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Lin Y, Cha X, Brennan C, Cao J, Shang Y. Contamination of Plant Foods with Bacillus cereus in a Province and Analysis of Its Traceability. Microorganisms 2023; 11:2763. [PMID: 38004774 PMCID: PMC10672870 DOI: 10.3390/microorganisms11112763] [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: 10/26/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Bacillus cereus is an important zoonotic foodborne conditional pathogen. It is found in vegetables, dairy products, rice, and other foods, thereby greatly endangering human health. Investigations on B. cereus contamination in China primarily focus on raw milk, dairy products, meat, and others, and limited research has been conducted on plant-based foodstuffs. The rapid development of sequencing technology and the application of bioinformatics-related techniques means that analysis based on whole-genome sequencing has become an important tool for the molecular-epidemiology investigation of B. cereus. In this study, we investigated the contamination of B. cereus in six types of commercially available plant foods from eight regions of a province. The molecular epidemiology of the isolated B. cereus was analyzed by whole-genome sequencing. We aimed to provide fundamental data for the surveillance and epidemiology analysis of B. cereus in food products in China. The rapid traceability system of B. cereus established in this study can provide a basis for rapid molecular epidemiology analysis of B. cereus, as well as for the prevention and surveillance of B. cereus. Moreover, it can also be expanded to monitoring and rapid tracing of more foodborne pathogens.
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Affiliation(s)
- Yingting Lin
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (Y.L.); (X.C.); (C.B.)
| | - Xiaoyan Cha
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (Y.L.); (X.C.); (C.B.)
| | - Charles Brennan
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (Y.L.); (X.C.); (C.B.)
- School of Science, Royal Melbourne Institute of Technology University, Melbourne 3000, Australia
| | - Jianxin Cao
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (Y.L.); (X.C.); (C.B.)
| | - Ying Shang
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (Y.L.); (X.C.); (C.B.)
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Cerar Kišek T, Pogačnik N, Godič Torkar K. Genetic diversity and the presence of circular plasmids in Bacillus cereus isolates of clinical and environmental origin. Arch Microbiol 2021; 203:3209-3217. [PMID: 33830284 DOI: 10.1007/s00203-021-02302-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
The diversity of 61 Bacillus cereus strains isolated from different clinical specimens, food including raw milk and milk products, and water was evaluated. PFGE analysis could discriminate 61 distinct pulsotypes with similarity levels from 25 to 82%, which were divided into 13 clonal complexes. The similarity between clonal complexes was at least 40%. Clinical strains were divided into 10 clonal complexes, while the strains, isolated from milk, food and water were included in 9, 6 and 6 clonal complexes, respectively. Three clonal complexes were dominated by clinical isolates, while they were absent in two complexes. Bacterial isolates from food, being a probable source of alimentary toxoinfection, showed low similarity to isolates from stool specimens. The isolates from both sources were classified together in only 4 out of 13 clonal complexes. The large circular and linear plasmids with the sizes between 50 and 200 kb were detected in 24 (39.3%) and 14 (23%) B. cereus strains, respectively. Thirteen (21.3%) strains contained only one plasmid, two plasmids were found in 6 (9.8%) of strains, and three or more plasmids were obtained in 5 (8.2%) of tested strains. The plasmids were confirmed in 30.8% and 40% of isolates from clinical specimens and food and milk samples, respectively. No clear correlation between the PFGE profiles, the source as well as plasmid content among all tested strains was observed.
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Affiliation(s)
- Tjaša Cerar Kišek
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Nežka Pogačnik
- Faculty of Health Sciences, University of Ljubljana, Zdravstvena pot 5, 1000, Ljubljana, Slovenia
| | - Karmen Godič Torkar
- Faculty of Health Sciences, University of Ljubljana, Zdravstvena pot 5, 1000, Ljubljana, Slovenia.
