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Frentzel H, Kraemer M, Kelner-Burgos Y, Uelze L, Bodi D. Cereulide production capacities and genetic properties of 31 emetic Bacillus cereus group strains. Int J Food Microbiol 2024; 417:110694. [PMID: 38614024 DOI: 10.1016/j.ijfoodmicro.2024.110694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/15/2024]
Abstract
The highly potent toxin cereulide is a frequent cause of foodborne intoxications. This extremely resistant toxin is produced by Bacillus cereus group strains carrying the plasmid encoded cesHPTABCD gene cluster. It is known that the capacities to produce cereulide vary greatly between different strains but the genetic background of these variations is not clear. In this study, cereulide production capacities were associated with genetic characteristics. For this, cereulide levels in cultures of 31 strains were determined after incubation in tryptic soy broth for 24 h at 24 °C, 30 °C and 37 °C. Whole genome sequencing based data were used for an in-depth characterization of gene sequences related to cereulide production. The taxonomy, population structure and phylogenetic relationships of the strains were evaluated based on average nucleotide identity, multi-locus sequence typing (MLST), core genome MLST and single nucleotide polymorphism analyses. Despite a limited strain number, the approach of a genome wide association study (GWAS) was tested to link genetic variation with cereulide quantities. Our study confirms strain-dependent differences in cereulide production. For most strains, these differences were not explainable by sequence variations in the cesHPTABCD gene cluster or the regulatory genes abrB, spo0A, codY and pagRBc. Likewise, the population structure and phylogeny of the tested strains did not comprehensively reflect the cereulide production capacities. GWAS yielded first hints for associated proteins, while their possible effect on cereulide synthesis remains to be further investigated.
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Affiliation(s)
- Hendrik Frentzel
- German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany.
| | - Marco Kraemer
- German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Ylanna Kelner-Burgos
- German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Laura Uelze
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Sequencing and Genotyping Service Unit, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Dorina Bodi
- German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
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Zhou Q, Li G, Cui Y, Xiang J, Zhu S, Li S, Huang J, Wang Y, Liu Y, Zhou L. Genomic characterization of Bacillus cereus isolated from food poisoning cases revealed the mechanism of toxin production. Front Microbiol 2024; 14:1238799. [PMID: 38282728 PMCID: PMC10822677 DOI: 10.3389/fmicb.2023.1238799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/12/2023] [Indexed: 01/30/2024] Open
Abstract
Introduction Bacillus cereus is a ubiquitous opportunistic human pathogen that causes food intoxications worldwide. However, the genomic characteristics and pathogenic mechanisms of B. cereus are still unclear. Methods Here, we isolated and purified nine strains of B. cereus (LY01-LY09) that caused vomiting, diarrhea and other symptoms from four foodborne outbreaks happened in Guizhou Province in southwest China from June to September 2021. After colony observation, Gram staining, microscopic examination and biochemical test, they were identified as B. cereus. The genomic characteristics, phylogenetic relationships and virulence factors of the isolated strains were analyzed at the genome level. Genome sequencing, comparative genomic analysis, secondary metabolite analysis and quantitative PCR were utilized to give a thorough exploration of the strains. Results We obtained the genome maps of LY01-LY09 and found that LY01-LY09 had a complex interspecific relationship with B. anthracis and B. thuringiensis. We also observed a contraction of gene families in LY01-LY09, and the contracted families were mainly associated with prophage, which contributed to the species diversity of B. cereus. The Hsp20 gene family underwent a rapid evolution in LY01-LY09, which facilitated the adaptation of the strains to adverse environmental conditions. Moreover, the LY01-LY09 strains exhibited a higher copy number in the non-ribosomal polypeptide synthetase (NRPS) genes and carried the complete cereulide synthetase (ces) gene cluster sequences. Considering that the NRPS system is a classical regulatory mechanism for emetic toxin synthesis, we hypothesized that LY01-LY09 could synthesize emetic toxins through the regulation of ces gene clusters by the NRPS system. Discussion These findings are important for further investigation into the evolutionary relationship between B. cereus and their related species, as well as the underlying mechanisms governing the synthesis and secretion of bacterial toxins.
