-1T (=MCCC 1A05942T=KCTC 33717T=LMG 28877T); Bacillus luti sp. nov., type strain TD41T (=MCCC 1A00359T=KCTC 33716T=LMG 28872T); Bacillus proteolyticus sp. nov., type strain TD42T (=MCCC 1A00365T=KCTC 33715T=LMG 28870T); Bacillus nitratireducens sp. nov., type strain 4049T (=MCCC 1A00732T=KCTC 33713T=LMG 28871T); and Bacillus paramycoides sp. nov., type strain NH24A2T (=MCCC 1A04098T=KCTC 33709T=LMG 28876T).
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Affiliation(s)
- Yang Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Juan Du
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Runying Zeng
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Dezan Ye
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Jun Xu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Institute of Oceanology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
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Abstract
BACKGROUND Bacillus cereus sensu lato (s. l.) is an ecologically diverse bacterial group of medical and agricultural significance. In this study, I use publicly available genomes and novel bioinformatic workflows to characterize the B. cereus s. l. pan-genome and perform the largest phylogenetic and population genetic analyses of this group to date in terms of the number of genes and taxa included. With these fundamental data in hand, I identify genes associated with particular phenotypic traits (i.e., "pan-GWAS" analysis), and quantify the degree to which taxa sharing common attributes are phylogenetically clustered. METHODS A rapid k-mer based approach (Mash) was used to create reduced representations of selected Bacillus genomes, and a fast distance-based phylogenetic analysis of this data (FastME) was performed to determine which species should be included in B. cereus s. l. The complete genomes of eight B. cereus s. l. species were annotated de novo with Prokka, and these annotations were used by Roary to produce the B. cereus s. l. pan-genome. Scoary was used to associate gene presence and absence patterns with various phenotypes. The orthologous protein sequence clusters produced by Roary were filtered and used to build HaMStR databases of gene models that were used in turn to construct phylogenetic data matrices. Phylogenetic analyses used RAxML, DendroPy, ClonalFrameML, PAUP*, and SplitsTree. Bayesian model-based population genetic analysis assigned taxa to clusters using hierBAPS. The genealogical sorting index was used to quantify the phylogenetic clustering of taxa sharing common attributes. RESULTS The B. cereus s. l. pan-genome currently consists of ≈60,000 genes, ≈600 of which are "core" (common to at least 99% of taxa sampled). Pan-GWAS analysis revealed genes associated with phenotypes such as isolation source, oxygen requirement, and ability to cause diseases such as anthrax or food poisoning. Extensive phylogenetic analyses using an unprecedented amount of data produced phylogenies that were largely concordant with each other and with previous studies. Phylogenetic support as measured by bootstrap probabilities increased markedly when all suitable pan-genome data was included in phylogenetic analyses, as opposed to when only core genes were used. Bayesian population genetic analysis recommended subdividing the three major clades of B. cereus s. l. into nine clusters. Taxa sharing common traits and species designations exhibited varying degrees of phylogenetic clustering. CONCLUSIONS All phylogenetic analyses recapitulated two previously used classification systems, and taxa were consistently assigned to the same major clade and group. By including accessory genes from the pan-genome in the phylogenetic analyses, I produced an exceptionally well-supported phylogeny of 114 complete B. cereus s. l. genomes. The best-performing methods were used to produce a phylogeny of all 498 publicly available B. cereus s. l. genomes, which was in turn used to compare three different classification systems and to test the monophyly status of various B. cereus s. l. species. The majority of the methodology used in this study is generic and could be leveraged to produce pan-genome estimates and similarly robust phylogenetic hypotheses for other bacterial groups.
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Affiliation(s)
- Adam L Bazinet
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, 21702, MD, USA.
