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Kompes G, Duvnjak S, Reil I, Mihaljević Ž, Habrun B, Benić M, Cvetnić L, Špičić S, Bagarić A. Antimicrobial Resistance Profile, Whole-Genome Sequencing and Core Genome Multilocus Sequence Typing of B. anthracis Isolates in Croatia from 2001 to 2022. Antibiotics (Basel) 2024; 13:639. [PMID: 39061321 PMCID: PMC11274125 DOI: 10.3390/antibiotics13070639] [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: 06/17/2024] [Revised: 07/07/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Bacillus anthracis, the causative agent of anthrax disease, is a worldwide threat to livestock, wildlife and public health. It is also considered one of the most important pathogens of bioterrorism. Rapid and reliable diagnosis and administration of antimicrobials are essential for effective anthrax treatment. In this study, we determined the in vitro susceptibilities of 40 isolates of B. anthracis isolated in Croatia over the recent two decades to 18 antimicrobials. Whole-genome sequencing was performed, and bioinformatics tools were used to determine virulence factors and antimicrobial resistance genes. Core genome-based multilocus sequence typing was used for isolate comparison and phylogenetic analysis. All isolates were susceptible to all antimicrobials recommended for post-exposure prophylaxis or anthrax therapy. Susceptibility was found to all other tested antimicrobials that are an alternative for primary therapy. We found two beta-lactamase genes, but their expression is not sufficient to confer resistance. In all isolates used in this study, we found 21 virulence genes, 8 of which are responsible for toxin and capsule production. As far as phylogenetic analysis is concerned, the B. anthracis isolates from Croatia are categorised into two clades. The first is clade A, subclade Trans Eurasia, and the other is clade B, subclade B2.
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Affiliation(s)
- Gordan Kompes
- Laboratory for General Bacteriology and Mycology, Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (G.K.); (B.H.); (A.B.)
| | - Sanja Duvnjak
- Laboratory for Bacterial Zoonoses and Molecular Diagnostics of Bacterial Diseases, Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia;
| | - Irena Reil
- Laboratory for Bacterial Zoonoses and Molecular Diagnostics of Bacterial Diseases, Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia;
| | - Željko Mihaljević
- Laboratory for Pathology, Department for Pathology, Croatian Veterinary Institute, 10000 Zagreb, Croatia;
| | - Boris Habrun
- Laboratory for General Bacteriology and Mycology, Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (G.K.); (B.H.); (A.B.)
| | - Miroslav Benić
- Laboratory for Mastitis and Raw Milk Quality, Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (M.B.); (L.C.)
| | - Luka Cvetnić
- Laboratory for Mastitis and Raw Milk Quality, Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (M.B.); (L.C.)
| | - Silvio Špičić
- Laboratory for Bacterial Zoonoses and Molecular Diagnostics of Bacterial Diseases, Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia;
| | - Antonela Bagarić
- Laboratory for General Bacteriology and Mycology, Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (G.K.); (B.H.); (A.B.)
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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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3
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Etter D, Biggel M, Greutmann M, Cernela N, Johler S. New insights into Bacillus cytotoxicus sources, screening, toxicity, and persistence in food production facilities. Food Microbiol 2024; 117:104399. [PMID: 37919007 DOI: 10.1016/j.fm.2023.104399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 11/04/2023]
Abstract
Bacillus cytotoxicus is a thermotolerant member of the Bacillus cereus group. It has been linked to rare, but at times fatal cases of diarrheal disease and might be missed at routine diagnostic screening temperatures commonly used for the B. cereus group. The pathogen is mostly found on dehydrated foods containing potato starch or insects. How it enters the food chain or whether it persists in food producing environments is largely unknown. Increased consumption of insects and convenience foods in Europe and the lack of information on the persistence of B. cytotoxicus in food environments and its virulence demand for further characterization. In this study, we aimed to obtain a better understanding of i) the food sources of B. cytotoxicus, ii) screening temperatures needed for its isolation from food matrices, iii) cytotoxicity of the organism, and iv) its ecological niche and potential epidemiological links. To this end, 112 food samples were collected, with a focus on foods exhibiting low water activity. The samples were screened for B. cytotoxicus at 42 °C and at 50 °C. Presumptive isolates were characterized by cytK-1 toxin gene PCR for differentiation of B. cytotoxicus from other B. cereus group members. Vero cell cytotoxicity assays were performed, and selected isolates were sequenced. Our results show that screening at 42 °C might be insufficient for detecting B. cytotoxicus in foods that harbor other less thermophilic Bacillus species. When screening at 50 °C, B. cytotoxicus was detected in 23% of the food samples (n = 26 isolates). The highest prevalence was detected in mashed potato products (82%) and potato flakes (67%). In contrast, a wide range of products not containing any potato ingredients did not yield B. cytotoxicus isolates. All B. cytotoxicus isolates exhibited either low or no detectable cytotoxicity. WGS analysis revealed that a highly toxic isolate is closely related to the French outbreak strain NVH 391-98. In addition, we could show that two isolates sampled 5 years apart from the same production facility only differed by seven SNPs, making it likely that B. cytotoxicus is able to persist in production facilities over a long time. Interestingly, the reoccurring strain possessed an additional plasmid and did not show cytotoxic potential when re-isolated after 5 years.
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Affiliation(s)
- Danai Etter
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Michael Biggel
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Mariella Greutmann
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Nicole Cernela
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Sophia Johler
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland.
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Vater J, Tam LTT, Jähne J, Herfort S, Blumenscheit C, Schneider A, Luong PT, Thao LTP, Blom J, Klee SR, Schweder T, Lasch P, Borriss R. Plant-Associated Representatives of the Bacillus cereus Group Are a Rich Source of Antimicrobial Compounds. Microorganisms 2023; 11:2677. [PMID: 38004689 PMCID: PMC10672896 DOI: 10.3390/microorganisms11112677] [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: 10/08/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Seventeen bacterial strains able to suppress plant pathogens have been isolated from healthy Vietnamese crop plants and taxonomically assigned as members of the Bacillus cereus group. In order to prove their potential as biocontrol agents, we perform a comprehensive analysis that included the whole-genome sequencing of selected strains and the mining for genes and gene clusters involved in the synthesis of endo- and exotoxins and secondary metabolites, such as antimicrobial peptides (AMPs). Kurstakin, thumolycin, and other AMPs were detected and characterized by different mass spectrometric methods, such as MALDI-TOF-MS and LIFT-MALDI-TOF/TOF fragment analysis. Based on their whole-genome sequences, the plant-associated isolates were assigned to the following species and subspecies: B. cereus subsp. cereus (6), B. cereus subsp. bombysepticus (5), Bacillus tropicus (2), and Bacillus pacificus. These three isolates represent novel genomospecies. Genes encoding entomopathogenic crystal and vegetative proteins were detected in B. cereus subsp. bombysepticus TK1. The in vitro assays revealed that many plant-associated isolates enhanced plant growth and suppressed plant pathogens. Our findings indicate that the plant-associated representatives of the B. cereus group are a rich source of putative antimicrobial compounds with potential in sustainable agriculture. However, the presence of virulence genes might restrict their application as biologicals in agriculture.