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Chang Y, Xie Q, Yang J, Ma L, Feng H. The prevalence and characterization of Bacillus cereus isolated from raw and pasteurized buffalo milk in southwestern China. J Dairy Sci 2021; 104:3980-3989. [DOI: 10.3168/jds.2020-19432] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 11/16/2020] [Indexed: 12/12/2022]
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Prevalence, toxigenic profiles, multidrug resistance, and biofilm formation of Bacillus cereus isolated from ready-to eat cooked rice in Penang, Malaysia. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107553] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Fei P, Xie Q, Jiang Y, Feng H, Chang Y, Kang H, Xing M, Chen J. Genotyping, Antimicrobial Susceptibility and Biofilm Formation of Bacillus cereus Isolated from Powdered Food Products in China. Foodborne Pathog Dis 2021; 18:8-15. [DOI: 10.1089/fpd.2020.2802] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Peng Fei
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Qinggang Xie
- Heilongjiang Feihe Dairy Co., Ltd., Beijing, China
| | - Yan Jiang
- Department of Market Supervision and Management, MuLing Food Inspection Testing Center, Mudanjiang, China
| | - Hongxia Feng
- Food and Pharmaceutical Engineering Institute, Guiyang University, Guiyang, China
| | - Yunhe Chang
- Food and Pharmaceutical Engineering Institute, Guiyang University, Guiyang, China
| | - Huaibin Kang
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Min Xing
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Junliang Chen
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
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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: 59] [Impact Index Per Article: 14.8] [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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Tran SL, Cormontagne D, Vidic J, André-Leroux G, Ramarao N. Structural Modeling of Cell Wall Peptidase CwpFM (EntFM) Reveals Distinct Intrinsically Disordered Extensions Specific to Pathogenic Bacillus cereus Strains. Toxins (Basel) 2020; 12:toxins12090593. [PMID: 32937845 PMCID: PMC7551459 DOI: 10.3390/toxins12090593] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/04/2020] [Accepted: 09/09/2020] [Indexed: 12/21/2022] Open
Abstract
The emergence of B. cereus as an opportunistic food-borne pathogen has intensified the need to distinguish strains of public health concern. The heterogeneity of the diseases associated with B. cereus infections emphasizes the versatility of these bacteria strains to colonize their host. Nevertheless, the molecular basis of these differences remains unclear. Several toxins are involved in virulence, particularly in gastrointestinal disorders, but there are currently no biological markers able to differentiate pathogenic from harmless strains. We have previously shown that CwpFM is a cell wall peptidase involved in B. cereus virulence. Here, we report a sequence/structure/function characterization of 39 CwpFM sequences, chosen from a collection of B. cereus with diverse virulence phenotypes, from harmless to highly pathogenic strains. CwpFM is homology-modeled in silico as an exported papain-like endopeptidase, with an N-terminal end composed of three successive bacterial Src Homology 3 domains (SH3b1–3) likely to control protein–protein interactions in signaling pathways, and a C-terminal end that contains a catalytic NLPC_P60 domain primed to form a competent active site. We confirmed in vitro that CwpFM is an endopeptidase with a moderate peptidoglycan hydrolase activity. Remarkably, CwpFMs from pathogenic strains harbor a specific stretch of twenty residues intrinsically disordered, inserted between the SH3b3 and the catalytic NLPC_P60 domain. This strongly suggests this linker as a marker of differentiation between B. cereus strains. We believe that our findings improve our understanding of the pathogenicity of B. cereus while advancing both clinical diagnosis and food safety.
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Affiliation(s)
- Seav-Ly Tran
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (S.-L.T.); (D.C.); (J.V.)
| | - Delphine Cormontagne
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (S.-L.T.); (D.C.); (J.V.)
| | - Jasmina Vidic
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (S.-L.T.); (D.C.); (J.V.)
| | - Gwenaëlle André-Leroux
- MaIAGE, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
- Correspondence: (G.A.-L.); (N.R.)
| | - Nalini Ramarao
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (S.-L.T.); (D.C.); (J.V.)
- Correspondence: (G.A.-L.); (N.R.)