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Affiliation(s)
- Qian Zhou
- Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, Guizhou, China
| | - Guanqiao Li
- College of Bioinformatics, Chongqing University of Post and Telecommunications, Chongqing, China
| | - Yinshan Cui
- Yunnan Pulis Biotechnology Co., Ltd., Kunming, Yunnan, China
| | - Jingshu Xiang
- Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, Guizhou, China
| | - Shu Zhu
- Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, Guizhou, China
| | - Shijun Li
- Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, Guizhou, China
| | - Jingyu Huang
- Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, Guizhou, China
| | - Yafang Wang
- Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, Guizhou, China
| | - Ying Liu
- Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, Guizhou, China
| | - Li Zhou
- Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, Guizhou, China
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Abdelli M, Falaise C, Morineaux-Hilaire V, Cumont A, Taysse L, Raynaud F, Ramisse V. Get to Know Your Neighbors: Characterization of Close Bacillus anthracis Isolates and Toxin Profile Diversity in the Bacillus cereus Group. Microorganisms 2023; 11:2721. [PMID: 38004733 PMCID: PMC10673079 DOI: 10.3390/microorganisms11112721] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Unexpected atypical isolates of Bacillus cereus s.l. occasionally challenge conventional microbiology and even the most advanced techniques for anthrax detection. For anticipating and gaining trust, 65 isolates of Bacillus cereus s.l. of diverse origin were sequenced and characterized. The BTyper3 tool was used for assignation to genomospecies B. mosaicus (34), B. cereus s.s (29) and B. toyonensis (2), as well as virulence factors and toxin profiling. None of them carried any capsule or anthrax-toxin genes. All harbored the non-hemolytic toxin nheABC and sphygomyelinase spH genes, whereas 41 (63%), 30 (46%), 11 (17%) and 6 (9%) isolates harbored cytK-2, hblABCD, cesABCD and at least one insecticidal toxin gene, respectively. Matrix-assisted laser desorption ionization-time of flight mass spectrometry confirmed the production of cereulide (ces genes). Phylogeny inferred from single-nucleotide polymorphisms positioned isolates relative to the B. anthracis lineage. One isolate (BC38B) was of particular interest as it appeared to be the closest B. anthracis neighbor described so far. It harbored a large plasmid similar to other previously described B. cereus s.l. megaplasmids and at a lower extent to pXO1. Whereas bacterial collection is enriched, these high-quality public genetic data offer additional knowledge for better risk assessment using future NGS-based technologies of detection.
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Affiliation(s)
- Mehdi Abdelli
- DGA CBRN Defence Center, Biology Division, French Ministry of the Armed Forces, 91710 Vert-le-Petit, France; (M.A.); (V.M.-H.); (A.C.); (L.T.); (F.R.)
- Institute for Integrative Biology of the Cell (I2BC), CNRS, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Charlotte Falaise
- DGA CBRN Defence Center, Biology Division, French Ministry of the Armed Forces, 91710 Vert-le-Petit, France; (M.A.); (V.M.-H.); (A.C.); (L.T.); (F.R.)
| | - Valérie Morineaux-Hilaire
- DGA CBRN Defence Center, Biology Division, French Ministry of the Armed Forces, 91710 Vert-le-Petit, France; (M.A.); (V.M.-H.); (A.C.); (L.T.); (F.R.)
| | - Amélie Cumont
- DGA CBRN Defence Center, Biology Division, French Ministry of the Armed Forces, 91710 Vert-le-Petit, France; (M.A.); (V.M.-H.); (A.C.); (L.T.); (F.R.)
| | - Laurent Taysse
- DGA CBRN Defence Center, Biology Division, French Ministry of the Armed Forces, 91710 Vert-le-Petit, France; (M.A.); (V.M.-H.); (A.C.); (L.T.); (F.R.)
| | - Françoise Raynaud
- DGA CBRN Defence Center, Biology Division, French Ministry of the Armed Forces, 91710 Vert-le-Petit, France; (M.A.); (V.M.-H.); (A.C.); (L.T.); (F.R.)
| | - Vincent Ramisse
- DGA CBRN Defence Center, Biology Division, French Ministry of the Armed Forces, 91710 Vert-le-Petit, France; (M.A.); (V.M.-H.); (A.C.); (L.T.); (F.R.)