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Affiliation(s)
- Joachim Vater
- Proteomics and Spectroscopy Unit (ZBS6), Center for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (J.V.); (J.J.); (S.H.); (C.B.); (A.S.); (P.L.)
| | - Le Thi Thanh Tam
- Division of Pathology and Phyto-Immunology, Plant Protection Research Institute (PPRI), Duc Thang, Bac Tu Liem, Hanoi, Vietnam; (L.T.T.T.); (P.T.L.); (L.T.P.T.)
| | - Jennifer Jähne
- Proteomics and Spectroscopy Unit (ZBS6), Center for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (J.V.); (J.J.); (S.H.); (C.B.); (A.S.); (P.L.)
| | - Stefanie Herfort
- Proteomics and Spectroscopy Unit (ZBS6), Center for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (J.V.); (J.J.); (S.H.); (C.B.); (A.S.); (P.L.)
| | - Christian Blumenscheit
- Proteomics and Spectroscopy Unit (ZBS6), Center for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (J.V.); (J.J.); (S.H.); (C.B.); (A.S.); (P.L.)
| | - Andy Schneider
- Proteomics and Spectroscopy Unit (ZBS6), Center for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (J.V.); (J.J.); (S.H.); (C.B.); (A.S.); (P.L.)
| | - Pham Thi Luong
- Division of Pathology and Phyto-Immunology, Plant Protection Research Institute (PPRI), Duc Thang, Bac Tu Liem, Hanoi, Vietnam; (L.T.T.T.); (P.T.L.); (L.T.P.T.)
| | - Le Thi Phuong Thao
- Division of Pathology and Phyto-Immunology, Plant Protection Research Institute (PPRI), Duc Thang, Bac Tu Liem, Hanoi, Vietnam; (L.T.T.T.); (P.T.L.); (L.T.P.T.)
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig Universität Giessen, 35392 Giessen, Germany;
| | - Silke R. Klee
- Highly Pathogenic Microorganisms Unit (ZBS2), Center for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany;
| | - Thomas Schweder
- Institute of Marine Biotechnology e.V. (IMaB), 17489 Greifswald, Germany;
- Pharmaceutical Biotechnology, University of Greifswald, 17489 Greifswald, Germany
| | - Peter Lasch
- Proteomics and Spectroscopy Unit (ZBS6), Center for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (J.V.); (J.J.); (S.H.); (C.B.); (A.S.); (P.L.)
| | - Rainer Borriss
- Institute of Marine Biotechnology e.V. (IMaB), 17489 Greifswald, Germany;
- Institute of Biology, Humboldt University Berlin, 10115 Berlin, Germany
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5
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Naudet J, d'Orbcastel ER, Bouvier T, Godreuil S, Dyall S, Bouvy S, Rieuvilleneuve F, Restrepo-Ortiz CX, Bettarel Y, Auguet JC. Identifying macroplastic pathobiomes and antibiotic resistance in a subtropical fish farm. MARINE POLLUTION BULLETIN 2023; 194:115267. [PMID: 37487429 DOI: 10.1016/j.marpolbul.2023.115267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/21/2023] [Accepted: 07/04/2023] [Indexed: 07/26/2023]
Abstract
Macroplastics are ubiquitous in aquaculture ecosystems. However, to date the potential role of plastics as a support for bacterial biofilm that can include potential human pathogenic bacteria (PHPB) and antibiotic-resistant bacteria (ARB) has been largely overlooked. In this study, we used a combination of metabarcoding and standard antibiotic susceptibility testing to study the pathobiome and resistome of macroplastics, fish guts and the environment in a marine aquaculture farm in Mauritius. Aquaculture macroplastics were found to be higher in PHPB, dominated by the Vibrionaceae family (0.34 % of the total community), compared with environmental samples. Moreover, isolates from aquaculture plastics showed higher significant multiple antibiotic resistance (MAR) compared to non-plastic samples of seawater, sediment and fish guts. These results suggest that plastics act as a reservoir and fomite of PHPB and ARB in aquaculture, potentially threatening the health of farmed fish and human consumers.
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Affiliation(s)
- Jeanne Naudet
- UMR MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France.
| | - Emmanuelle Roque d'Orbcastel
- UMR MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France; IOC, Indian Ocean Commission, Blue Tower, Rue de l'Institut, Ebène, Mauritius
| | - Thierry Bouvier
- UMR MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Sylvain Godreuil
- UMR MIVEGEC IRD-CNRS-Université de Montpellier, IRD, Montpellier, France
| | - Sabrina Dyall
- Molecular Life Sciences Pole of Research Excellence, Department of Biosciences and Ocean Studies, Faculty of Science, University of Mauritius, Réduit 80837, Mauritius
| | - Simon Bouvy
- Ferme Marine de Mahébourg Ltd. Royal Road, Pointe aux Feuilles, Mauritius
| | | | | | - Yvan Bettarel
- UMR MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
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6
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Wales A, Mackintosh A. JMM Profile: Bacillus anthracis. J Med Microbiol 2023; 72. [PMID: 37602808 DOI: 10.1099/jmm.0.001747] [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] [Indexed: 08/22/2023] Open
Abstract
Graphical abstract
Principal routes of
Bacillus anthracis
infection and stages of anthrax pathogenesis, consistent with current understandings. Depending on the route of infection, germination of spores may happen in extracellular tissue fluid, or following phagocytosis (a). Successful infection of host cells leads to toxin-associated cell death and release of vegetative cells and toxin (b). Toxin binds and enters other host cells (c), including those of the immune system, disrupting function. In some cases this leads to systemic disease, which typically is fatal.