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Cereulide Synthetase Acquisition and Loss Events within the Evolutionary History of Group III Bacillus cereus Sensu Lato Facilitate the Transition between Emetic and Diarrheal Foodborne Pathogens. mBio 2020; 11:mBio.01263-20. [PMID: 32843545 PMCID: PMC7448271 DOI: 10.1128/mbio.01263-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cereulide-producing members of Bacillus cereus sensu lato group III (also known as emetic B. cereus) possess cereulide synthetase, a plasmid-encoded, nonribosomal peptide synthetase encoded by the ces gene cluster. Despite the documented risks that cereulide-producing strains pose to public health, the level of genomic diversity encompassed by emetic B. cereus has never been evaluated at a whole-genome scale. Here, we employ a phylogenomic approach to characterize group III B. cereus sensu lato genomes which possess ces (ces positive) alongside their closely related, ces-negative counterparts (i) to assess the genomic diversity encompassed by emetic B. cereus and (ii) to identify potential ces loss and/or gain events within the evolutionary history of the high-risk and medically relevant sequence type (ST) 26 lineage often associated with emetic foodborne illness. Using all publicly available ces-positive group III B. cereus sensu lato genomes and the ces-negative genomes interspersed among them (n = 159), we show that emetic B. cereus is not clonal; rather, multiple lineages within group III harbor cereulide-producing strains, all of which share an ancestor incapable of producing cereulide (posterior probability = 0.86 to 0.89). Members of ST 26 share an ancestor that existed circa 1748 (95% highest posterior density [HPD] interval = 1246.89 to 1915.64) and first acquired the ability to produce cereulide before 1876 (95% HPD = 1641.43 to 1946.70). Within ST 26 alone, two subsequent ces gain events were observed, as well as three ces loss events, including among isolates responsible for B. cereus sensu lato toxicoinfection (i.e., "diarrheal" illness).IMPORTANCE B. cereus is responsible for thousands of cases of foodborne disease each year worldwide, causing two distinct forms of illness: (i) intoxication via cereulide (i.e., emetic syndrome) or (ii) toxicoinfection via multiple enterotoxins (i.e., diarrheal syndrome). Here, we show that emetic B. cereus is not a clonal, homogenous unit that resulted from a single cereulide synthetase gain event followed by subsequent proliferation; rather, cereulide synthetase acquisition and loss is a dynamic, ongoing process that occurs across lineages, allowing some group III B. cereus sensu lato populations to oscillate between diarrheal and emetic foodborne pathogens over the course of their evolutionary histories. We also highlight the care that must be taken when selecting a reference genome for whole-genome sequencing-based investigation of emetic B. cereus sensu lato outbreaks, since some reference genome selections can lead to a confounding loss of resolution and potentially hinder epidemiological investigations.
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Zhao S, Chen J, Fei P, Feng H, Wang Y, Ali MA, Li S, Jing H, Yang W. Prevalence, molecular characterization, and antibiotic susceptibility of Bacillus cereus isolated from dairy products in China. J Dairy Sci 2020; 103:3994-4001. [DOI: 10.3168/jds.2019-17541] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/17/2019] [Indexed: 12/15/2022]
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Sánchez Chica J, Correa MM, Aceves-Diez AE, Rasschaert G, Heyndrickx M, Castañeda-Sandoval LM. Genomic and Toxigenic Heterogeneity of Bacillus cereus sensu lato Isolated from Ready-to-Eat Foods and Powdered Milk in Day Care Centers in Colombia. Foodborne Pathog Dis 2019; 17:340-347. [PMID: 31738585 DOI: 10.1089/fpd.2019.2709] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bacillus cereus sensu lato (s.l.) is a group of bacteria commonly found in diverse environments, including foods, with potential to cause emesis and diarrhea. In Colombia, it is one of the main foodborne pathogens. The aim of this study was to determine the genomic and toxigenic heterogeneity of B. cereus s.l. isolated from ready-to-eat foods and powdered milk collected in day care centers of Medellin, Colombia. Of 112 B. cereus s.l. isolates obtained, 94% were β-hemolytic. Toxigenic heterogeneity was established by the presence of nheABC, hblCDAB, cytK2, entFM, and cesB toxigenic genes. The nheABC operon and entFM gene were most frequently detected in the isolates, whereas the cesB gene was not found. According to the toxin genes content, nine toxigenic profiles were identified. A 44% of isolates had profiles with all genes for nonhemolytic enterotoxin, hemolysin BL, and enterotoxin FM production (profiles II and IV). Pulsed-field gel electrophoresis analysis indicated a high genomic heterogeneity among the B. cereus s.l., with 68 isolates grouping into 16 clusters and 33 placed separately in the dendrogram. This study provides useful information on the safety of ready-to-eat foods and powdered milk in day care centers where children, a susceptible population, are exposed and it should incentive for more studies to understand the distribution of different toxin-encoding genes among B. cereus s.l. isolates, enabling detailed risk assessment.