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Liu B, Liu GH, Sengonca C, Schumann P, Wang JP, Zhu YJ, Zhang HF. Bacillus wudalianchiensis sp. nov., isolated from grass soils of the Wudalianchi scenic area. Int J Syst Evol Microbiol 2017; 67:2897-2902. [DOI: 10.1099/ijsem.0.002042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Bo Liu
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Guo-Hong Liu
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Cetin Sengonca
- Institute of Crop Sciences and Resource Conservation (INRES), University of Bonn, Meckenheimer Allee 166A D-53115 Bonn, Germany
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße7B, 38124 Braunschweig, Germany
| | - Jie-Ping Wang
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Yu-Jing Zhu
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Hai-Feng Zhang
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
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Liu B, Liu GH, Sengonca C, Schumann P, Wang JP, Zhu YJ, Liu QY, Wang MK. Bacillus praedii sp. nov., isolated from purplish paddy soil. Int J Syst Evol Microbiol 2017; 67:2823-2828. [DOI: 10.1099/ijsem.0.002030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Bo Liu
- Agricultural Bio-resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Guo-Hong Liu
- Agricultural Bio-resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Cetin Sengonca
- Institute of Crop Sciences and Resource Conservation (INRES), University of Bonn, Meckenheimer Allee 166A D-53115 Bonn, Germany
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße7B, 38124, Braunschweig, Germany
| | - Jie-Ping Wang
- Agricultural Bio-resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Yu-Jing Zhu
- Agricultural Bio-resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Qin-Ying Liu
- Agricultural Bio-resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
- College of Life Science, Fujian Normal University, Fuzhou, Fujian 350117, PR China
| | - Ming-Kuang Wang
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan, ROC
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Yan S, Zhao W, Shi C, Tong Q, Zhai Z, Wang Y. Isolation and characterization of a high salt-tolerant and glyphosate-degrading strain of Agrobacterium tumefaciens BZ8. BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING 2017. [DOI: 10.1590/0104-6632.20170343s20150803] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Shoubao Yan
- Huainan Normal University, China; Liquor Making Biological Technology and Application of Key Laboratory of Sichuan Province, People's Republic of China
| | - Wei Zhao
- Huainan Normal University, China
| | - Cuie Shi
- Huainan Normal University, China
| | | | - Zhijun Zhai
- Jiangxi agricultural University, People's Republic of China
| | - Yun Wang
- Huainan Normal University, China
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Fiedoruk K, Drewnowska JM, Daniluk T, Leszczynska K, Iwaniuk P, Swiecicka I. Ribosomal background of the Bacillus cereus group thermotypes. Sci Rep 2017; 7:46430. [PMID: 28406161 PMCID: PMC5390287 DOI: 10.1038/srep46430] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/08/2017] [Indexed: 11/09/2022] Open
Abstract
In this study we reconstructed the architecture of Bacillus cereus sensu lato population based on ribosomal proteins, and identified a link between the ribosomal proteins’ variants and thermal groups (thermotypes) of the bacilli. The in silico phyloproteomic analysis of 55 ribosomal proteins (34 large and 21 small subunit r-proteins) of 421 strains, representing 14 well-established or plausible B. cereus sensu lato species, revealed several ribosomal clusters (r-clusters), which in general were well correlated with the strains’ affiliation to phylogenetic/thermal groups I–VII. However, a conformity and possibly a thermal characteristic of certain phylogenetic groups, e.g. the group IV, were not supported by a distribution of the corresponding r-clusters, and consequently neither by the analysis of cold-shock proteins (CSPs) nor by a content of heat shock proteins (HSPs). Furthermore, a preference for isoleucine and serine over valine and alanine in r-proteins along with a lack of HSP16.4 were recognized in non-mesophilic thermotypes. In conclusion, we suggest that the observed divergence in ribosomal proteins may be connected with an adaptation of B. cereus sensu lato members to various thermal niches.
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Affiliation(s)
- Krzysztof Fiedoruk
- Department of Microbiology, Medical University of Bialystok, Bialystok, Poland
| | - Justyna M Drewnowska
- Department of Microbiology, Institute of Biology, University of Bialystok, Bialystok, Poland
| | - Tamara Daniluk
- Department of Microbiology, Medical University of Bialystok, Bialystok, Poland
| | | | - Piotr Iwaniuk
- Department of Microbiology, Institute of Biology, University of Bialystok, Bialystok, Poland
| | - Izabela Swiecicka
- Department of Microbiology, Institute of Biology, University of Bialystok, Bialystok, Poland.,Laboratory of Applied Microbiology, University of Bialystok, Bialystok, Poland
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Glenwright H, Pohl S, Navarro F, Miro E, Jiménez G, Blanch AR, Harwood CR. The Identification of Intrinsic Chloramphenicol and Tetracycline Resistance Genes in Members of the Bacillus cereus Group ( sensu lato). Front Microbiol 2017; 7:2122. [PMID: 28101085 PMCID: PMC5209696 DOI: 10.3389/fmicb.2016.02122] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/15/2016] [Indexed: 11/24/2022] Open
Abstract
Bacillus toyonensis strain BCT-7112T (NCIMB 14858T) has been widely used as an additive in animal nutrition for more than 30 years without reports of adverse toxigenic effects. However, this strain is resistant to chloramphenicol and tetracycline and it is generally considered inadvisable to introduce into the food chain resistance determinants capable of being transferred to other bacterial strains, thereby adding to the pool of such determinants in the gastro-enteric systems of livestock species. We therefore characterized the resistance phenotypes of this strain and its close relatives to determine whether they were of recent origin, and therefore likely to be transmissible. To this end we identified the genes responsible for chloramphenicol (catQ) and tetracycline (tetM) resistance and confirmed the presence of homologs in other members of the B. toyonensis taxonomic unit. Unexpectedly, closely related strains encoding these genes did not exhibit chloramphenicol and tetracycline resistance phenotypes. To understand the differences in the behaviors, we cloned and expressed the genes, together with their upstream regulatory regions, into Bacillus subtilis. The data showed that the genes encoded functional proteins, but were expressed inefficiently from their native promoters. B. toyonensis is a taxonomic unit member of the Bacillus cereus group (sensu lato). We therefore extended the analysis to determine the extent to which homologous chloramphenicol and tetracycline resistance genes were present in other species within this group. This analysis revealed that homologous genes were present in nearly all representative species within the B. cereus group (sensu lato). The absence of known transposition elements and the observations that they are found at the same genomic locations, indicates that these chloramphenicol and tetracycline resistance genes are of ancient origin and intrinsic to this taxonomic group, rather than recent acquisitions. In this context we discuss definitions of what are and are not intrinsic genes, an issue that is of fundamental importance to both Regulatory Authorities, and the animal feed and related industries.