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Affiliation(s)
- Andrew Wales
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, GU2 7AL, UK
| | - Adrienne Mackintosh
- Department of Bacteriology, Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone Surrey, KT15 3LJ, UK
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Oh SY, Château A, Tomatsidou A, Elli D, Gula H, Schneewind O, Missiakas D. Modeling gastrointestinal anthrax disease. Res Microbiol 2023; 174:104026. [PMID: 36646261 PMCID: PMC10338639 DOI: 10.1016/j.resmic.2023.104026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/28/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023]
Abstract
Bacillus anthracis is a spore-forming microbe that persists in soil and causes anthrax disease. The most natural route of infection is ingestion by grazing animals. Gastrointestinal (GI) anthrax also occurs in their monogastric predators, including humans. Exposure of carcasses to oxygen triggers sporulation and contamination of the surrounding soil completing the unusual life cycle of this microbe. The pathogenesis of GI anthrax is poorly characterized. Here, we use B. anthracis carrying the virulence plasmids pXO1 and pXO2, to model gastrointestinal disease in Guinea pigs and mice. We find that spores germinate in the GI tract and precipitate disease in a dose-dependent manner. Inoculation of vegetative bacilli also results in GI anthrax. Virulence is impacted severely by the loss of capsule (pXO2-encoded) but only moderately in absence of toxins (pXO1-encoded). Nonetheless, the lack of toxins leads to reduced bacterial replication in infected hosts. B. cereus Elc4, a strain isolated from a fatal case of inhalational anthrax-like disease, was also found to cause GI anthrax. Because transmission to new hosts depends on the release of large numbers of spores in the environment, we propose that the acquisition of pXO1- and pXO2-like plasmids may promote the successful expansion of members of the Bacillus cereus sensu lato group able to cause anthrax-like disease.
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Affiliation(s)
- So Young Oh
- The University of Chicago, Department of Microbiology, Howard Taylor Ricketts Laboratory, Lemont, IL, USA
| | - Alice Château
- The University of Chicago, Department of Microbiology, Howard Taylor Ricketts Laboratory, Lemont, IL, USA
| | - Anastasia Tomatsidou
- The University of Chicago, Department of Microbiology, Howard Taylor Ricketts Laboratory, Lemont, IL, USA
| | - Derek Elli
- The University of Chicago, Department of Microbiology, Howard Taylor Ricketts Laboratory, Lemont, IL, USA
| | - Haley Gula
- The University of Chicago, Department of Microbiology, Howard Taylor Ricketts Laboratory, Lemont, IL, USA
| | - Olaf Schneewind
- The University of Chicago, Department of Microbiology, Howard Taylor Ricketts Laboratory, Lemont, IL, USA
| | - Dominique Missiakas
- The University of Chicago, Department of Microbiology, Howard Taylor Ricketts Laboratory, Lemont, IL, USA.
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8
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Nevers A, Kranzler M, Perchat S, Gohar M, Sorokin A, Lereclus D, Ehling-Schulz M, Sanchis-Borja V. Plasmid - Chromosome interplay in natural and non-natural hosts: global transcription study of three Bacillus cereus group strains carrying pCER270 plasmid. Res Microbiol 2023; 174:104074. [PMID: 37149076 DOI: 10.1016/j.resmic.2023.104074] [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: 12/12/2022] [Revised: 04/12/2023] [Accepted: 04/25/2023] [Indexed: 05/08/2023]
Abstract
The Bacillus cereus group comprises genetically related Gram-positive spore-forming bacteria that colonize a wide range of ecological niches and hosts. Despite their high degree of genome conservation, extrachromosomal genetic material diverges between these species. The discriminating properties of the B. cereus group strains are mainly due to plasmid-borne toxins, reflecting the importance of horizontal gene transfers in bacterial evolution and species definition. To investigate how a newly acquired megaplasmid can impact the transcriptome of its host, we transferred the pCER270 from the emetic B. cereus strains to phylogenetically distant B. cereus group strains. RNA-sequencing experiments allowed us to determine the transcriptional influence of the plasmid on host gene expression and the impact of the host genomic background on the pCER270 gene expression. Our results show a transcriptional cross-regulation between the megaplasmid and the host genome. pCER270 impacted carbohydrate metabolism and sporulation genes expression, with a higher effect in the natural host of the plasmid, suggesting a role of the plasmid in the adaptation of the carrying strain to its environment. In addition, the host genomes also modulated the expression of pCER270 genes. Altogether, these results provide an example of the involvement of megaplasmids in the emergence of new pathogenic strains.
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Affiliation(s)
- Alicia Nevers
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Markus Kranzler
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine Vienna; Vienna, Austria
| | - Stéphane Perchat
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Michel Gohar
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Alexei Sorokin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Didier Lereclus
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Monika Ehling-Schulz
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine Vienna; Vienna, Austria.
| | - Vincent Sanchis-Borja
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
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9
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Hinnekens P, Fayad N, Gillis A, Mahillon J. Conjugation across Bacillus cereus and kin: A review. Front Microbiol 2022; 13:1034440. [PMID: 36406448 PMCID: PMC9673590 DOI: 10.3389/fmicb.2022.1034440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Horizontal gene transfer (HGT) is a major driving force in shaping bacterial communities. Key elements responsible for HGT are conjugation-like events and transmissible plasmids. Conjugative plasmids can promote their own transfer as well as that of co-resident plasmids. Bacillus cereus and relatives harbor a plethora of plasmids, including conjugative plasmids, which are at the heart of the group species differentiation and specification. Since the first report of a conjugation-like event between strains of B. cereus sensu lato (s.l.) 40 years ago, many have studied the potential of plasmid transfer across the group, especially for plasmids encoding major toxins. Over the years, more than 20 plasmids from B. cereus isolates have been reported as conjugative. However, with the increasing number of genomic data available, in silico analyses indicate that more plasmids from B. cereus s.l. genomes present self-transfer potential. B. cereus s.l. bacteria occupy diverse environmental niches, which were mimicked in laboratory conditions to study conjugation-related mechanisms. Laboratory mating conditions remain nonetheless simplistic compared to the complex interactions occurring in natural environments. Given the health, economic and ecological importance of strains of B. cereus s.l., it is of prime importance to consider the impact of conjugation within this bacterial group.
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Affiliation(s)
- Pauline Hinnekens
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Louvain-la-Neuve, Belgium
| | - Nancy Fayad
- Multi-Omics Laboratory, School of Pharmacy, Lebanese American University, Byblos, Lebanon
| | - 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
- *Correspondence: Jacques Mahillon,
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Mondange L, Tessier É, Tournier JN. Pathogenic Bacilli as an Emerging Biothreat? Pathogens 2022; 11:pathogens11101186. [PMID: 36297243 PMCID: PMC9609551 DOI: 10.3390/pathogens11101186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022] Open
Abstract
Bacillus anthracis, present as a very durable endospore in soil, causes zoonotic illness which is mainly associated with herbivores and domestic animals. Human cases are scarce and often involve populations close to infected livestock. If anthrax is no longer of public health concern in developed countries, B. anthracis is one of the top-tier biological weapon agents. It is classified by the CDC as a category A agent. Since 1994, emerging strains of Bacillus cereus have been associated with anthrax-like disease in mammals. Some clinical strains of B. cereus harbor anthrax-like plasmid genes (pXO1 and pXO2) associated with non-human primate and human infections, with the same clinical presentation of inhalation anthrax and mortality rates. Although currently restricted to certain limited areas of circulation, the emergence of these new strains of B. cereus extends the list of potential agents possibly usable for bioterrorism or as a biological weapon. It is therefore important to improve our knowledge of the phylogeny within the B. cereus sensu lato group to better understand the origin of these strains. We can then more efficiently monitor the emergence of new strains to better control the risk of infection and limit potentially malicious uses.