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Affiliation(s)
- Jennifer Sánchez Chica
- Grupo de Microbiología Molecular, Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia
| | - Margarita M Correa
- Grupo de Microbiología Molecular, Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia
| | - Angel E Aceves-Diez
- Laboratorios Minkab, Departamento de Investigación y Desarrollo, Guadalajara, Jalisco, Mexico
| | - Geertrui Rasschaert
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Melle, Belgium
| | - Marc Heyndrickx
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Melle, Belgium.,Department of Pathology, Bacteriology and Avian Diseases, Ghent University, Merelbeke, Belgium
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Gdoura-Ben Amor M, Jan S, Baron F, Grosset N, Culot A, Gdoura R, Gautier M, Techer C. Toxigenic potential and antimicrobial susceptibility of Bacillus cereus group bacteria isolated from Tunisian foodstuffs. BMC Microbiol 2019; 19:196. [PMID: 31445510 PMCID: PMC6708205 DOI: 10.1186/s12866-019-1571-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/14/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Despite the importance of the B. cereus group as major foodborne pathogens that may cause diarrheal and/or emetic syndrome(s), no study in Tunisia has been conducted in order to characterize the pathogenic potential of the B. cereus group. The aim of this study was to assess the sanitary potential risks of 174 B. cereus group strains isolated from different foodstuffs by detecting and profiling virulence genes (hblA, hblB, hblC, hblD, nheA, nheB, nheC, cytK, bceT and ces), testing the isolates cytotoxic activity on Caco-2 cells and antimicrobial susceptibility towards 11 antibiotics. RESULTS The entertoxin genes detected among B. cereus isolates were, in decreasing order, nheA (98.9%), nheC (97.7%) and nheB (86.8%) versus hblC (54.6%), hblD (54.6%), hblA (29.9%) and hblB (14.9%), respectively encoding for Non-hemolytic enterotoxin (NHE) and Hemolysin BL (HBL). The isolates are multi-toxigenic, harbouring at least one gene of each NHE and HBL complexes associated or not to bceT, cytK-2 and ces genes. Based on the incidence of virulence genes, the strains were separated into 12 toxigenic groups. Isolates positive for cytK (37,9%) harbored the cytK-2 variant. The detection rates of bceT and ces genes were 50.6 and 4%, respectively. When bacteria were incubated in BHI-YE at 30 °C for 18 h and for 5 d, 70.7 and 35% of the strains were shown to be cytotoxic to Caco-2 cells, respectively. The cytotoxicity of B. cereus strains depended on the food source of isolation. The presence of virulence factors is not always consistent with cytotoxicity. However, different combinations of enterotoxin genetic determinants are significantly associated to the cytotoxic potential of the bacteria. All strains were fully sensitive to rifampicin, chloramphenicol, ciprofloxacin, and gentamycin. The majority of the isolates were susceptible to streptomycin, kanamycin, erythromycin, vancomycin and tetracycline but showed resistance to ampicillin and novobiocin. CONCLUSION Our results contribute data that are primary to facilitate risk assessments in order to prevent food poisoning due to B. cereus group.
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Affiliation(s)
- Maroua Gdoura-Ben Amor
- Laboratory Research of Toxicology-Microbiology Environmental and Health LR17ES06, Sciences Faculty of Sfax, University of Sfax, Sfax, Tunisia.