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4
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Sun S, Xu Z, Hu H, Zheng M, Zhang L, Xie W, Sun L, Liu P, Li T, Zhang L, Chen M, Zhu X, Liu M, Yang Y, Zhou J. The Bacillus cereus toxin alveolysin disrupts the intestinal epithelial barrier by inducing microtubule disorganization through CFAP100. Sci Signal 2023; 16:eade8111. [PMID: 37192300 DOI: 10.1126/scisignal.ade8111] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 04/18/2023] [Indexed: 05/18/2023]
Abstract
Bacillus cereus is a Gram-positive bacterium that mainly causes self-limiting emetic or diarrheal illness but can also cause skin infections and bacteremia. Symptoms of B. cereus ingestion depend on the production of various toxins that target the gastric and intestinal epithelia. From a screen of bacterial isolates from human stool samples that compromised intestinal barrier function in mice, we identified a strain of B. cereus that disrupted tight and adherens junctions in the intestinal epithelium. This activity was mediated by the pore-forming exotoxin alveolysin, which increased the production of the membrane-anchored protein CD59 and of cilia- and flagella-associated protein 100 (CFAP100) in intestinal epithelial cells. In vitro, CFAP100 interacted with microtubules and promoted microtubule polymerization. CFAP100 overexpression stabilized microtubules in intestinal epithelial cells, leading to disorganization of the microtubule network and perturbation of tight and adherens junctions. The disruption of cell junctions by alveolysin depended on the increase in CFAP100, which in turn depended on CD59 and the activation of PI3K-AKT signaling. These findings demonstrate that, in addition to forming membrane pores, B. cereus alveolysin can permeabilize the intestinal epithelium by disrupting epithelial cell junctions in a manner that is consistent with intestinal symptoms and may allow the bacteria to escape the intestine and cause systemic infections. Our results suggest the potential value of targeting alveolysin or CFAP100 to prevent B. cereus-associated intestinal diseases and systemic infections.
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Affiliation(s)
- Shuang Sun
- Center for Cell Structure and Function, Haihe Laboratory of Cell Ecosystem, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Zhaoyang Xu
- Center for Cell Structure and Function, Haihe Laboratory of Cell Ecosystem, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Haijie Hu
- Center for Cell Structure and Function, Haihe Laboratory of Cell Ecosystem, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Manxi Zheng
- Center for Cell Structure and Function, Haihe Laboratory of Cell Ecosystem, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Liang Zhang
- Center for Cell Structure and Function, Haihe Laboratory of Cell Ecosystem, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Wei Xie
- Center for Cell Structure and Function, Haihe Laboratory of Cell Ecosystem, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Lei Sun
- Center for Cell Structure and Function, Haihe Laboratory of Cell Ecosystem, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Peiwei Liu
- Center for Cell Structure and Function, Haihe Laboratory of Cell Ecosystem, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Tianliang Li
- Center for Cell Structure and Function, Haihe Laboratory of Cell Ecosystem, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Liangran Zhang
- Center for Cell Structure and Function, Haihe Laboratory of Cell Ecosystem, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Min Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xueliang Zhu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Min Liu
- Center for Cell Structure and Function, Haihe Laboratory of Cell Ecosystem, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Yunfan Yang
- Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Jun Zhou
- Center for Cell Structure and Function, Haihe Laboratory of Cell Ecosystem, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, Jinan 250014, China
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
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5
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Carroll LM, Matle I, Kovac J, Cheng RA, Wiedmann M. Laboratory Misidentifications Resulting from Taxonomic Changes to Bacillus cereus Group Species, 2018-2022. Emerg Infect Dis 2022; 28:1877-1881. [PMID: 35997597 PMCID: PMC9423903 DOI: 10.3201/eid2809.220293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Whole-genome sequencing (WGS) is being applied increasingly to Bacillus cereus group species; however, misinterpretation of WGS results may have severe consequences. We report 3 cases, 1 of which was an outbreak, in which misinterpretation of B. cereus group WGS results hindered communication within public health and industrial laboratories.