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Affiliation(s)
- Lou Mondange
- Bacteriology Unit, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 91220 Brétigny-sur-Orge, France
- Yersinia Unit, Institut Pasteur, 75015 Paris, France
- Correspondence: (L.M.); (J.-N.T.)
| | - Émilie Tessier
- Immunopathology Unit, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 91220 Brétigny-sur-Orge, France
| | - Jean-Nicolas Tournier
- CNR-LE Charbon, Institut de Recherche Biomédicale des Armées, 91220 Brétigny-sur-Orge, France
- Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 91220 Brétigny-sur-Orge, France
- École du Val-de-Grâce, 75015 Paris, France
- Correspondence: (L.M.); (J.-N.T.)
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11
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Identification of Universally Applicable and Species-Specific Marker Peptides for Bacillus anthracis. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101549. [PMID: 36294983 PMCID: PMC9605612 DOI: 10.3390/life12101549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/09/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022]
Abstract
Anthrax is a zoonotic infection caused by the bacterium Bacillus anthracis (BA). Specific identification of this pathogen often relies on targeting genes located on two extrachromosomal plasmids, which represent the major pathogenicity factors of BA. However, more recent findings show that these plasmids have also been found in other closely related Bacillus species. In this study, we investigated the possibility of identifying species-specific and universally applicable marker peptides for BA. For this purpose, we applied a high-resolution mass spectrometry-based approach for 42 BA isolates. Along with the genomic sequencing data and by developing a bioinformatics data evaluation pipeline, which uses a database containing most of the publicly available protein sequences worldwide (UniParc), we were able to identify eleven universal marker peptides unique to BA. These markers are located on the chromosome and therefore, might overcome known problems, such as observable loss of plasmids in environmental species, plasmid loss during cultivation in the lab, and the fact that the virulence plasmids are not necessarily a unique feature of BA. The identified chromosomally encoded markers in this study could extend the small panel of already existing chromosomal targets and along with targets for the virulence plasmids, may pave the way to an even more reliable identification of BA using genomics- as well as proteomics-based techniques.
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12
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Tomatsidou A, Krunic M, Missiakas D. Contribution of TagA-Like Glycosyltransferases to the Assembly of the Secondary Cell Wall Polysaccharide in Bacillus anthracis. J Bacteriol 2022; 204:e0025322. [PMID: 35997505 PMCID: PMC9487633 DOI: 10.1128/jb.00253-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/01/2022] [Indexed: 11/20/2022] Open
Abstract
Bacillus anthracis elaborates a secondary cell wall polysaccharide (SCWP) made of 6 to 12 trisaccharide units. Pyruvyl and acetyl substitutions of the distal unit are prerequisites for the noncovalent retention of 22 secreted Bacillus S-layer (Bsl)-associated proteins bearing an S-layer homology (SLH) domain. Surface display of Bsl proteins contributes to cell separation as well as virulence. Earlier work suggested that TagO initiates the synthesis of SCWP while GneY and GneZ, two UDP-GlcNAc 2-epimerases, synthesize ManNAc that is later incorporated in the repeat unit (→4)-ManNAc-(β1→4)-GlcNAc-(β1→6)-GlcNAc-(α1→). In organisms that synthesize wall teichoic acid, TagA catalysts have been shown to form the glycosidic bond ManNAc-(β1→4)-GlcNAc. Here, we show that genes bas2675 and bas5272, predicted to encode glycosyltransferases of the WecB/TagA/CpsF family (PFAM03808; CAZy GT26), are required for B. anthracis SCWP synthesis and S-layer assembly. Similar to tagO or gneY gneZ mutants, B. anthracis strains depleted of tagA1 (bas5272) cannot maintain cell shape, support vegetative growth, or synthesize SCWP. Expression of tagA2 (bas2675), or Staphylococcus aureus tagA on a plasmid, rescues the nonviable tagA1 mutant. We propose that TagA1 and TagA2 fulfill overlapping and key glycosyltransferase functions for the synthesis of repeat units of the SCWP of B. anthracis. IMPORTANCE Glycosyltransferases (GTs) catalyze the transfer of sugar moieties from activated donor molecules to acceptor molecules to form glycosidic bonds using a retaining or inverting mechanism. Based on the structural relatedness of their catalytic and carbohydrate-binding modules, GTs have been grouped into 115 families in the Carbohydrate-Active EnZyme (CAZy) database. For complex products, the functional assignment of GTs remains highly challenging without the knowledge of the chemical structure of the assembled polymer. Here, we propose that two uncharacterized GTs of B. anthracis belonging to the WecB/TagA/CpsF family incorporate ManNAc in repeat units of the secondary cell wall polymer of bacilli species.
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Affiliation(s)
- Anastasia Tomatsidou
- Department of Microbiology, Howard Taylor Ricketts Laboratory, The University of Chicago, Lemont, Illinois, USA
| | - Maria Krunic
- Department of Microbiology, Howard Taylor Ricketts Laboratory, The University of Chicago, Lemont, Illinois, USA
| | - Dominique Missiakas
- Department of Microbiology, Howard Taylor Ricketts Laboratory, The University of Chicago, Lemont, Illinois, USA
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13
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A Comparative Analysis of the Core Proteomes within and among the Bacillus subtilis and Bacillus cereus Evolutionary Groups Reveals the Patterns of Lineage- and Species-Specific Adaptations. Microorganisms 2022; 10:microorganisms10091720. [PMID: 36144322 PMCID: PMC9505155 DOI: 10.3390/microorganisms10091720] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
By integrating phylogenomic and comparative analyses of 1104 high-quality genome sequences, we identify the core proteins and the lineage-specific fingerprint proteins of the various evolutionary clusters (clades/groups/species) of the Bacillus genus. As fingerprints, we denote those core proteins of a certain lineage that are present only in that particular lineage and absent in any other Bacillus lineage. Thus, these lineage-specific fingerprints are expected to be involved in particular adaptations of that lineage. Intriguingly, with a few notable exceptions, the majority of the Bacillus species demonstrate a rather low number of species-specific fingerprints, with the majority of them being of unknown function. Therefore, species-specific adaptations are mostly attributed to highly unstable (in evolutionary terms) accessory proteomes and possibly to changes at the gene regulation level. A series of comparative analyses consistently demonstrated that the progenitor of the Cereus Clade underwent an extensive genomic expansion of chromosomal protein-coding genes. In addition, the majority (76–82%) of the B. subtilis proteins that are essential or play a significant role in sporulation have close homologs in most species of both the Subtilis and the Cereus Clades. Finally, the identification of lineage-specific fingerprints by this study may allow for the future development of highly specific vaccines, therapeutic molecules, or rapid and low-cost molecular tests for species identification.