- Equipe Microbiologie, Agrocampus Ouest, INRA, UMR1253 Science et Technologie du Lait et de l'Œuf, Rennes, France.
| | - Sophie Jan
- Equipe Microbiologie, Agrocampus Ouest, INRA, UMR1253 Science et Technologie du Lait et de l'Œuf, Rennes, France
| | - Florence Baron
- Equipe Microbiologie, Agrocampus Ouest, INRA, UMR1253 Science et Technologie du Lait et de l'Œuf, Rennes, France
| | - Noël Grosset
- Equipe Microbiologie, Agrocampus Ouest, INRA, UMR1253 Science et Technologie du Lait et de l'Œuf, Rennes, France
| | - Antoine Culot
- Equipe Microbiologie, Agrocampus Ouest, INRA, UMR1253 Science et Technologie du Lait et de l'Œuf, Rennes, France
- Mixscience, Rue des Courtillons, ZAC Cissé Blossac, 35712, Bruz, France
| | - Radhouane Gdoura
- Laboratory Research of Toxicology-Microbiology Environmental and Health LR17ES06, Sciences Faculty of Sfax, University of Sfax, Sfax, Tunisia
| | - Michel Gautier
- Equipe Microbiologie, Agrocampus Ouest, INRA, UMR1253 Science et Technologie du Lait et de l'Œuf, Rennes, France
| | - Clarisse Techer
- Mixscience, Rue des Courtillons, ZAC Cissé Blossac, 35712, Bruz, France
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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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Rapid, High-Throughput Identification of Anthrax-Causing and Emetic Bacillus cereus Group Genome Assemblies via BTyper, a Computational Tool for Virulence-Based Classification of Bacillus cereus Group Isolates by Using Nucleotide Sequencing Data. Appl Environ Microbiol 2017. [PMID: 28625989 PMCID: PMC5561296 DOI: 10.1128/aem.01096-17] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The Bacillus cereus group comprises nine species, several of which are pathogenic. Differentiating between isolates that may cause disease and those that do not is a matter of public health and economic importance, but it can be particularly challenging due to the high genomic similarity within the group. To this end, we have developed BTyper, a computational tool that employs a combination of (i) virulence gene-based typing, (ii) multilocus sequence typing (MLST), (iii) panC clade typing, and (iv) rpoB allelic typing to rapidly classify B. cereus group isolates using nucleotide sequencing data. BTyper was applied to a set of 662 B. cereus group genome assemblies to (i) identify anthrax-associated genes in non-B. anthracis members of the B. cereus group, and (ii) identify assemblies from B. cereus group strains with emetic potential. With BTyper, the anthrax toxin genes cya, lef, and pagA were detected in 8 genomes classified by the NCBI as B. cereus that clustered into two distinct groups using k-medoids clustering, while either the B. anthracis poly-γ-d-glutamate capsule biosynthesis genes capABCDE or the hyaluronic acid capsule hasA gene was detected in an additional 16 assemblies classified as either B. cereus or Bacillus thuringiensis isolated from clinical, environmental, and food sources. The emetic toxin genes cesABCD were detected in 24 assemblies belonging to panC clades III and VI that had been isolated from food, clinical, and environmental settings. The command line version of BTyper is available at https://github.com/lmc297/BTyper. In addition, BMiner, a companion application for analyzing multiple BTyper output files in aggregate, can be found at https://github.com/lmc297/BMiner. IMPORTANCEBacillus cereus is a foodborne pathogen that is estimated to cause tens of thousands of illnesses each year in the United States alone. Even with molecular methods, it can be difficult to distinguish nonpathogenic B. cereus group isolates from their pathogenic counterparts, including the human pathogen Bacillus anthracis, which is responsible for anthrax, as well as the insect pathogen B. thuringiensis. By using the variety of typing schemes employed by BTyper, users can rapidly classify, characterize, and assess the virulence potential of any isolate using its nucleotide sequencing data.
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