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Affiliation(s)
- Helen Glenwright
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biology, Newcastle UniversityNewcastle upon Tyne, UK
| | - Susanne Pohl
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biology, Newcastle UniversityNewcastle upon Tyne, UK
| | - Ferran Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant PauBarcelona, Spain
| | - Elisenda Miro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant PauBarcelona, Spain
| | | | - Anicet R. Blanch
- Department of Microbiology, University of BarcelonaBarcelona, Spain
| | - Colin R. Harwood
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biology, Newcastle UniversityNewcastle upon Tyne, UK
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Miller RA, Beno SM, Kent DJ, Carroll LM, Martin NH, Boor KJ, Kovac J. Bacillus wiedmannii sp. nov., a psychrotolerant and cytotoxic Bacillus cereus group species isolated from dairy foods and dairy environments. Int J Syst Evol Microbiol 2016; 66:4744-4753. [PMID: 27520992 DOI: 10.1099/ijsem.0.001421] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A facultatively anaerobic, spore-forming Bacillus strain, FSL W8-0169T, collected from raw milk stored in a silo at a dairy powder processing plant in the north-eastern USA was initially identified as a Bacillus cereus group species based on a partial sequence of the rpoB gene and 16S rRNA gene sequence. Analysis of core genome single nucleotide polymorphisms clustered this strain separately from known B. cereus group species. Pairwise average nucleotide identity blast values obtained for FSL W8-0169T compared to the type strains of existing B. cereus group species were <95 % and predicted DNA-DNA hybridization values were <70 %, suggesting that this strain represents a novel B. cereus group species. We characterized 10 additional strains with the same or closely related rpoB allelic type, by whole genome sequencing and phenotypic analyses. Phenotypic characterization identified a higher content of iso-C16 : 0 fatty acid and the combined inability to ferment sucrose or to hydrolyse arginine as the key characteristics differentiating FSL W8-0169T from other B. cereus group species. FSL W8-0169T is psychrotolerant, produces haemolysin BL and non-haemolytic enterotoxin, and is cytotoxic in a HeLa cell model. The name Bacillus wiedmannii sp. nov. is proposed for the novel species represented by the type strain FSL W8-0169T (=DSM 102050T=LMG 29269T).
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Affiliation(s)
- Rachel A Miller
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Sarah M Beno
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - David J Kent
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Laura M Carroll
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Nicole H Martin
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Kathryn J Boor
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Jasna Kovac
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
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Liu B, Liu GH, Zhu YJ, Wang JP, Che JM, Chen QQ, Chen Z. Bacillus loiseleuriae sp. nov., isolated from rhizosphere soil from a loiseleuria plant. Int J Syst Evol Microbiol 2016; 66:2678-2683. [DOI: 10.1099/ijsem.0.001107] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Bo Liu
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Guo-Hong Liu
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Yu-Jing Zhu
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Jie-Ping Wang
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Jian-Mei Che
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Qian-Qian Chen
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Zheng Chen
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
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42
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Liu Y, Lai Q, Göker M, Meier-Kolthoff JP, Wang M, Sun Y, Wang L, Shao Z. Genomic insights into the taxonomic status of the Bacillus cereus group. Sci Rep 2015; 5:14082. [PMID: 26373441 PMCID: PMC4571650 DOI: 10.1038/srep14082] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 08/17/2015] [Indexed: 02/01/2023] Open
Abstract
The identification and phylogenetic relationships of bacteria within the Bacillus cereus group are controversial. This study aimed at determining the taxonomic affiliations of these strains using the whole-genome sequence-based Genome BLAST Distance Phylogeny (GBDP) approach. The GBDP analysis clearly separated 224 strains into 30 clusters, representing eleven known, partially merged species and accordingly 19–20 putative novel species. Additionally, 16S rRNA gene analysis, a novel variant of multi-locus sequence analysis (nMLSA) and screening of virulence genes were performed. The 16S rRNA gene sequence was not sufficient to differentiate the bacteria within this group due to its high conservation. The nMLSA results were consistent with GBDP. Moreover, a fast typing method was proposed using the pycA gene, and where necessary, the ccpA gene. The pXO plasmids and cry genes were widely distributed, suggesting little correlation with the phylogenetic positions of the host bacteria. This might explain why classifications based on virulence characteristics proved unsatisfactory in the past. In summary, this is the first large-scale and systematic study of the taxonomic status of the bacteria within the B. cereus group using whole-genome sequences, and is likely to contribute to further insights into their pathogenicity, phylogeny and adaptation to diverse environments.
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Affiliation(s)
- Yang Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Centre; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Centre; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
| | - Markus Göker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraβe 7B, 38124, Braunschweig, Germany
| | - Jan P Meier-Kolthoff
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraβe 7B, 38124, Braunschweig, Germany
| | - Meng Wang
- TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China
| | - Yamin Sun
- TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China
| | - Lei Wang
- TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Centre; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
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