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14
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Goncharova YO, Bogun AG, Bahtejeva IV, Titareva GM, Mironova RI, Kravchenko TB, Ostarkov NA, Brushkov AV, Timofeev VS, Ignatov SG. Allelic Polymorphism of Anthrax Pathogenicity Factor Genes as a Means of Estimating Microbiological Risks Associated with Climate Change. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822040056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Climate change brings new risks of emergence of especially dangerous diseases. The paper reports the possibility of assessing the pathogenic potential of bacteria as demonstrated by studying the allelic polymorphism of anthrax bacterium pathogenicity factor genes, which is a prerequisite for assessing the associated microbiological risks. The allelic polymorphism of the capBCADE operon (capB, capC, capA, capD, and capE genes) encoding the capsule biosynthesis proteins of Bacillus anthracis, and the acpA and acpB genes encoding the expression regulators of this operon have been studied for the first time. A number of single nucleotide polymorphisms (SNPs) were described in the strains of the studied sample, including 5 SNPs in the capB gene, 3 in capC, 4 in capA, 14 in capD, 2 in capE, and 15 in acpB, as well as 7 SNPs and one insertion in the acpA gene. As a result, the sample has been divided into sequence types for each gene and 17 genotypes, which are combinations of the identified sequence types. In silico translation of the detected alleles of the studied genes revealed three isoforms of the CapB and CapA proteins, two isoforms of the CapC and CapE proteins, six isoforms of the CapD protein, five isoforms of the AcpA protein, and four isoforms in the AcpB protein. It has been demonstrated that the SNP in the 351A → G position of capC is a marker of A.Br.Aust94 group strains. Based on the results, A.Br.Vollum group strains were divided into two subgroups. The strains in the evolutionary lines B and C differed from the line A strains by the presence of an 853G → A SNP in the acpA gene. In addition, a previously unknown variable number tandem repeat (VNTR), has been found in the acpA gene and the possibility of using it for differentiating and genotyping of B. anthracis strains has been demonstrated.
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15
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Hinnekens P, Mahillon J. Conjugation-mediated transfer of pXO16, a large plasmid from Bacillus thuringiensis sv. israelensis, across the Bacillus cereus group and its impact on host phenotype. Plasmid 2022; 122:102639. [PMID: 35842001 DOI: 10.1016/j.plasmid.2022.102639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/27/2022] [Accepted: 07/10/2022] [Indexed: 11/17/2022]
Abstract
pXO16, the 350 kb-conjugative plasmid from Bacillus thuringiensis sv. israelensis promotes its own transfer at high efficiency, triggers the transfer of mobilizable and non-mobilizable plasmids, as well as the transfer of host chromosomal loci. Naturally found in B. thuringiensis sv. israelensis, pXO16 transfers to various strains of Bacillus cereus sensu lato (s.l.) at a wide range of frequencies. Despite this host diversity, a paradox remains between the relatively large host spectrum and the natural occurrence of pXO16, so far restricted to B. thuringiensis sv. israelensis. Proposing first insights exploring this paradox, we investigated the behaviour of pXO16 amongst different members of the B. cereus group. We first looked at the transfer of pXO16 to two new host clusters of B. cereus s.l., Bacillus mycoides and Bacillus anthracis clusters. This examination brought to light the impairment of the characteristic rhizoidal phenotype of B. mycoides in presence of pXO16. We also explored the stability of pXO16 at different temperatures as some B. cereus group members are well-known for their psychro- or thermo-tolerance. This shed light on the thermo-sensitivity of the plasmid. The influence of pXO16 on its host cell growth and on swimming capacity also revealed no or limited impact on its natural host B. thuringiensis sv. israelensis. On the contrary, pXO16 affected more strongly both the growth and swimming capacity of other B. cereus s.l. hosts. This reinforced the running hypothesis of a co-evolution between pXO16 and B. thuringiensis sv. israelensis, enabling the plasmid maintenance without impairing the host strain development.
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Affiliation(s)
- Pauline Hinnekens
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium.
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16
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Gonçalves KB, Appel RJC, Bôas LAV, Cardoso PF, Bôas GTV. Genomic insights into the diversity of non-coding RNAs in Bacillus cereus sensu lato. Curr Genet 2022; 68:449-466. [PMID: 35552506 DOI: 10.1007/s00294-022-01240-4] [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: 12/19/2021] [Revised: 03/20/2022] [Accepted: 03/30/2022] [Indexed: 11/28/2022]
Abstract
Bacillus cereus sensu lato is a group of bacteria of medical and agricultural importance in different ecological niches and with controversial taxonomic relationships. Studying the composition of non-coding RNAs (ncRNAs) in several bacterial groups has been an important tool for identifying genetic information and better understanding genetic regulation towards environment adaptation. However, to date, no comparative genomics study of ncRNA has been performed in this group. Thus, this study aimed to identify and characterize the set of ncRNAs from 132 strains of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis to obtain an overview of the diversity and distribution of these genetic elements in these species. We observed that the number of ncRNAs differs in the chromosomes of the three species, but not in the plasmids, when species or phylogenetic clusters were compared. The prevailing functional/structural category was Cis-reg and the most frequent class was Riboswitch. However, in plasmids, the class Group II intron was the most frequent. Also, nine ncRNAs were selected for validation in the strain B. thuringiensis 407 by RT-PCR, which allowed to identify the expression of the ncRNAs. The wide distribution and diversity of ncRNAs in the B. cereus group, and more intensely in B. thuringiensis, may help improve the abilities of these species to adapt to various environmental changes. Further studies should address the expression of these genetic elements in different conditions.