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6
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Takahashi N, Nagai S, Tomimatsu Y, Saito A, Kaneta N, Tsujimoto Y, Tamura H. Simultaneous Discrimination of Cereulide-Producing Bacillus cereus and Psychrotolerant B. cereus Group by Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry. J Food Prot 2022; 85:1192-1202. [PMID: 35687734 DOI: 10.4315/jfp-21-450] [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: 12/17/2021] [Accepted: 06/01/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT Cereulide-producing Bacillus cereus, which causes foodborne illnesses with vomiting, and psychrotolerant B. cereus group strains such as Bacillus mycoides, which can grow at ≥7°C and cause spoilage of refrigerated foods, are significant concerns for the food industry. Rapid and simple methods to discriminate the cereulide-producing B. cereus and psychrotolerant B. cereus group strains from other B. cereus group strains are needed. We developed a novel, rapid, and simple method with matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) analysis for simultaneous discrimination of these two groups from other B. cereus group strains. A potassium adduct of cereulide was used to detect cereulide-producing B. cereus, and three ribosomal subunit proteins (L30, S16, and S20) were used to detect psychrotolerant B. cereus group. A total of 51 B. cereus group strains were analyzed by MALDI-TOF MS. The biomarkers allowed successful discrimination of 16 cereulide-producing B. cereus and 15 psychrotolerant B. cereus group strains from other B. cereus group strains. The results showed that this MALDI-TOF MS analysis allows simultaneous discrimination of cereulide-producing B. cereus and psychrotolerant B. cereus group strains from other B. cereus group strains. This efficient method has the potential to be a valuable tool for ensuring food safety. HIGHLIGHTS
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Affiliation(s)
- Naomi Takahashi
- Food Quality and Safety Research Laboratories, Meiji Co., Ltd., 1-29-1 Nanakuni, Hachioji, Tokyo, 192-0919, Japan
| | - Satomi Nagai
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi 468-8502, Japan
| | - Yumiko Tomimatsu
- Food Quality and Safety Research Laboratories, Meiji Co., Ltd., 1-29-1 Nanakuni, Hachioji, Tokyo, 192-0919, Japan
| | - Ayumi Saito
- Food Quality and Safety Research Laboratories, Meiji Co., Ltd., 1-29-1 Nanakuni, Hachioji, Tokyo, 192-0919, Japan
| | - Naoko Kaneta
- Food Quality and Safety Research Laboratories, Meiji Co., Ltd., 1-29-1 Nanakuni, Hachioji, Tokyo, 192-0919, Japan
| | - Yoshinori Tsujimoto
- Food Quality and Safety Research Laboratories, Meiji Co., Ltd., 1-29-1 Nanakuni, Hachioji, Tokyo, 192-0919, Japan
| | - Hiroto Tamura
- Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi 468-8502, Japan
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7
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Biggel M, Jessberger N, Kovac J, Johler S. Recent paradigm shifts in the perception of the role of Bacillus thuringiensis in foodborne disease. Food Microbiol 2022; 105:104025. [DOI: 10.1016/j.fm.2022.104025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 12/16/2022]
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8
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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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9
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Xiong Q, Liu J, Xie G, Mu D, Feng X, Xu H. Blocker-tailed PCR coupled with rolling circle amplification for fluorescent detection of emetic Bacillus cereus in milk. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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Le Marc Y, Postollec F, Huchet V, Ellouze M. Modelling the thermal inactivation of spores from different phylogenetic groups of Bacillus cereus. Int J Food Microbiol 2022; 368:109607. [DOI: 10.1016/j.ijfoodmicro.2022.109607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 11/29/2021] [Accepted: 02/27/2022] [Indexed: 11/29/2022]
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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: 39] [Impact Index Per Article: 13.0] [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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12
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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: 19] [Impact Index Per Article: 4.8] [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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