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Affiliation(s)
- Kátia B Gonçalves
- Depto Biologia Geral, Universidade Estadual de Londrina, Londrina, Brazil
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17
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Chen H, Verplaetse E, Jauslin T, Cosson P, Slamti L, Lereclus D. The Fate of Bacteria of the Bacillus cereus Group in the Amoeba Environment. MICROBIAL ECOLOGY 2022; 83:1088-1104. [PMID: 34342700 DOI: 10.1007/s00248-021-01828-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
The Bacillus cereus sensu lato group consists of several closely related species, including B. anthracis, B. cereus sensu stricto, and B. thuringiensis. Spores of these pathogenic bacteria are commonly found in the soil but evidence suggests that they are unable to grow in such a natural environment in the absence of nutrient input. Amoebas have been reported to be an amplifier for several species of pathogenic bacteria and their potential involvement to explain the large amount of B. thuringiensis and B. cereus spores in soil has been frequently proposed. Here, we studied the fate of Bacillus and amoebas when cultured together. We show that the virulence factors produced by B. thuringiensis and B. cereus do not affect the amoeba Acanthamoeba castellanii, which, on the contrary, can phagocytose and effectively digest vegetative Bacillus cells to grow and prevent the formation of cysts. Bacterial spores can germinate in the amoeba environment and the vegetative cells can then form chains or aggregates that appear to be less efficiently phagocyted by the amoeba. The use of transcriptional fusions between fluorescent reporter genes and stationary phase- and sporulation-specific promoters showed that the sporulation process occurs more efficiently in the presence of amoebas than in their absence. Moreover, our results showed the amoeba environment to promote spore germination and allow the bacteria to complete their developmental cycle. Overall, this study suggests that the amoeba-Bacillus interaction creates a virtuous circle in which each protagonist helps the other to develop.
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Affiliation(s)
- Haibo Chen
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Emilie Verplaetse
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Tania Jauslin
- Cell Physiology and Metabolism Dpt, Faculty of Medicine, University of Geneva, 1 rue Michel Servet, CH-1211, Geneva 4, Switzerland
| | - Pierre Cosson
- Cell Physiology and Metabolism Dpt, Faculty of Medicine, University of Geneva, 1 rue Michel Servet, CH-1211, Geneva 4, Switzerland
| | - Leyla Slamti
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Didier Lereclus
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
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18
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Yudianingtyas DW, Sumiarto B, Susetya H, Salman M, Djatmikowati TF, Haeriah H, Rahman A, Mangidi R. Identification of the molecular characteristics of Bacillus anthracis (1982-2020) isolates in East Indonesia using multilocus variable-number tandem repeat analysis. Vet World 2022; 15:953-961. [PMID: 35698492 PMCID: PMC9178602 DOI: 10.14202/vetworld.2022.953-961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/09/2022] [Indexed: 11/30/2022] Open
Abstract
Background and Aim: Anthrax is one of the endemic strategic diseases in East Indonesia, particularly in the provinces of South Sulawesi, West Sulawesi, Gorontalo, East Nusa Tenggara, and West Nusa Tenggara. Anthrax is an important disease due to its zoonotic and economic impact on the livestock industry. This study aimed to identify the molecular characteristics of Bacillus anthracis in East Indonesia using multilocus variable-number tandem repeat (VNTR) analysis (MLVA). Materials and Methods: Isolates were obtained from an investigation of anthrax outbreaks in five provinces of East Indonesia from 1982 to 2020. Conventional polymerase chain reaction for B. anthracis was used to identify MLVA-8. Deoxyribonucleic acid sequencing analysis was based on MLVA-8 primers for VNTR identification of the phylogenetic relationship among 24 isolates of B. anthracis obtained from 17 distinct districts/cities in East Indonesia. Tandem Repeats Finder was used for VNTR identification, and Molecular Evolutionary Genetics Analysis X was used to construct phylogenetic analysis. Results: In this study, 24 isolates were classified as genotype or lineage A. There were four subgroups of B. anthracis circulating in East Indonesia based on eight molecular marker loci sequence results. Conclusion: The findings of this study show that MLVA-8 typing might be useful as a subtyping tool for the epidemiological investigation of identical genotypes and low genetic diversity of B. anthracis. No other lineage of B. anthracis was circulating in East Indonesia. Other molecular methods are needed, such as extended MLVA, whole-genome sequencing, and canonical single-nucleotide polymorphism, for a more precise study of B. anthracis genetic diversity.
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Affiliation(s)
- D. W. Yudianingtyas
- Doctoral Study Program, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia; Department of Epidemiology and Veterinary Information, Disease Investigation Centre Maros, Directorate General of Livestock Services and Animal Health, Ministry of Agriculture, The Republic of Indonesia, Indonesia
| | - B. Sumiarto
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - H. Susetya
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mo Salman
- Department of of Clinical Sciences, Animal Population Health Institute, College of Veterinary Medicine and Biomedical Science, Colorado State University, Fort Collins, United States of America
| | - T. F. Djatmikowati
- Bacteriology laboratory, Disease Investigation Centre Maros, Directorate General of Livestock Services and Animal Health, Ministry of Agriculture, Indonesia, The Republic of Indonesia, Indonesia
| | - Haeriah Haeriah
- Bacteriology laboratory, Disease Investigation Centre Maros, Directorate General of Livestock Services and Animal Health, Ministry of Agriculture, Indonesia, The Republic of Indonesia, Indonesia
| | - Abdul Rahman
- Bacteriology laboratory, Disease Investigation Centre Maros, Directorate General of Livestock Services and Animal Health, Ministry of Agriculture, Indonesia, The Republic of Indonesia, Indonesia
| | - R. Mangidi
- Disease Investigation Centre Maros, Directorate General of Livestock Services and Animal Health, Ministry of Agriculture, The Republic of Indonesia, Indonesia
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19
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Nakonieczna A, Rutyna P, Fedorowicz M, Kwiatek M, Mizak L, Łobocka M. Three Novel Bacteriophages, J5a, F16Ba, and z1a, Specific for Bacillus anthracis, Define a New Clade of Historical Wbeta Phage Relatives. Viruses 2022; 14:213. [PMID: 35215807 PMCID: PMC8878798 DOI: 10.3390/v14020213] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 11/16/2022] Open
Abstract
Bacillus anthracis is a potent biowarfare agent, able to be highly lethal. The bacteria dwell in the soil of certain regions, as natural flora. Bacteriophages or their lytic enzymes, endolysins, may be an alternative for antibiotics and other antibacterials to fight this pathogen in infections and to minimize environmental contamination with anthrax endospores. Upon screening environmental samples from various regions in Poland, we isolated three new siphophages, J5a, F16Ba, and z1a, specific for B. anthracis. They represent new species related to historical anthrax phages Gamma, Cherry, and Fah, and to phage Wbeta of Wbetavirus genus. We show that the new phages and their closest relatives, phages Tavor_SA, Negev_SA, and Carmel_SA, form a separate clade of the Wbetavirus genus, designated as J5a clade. The most distinctive feature of J5a clade phages is their cell lysis module. While in the historical phages it encodes a canonical endolysin and a class III holin, in J5a clade phages it encodes an endolysin with a signal peptide and two putative holins. We present the basic characteristic of the isolated phages. Their comparative genomic analysis indicates that they encode two receptor-binding proteins, of which one may bind a sugar moiety of B. anthracis cell surface.
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Affiliation(s)
- Aleksandra Nakonieczna
- Biological Threats Identification and Countermeasure Center, Military Institute of Hygiene and Epidemiology, 24-100 Pulawy, Poland; (P.R.); (M.F.); (M.K.); (L.M.)
| | - Paweł Rutyna
- Biological Threats Identification and Countermeasure Center, Military Institute of Hygiene and Epidemiology, 24-100 Pulawy, Poland; (P.R.); (M.F.); (M.K.); (L.M.)
| | - Magdalena Fedorowicz
- Biological Threats Identification and Countermeasure Center, Military Institute of Hygiene and Epidemiology, 24-100 Pulawy, Poland; (P.R.); (M.F.); (M.K.); (L.M.)
| | - Magdalena Kwiatek
- Biological Threats Identification and Countermeasure Center, Military Institute of Hygiene and Epidemiology, 24-100 Pulawy, Poland; (P.R.); (M.F.); (M.K.); (L.M.)
| | - Lidia Mizak
- Biological Threats Identification and Countermeasure Center, Military Institute of Hygiene and Epidemiology, 24-100 Pulawy, Poland; (P.R.); (M.F.); (M.K.); (L.M.)
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02-106 Warsaw, Poland
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20
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Chang JD, Vaughan EE, Liu CG, Jelinski JW, Terwilliger AL, Maresso AW. Metabolic profiling reveals nutrient preferences during carbon utilization in Bacillus species. Sci Rep 2021; 11:23917. [PMID: 34903830 PMCID: PMC8669014 DOI: 10.1038/s41598-021-03420-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 11/29/2021] [Indexed: 11/18/2022] Open
Abstract
The genus Bacillus includes species with diverse natural histories, including free-living nonpathogenic heterotrophs such as B. subtilis and host-dependent pathogens such as B. anthracis (the etiological agent of the disease anthrax) and B. cereus, a cause of food poisoning. Although highly similar genotypically, the ecological niches of these three species are mutually exclusive, which raises the untested hypothesis that their metabolism has speciated along a nutritional tract. Here, we developed a pipeline for quantitative total assessment of the use of diverse sources of carbon for general metabolism to better appreciate the "culinary preferences" of three distinct Bacillus species, as well as related Staphylococcus aureus. We show that each species has widely varying metabolic ability to utilize diverse sources of carbon that correlated to their ecological niches. This approach was applied to the growth and survival of B. anthracis in a blood-like environment and find metabolism shifts from sugar to amino acids as the preferred source of energy. Finally, various nutrients in broth and host-like environments are identified that may promote or interfere with bacterial metabolism during infection.
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Affiliation(s)
- James D Chang
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Ellen E Vaughan
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Carmen Gu Liu
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Joseph W Jelinski
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Austen L Terwilliger
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Anthony W Maresso
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
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21
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Sequence Variability of pXO1-Located Pathogenicity Genes of Bacillus anthracis Natural Strains of Different Geographic Origin. Pathogens 2021; 10:pathogens10121556. [PMID: 34959512 PMCID: PMC8703917 DOI: 10.3390/pathogens10121556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/11/2021] [Accepted: 11/26/2021] [Indexed: 11/18/2022] Open
Abstract
The main pathogenic factor of Bacillus anthracis is a three-component toxin encoded by the pagA, lef, and cya genes, which are located on the pXO1 plasmid. The atxA gene, which encodes the primary regulator of pathogenicity factor expression, is located on the same plasmid. In this work, we evaluated the polymorphism of the pagA, lef, cya, and atxA genes for 85 B. anthracis strains from different evolutionary lineages and canSNP groups. We have found a strong correlation of 19 genotypes with the main evolutionary lineages, but the correlation with the canSNP group of the strain was not as strong. We have detected several genetic markers indicating the geographical origin of the strains, for example, their source from the steppe zone of the former USSR. We also found that strains of the B.Br.001/002 group caused an anthrax epidemic in Russia in 2016 and strains isolated during paleontological excavations in the Russian Arctic have the same genotype as the strains of the B.Br.CNEVA group circulating in Central Europe. This data could testify in favor of the genetic relationship of these two groups of strains and hypothesize the ways of distribution of their ancestral forms between Europe and the Arctic.
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Gupta M, Kumar H, Kaur S. Vegetative Insecticidal Protein (Vip): A Potential Contender From Bacillus thuringiensis for Efficient Management of Various Detrimental Agricultural Pests. Front Microbiol 2021; 12:659736. [PMID: 34054756 PMCID: PMC8158940 DOI: 10.3389/fmicb.2021.659736] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/19/2021] [Indexed: 11/25/2022] Open
Abstract
Bacillus thuringiensis (Bt) bacterium is found in various ecological habitats, and has natural entomo-pesticidal properties, due to the production of crystalline and soluble proteins during different growth phases. In addition to Cry and Cyt proteins, this bacterium also produces Vegetative insecticidal protein (Vip) during its vegetative growth phase, which is considered an excellent toxic candidate because of the difference in sequence homology and receptor sites from Cry proteins. Vip proteins are referred as second-generation insecticidal proteins, which can be used either alone or in complementarity with Cry proteins for the management of various detrimental pests. Among these Vip proteins, Vip1 and Vip2 act as binary toxins and have toxicity toward pests belonging to Hemiptera and Coleoptera orders, whereas the most important Vip3 proteins have insecticidal activity against Lepidopteran pests. These Vip3 proteins are similar to Cry proteins in terms of toxicity potential against susceptible insects. They are reported to be toxic toward pests, which can’t be controlled with Cry proteins. The Vip3 proteins have been successfully pyramided along with Cry proteins in transgenic rice, corn, and cotton to combat resistant pest populations. This review provides detailed information about the history and importance of Vip proteins, their types, structure, newly identified specific receptors, and action mechanism of this specific class of proteins. Various studies conducted on Vip proteins all over the world and the current status have been discussed. This review will give insights into the significance of Vip proteins as alternative promising candidate toxic proteins from Bt for the management of pests in most sustainable manner.
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Affiliation(s)
- Mamta Gupta
- ICAR-National Institute for Plant Biotechnology, New Delhi, India.,ICAR-Indian Institute of Maize Research, Ludhiana, India
| | - Harish Kumar
- Punjab Agricultural University, Regional Research Station, Faridkot, India
| | - Sarvjeet Kaur
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
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Smith V, Josefsen M, Lindbäck T, Hegna IK, Finke S, Tourasse NJ, Nielsen-LeRoux C, Økstad OA, Fagerlund A. MogR Is a Ubiquitous Transcriptional Repressor Affecting Motility, Biofilm Formation and Virulence in Bacillus thuringiensis. Front Microbiol 2020; 11:610650. [PMID: 33424814 PMCID: PMC7793685 DOI: 10.3389/fmicb.2020.610650] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/01/2020] [Indexed: 12/16/2022] Open
Abstract
Flagellar motility is considered an important virulence factor in different pathogenic bacteria. In Listeria monocytogenes the transcriptional repressor MogR regulates motility in a temperature-dependent manner, directly repressing flagellar- and chemotaxis genes. The only other bacteria known to carry a mogR homolog are members of the Bacillus cereus group, which includes motile species such as B. cereus and Bacillus thuringiensis as well as the non-motile species Bacillus anthracis, Bacillus mycoides and Bacillus pseudomycoides. Furthermore, the main motility locus in B. cereus group bacteria, carrying the genes for flagellar synthesis, appears to be more closely related to L. monocytogenes than to Bacillus subtilis, which belongs to a separate phylogenetic group of Bacilli and does not carry a mogR ortholog. Here, we show that in B. thuringiensis, MogR overexpression results in non-motile cells devoid of flagella. Global gene expression profiling showed that 110 genes were differentially regulated by MogR overexpression, including flagellar motility genes, but also genes associated with virulence, stress response and biofilm lifestyle. Accordingly, phenotypic assays showed that MogR also affects cytotoxicity and biofilm formation in B. thuringiensis. Overexpression of a MogR variant mutated in two amino acids within the putative DNA binding domain restored phenotypes to those of an empty vector control. In accordance, introduction of these mutations resulted in complete loss in MogR binding to its candidate flagellar locus target site in vitro. In contrast to L. monocytogenes, MogR appears to be regulated in a growth-phase dependent and temperature-independent manner in B. thuringiensis 407. Interestingly, mogR was found to be conserved also in non-motile B. cereus group species such as B. mycoides and B. pseudomycoides, which both carry major gene deletions in the flagellar motility locus and where in B. pseudomycoides mogR is the only gene retained. Furthermore, mogR is expressed in non-motile B. anthracis. Altogether this provides indications of an expanded set of functions for MogR in B. cereus group species, beyond motility regulation. In conclusion, MogR constitutes a novel B. thuringiensis pleiotropic transcriptional regulator, acting as a repressor of motility genes, and affecting the expression of a variety of additional genes involved in biofilm formation and virulence.
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Affiliation(s)
- Veronika Smith
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, Oslo, Norway
- Centre for Integrative Microbial Evolution (CIME), Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Malin Josefsen
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Toril Lindbäck
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Ida K Hegna
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Sarah Finke
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, Oslo, Norway
- Centre for Integrative Microbial Evolution (CIME), Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Nicolas J Tourasse
- CNRS, INSERM, ARNA, UMR 5320, U1212, University of Bordeaux, Bordeaux, France
| | | | - Ole Andreas Økstad
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, Oslo, Norway
- Centre for Integrative Microbial Evolution (CIME), Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Annette Fagerlund
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, Oslo, Norway
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
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Novel Strategy for Rapidly and Safely Distinguishing Bacillus anthracis and Bacillus cereus by Use of Peptide Mass Fingerprints Based on Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. J Clin Microbiol 2020; 59:JCM.02358-20. [PMID: 33115846 DOI: 10.1128/jcm.02358-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 10/19/2020] [Indexed: 12/28/2022] Open
Abstract
The objective of this study was to construct a rapid, high-throughput, and biosafety-compatible screening method for Bacillus anthracis and Bacillus cereus based on matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). MALDI-TOF MS coupled to ClinProTools was used to discover MALDI-TOF MS biomarker peaks and generate a classification model based on a genetic algorithm (GA) to differentiate between different Bacillus anthracis and Bacillus cereus isolates. Thirty Bacillus anthracis and 19 Bacillus cereus strains were used to construct and analyze the model, and 40 Bacillus strains were used for validation. For the GA screening model, the cross-validation values, which reflect the ability of the model to handle variability among the test spectra, and the recognition capability values, which reflect the model's ability to correctly identify its component spectra, were all 100%. This model contained 10 biomarker peaks (m/z 3,339.9, 3,396.3, 3,682.4, 5,476.7, 6,610.6, 6,680.1, 7,365.3, 7,792.4, 9,475.8, and 10,934.1) used to correctly identify 28 Bacillus anthracis and 12 Bacillus cereus isolates from 40 Bacillus isolates, with a sensitivity and specificity of 100%. With the obvious advantages of being rapid, highly accurate, and highly sensitive and having a low cost and high throughput, MALDI-TOF MS ClinProTools is a powerful and reliable tool for screening Bacillus anthracis and Bacillus cereus strains.
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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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Salam LB, Obayori OS. Remarkable shift in structural and functional properties of an animal charcoal-polluted soil accentuated by inorganic nutrient amendment. J Genet Eng Biotechnol 2020; 18:70. [PMID: 33175233 PMCID: PMC7658278 DOI: 10.1186/s43141-020-00089-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/02/2020] [Indexed: 12/02/2022]
Abstract
Background Soils polluted with animal charcoal from skin and hide cottage industries harbour extremely toxic and carcinogenic hydrocarbon pollutants and thus require a bio-based eco-friendly strategy for their depuration. The effects of carbon-free mineral medium (CFMM) amendment on hydrocarbon degradation and microbial community structure and function in an animal charcoal-polluted soil was monitored for 6 weeks in field moist microcosms consisting of CFMM-treated soil (FN4) and an untreated control (FN1). Hydrocarbon degradation was monitored using gas chromatography-flame ionization detector (GC-FID), and changes in microbial community structure were monitored using Kraken, while functional annotation of putative open reading frames (ORFs) was done using KEGG KofamKOALA and NCBI’s conserved domain database (CDD). Results Gas chromatographic analysis of hydrocarbon fractions revealed the removal of 84.02% and 82.38% aliphatic and 70.09% and 70.14% aromatic fractions in FN4 and FN1 microcosms in 42 days. Shotgun metagenomic analysis of the two metagenomes revealed a remarkable shift in the microbial community structure. In the FN4 metagenome, 92.97% of the population belong to the phylum Firmicutes and its dominant representative genera Anoxybacillus (64.58%), Bacillus (21.47%) and Solibacillus (2.39%). In untreated FN1 metagenome, the phyla Proteobacteria (56.12%), Actinobacteria (23.79%) and Firmicutes (11.20%), and the genera Xanthobacter (9.73%), Rhizobium (7.49%) and Corynebacterium (7.35%), were preponderant. Functional annotation of putative ORFs from the two metagenomes revealed the detection of degradation genes for aromatic hydrocarbons, benzoate, xylene, chlorocyclohexane/chlorobenzene, toluene and several others in FN1 metagenome. In the FN4 metagenome, only seven hydrocarbon degradation genes were detected. Conclusion This study revealed that though CFMM amendment slightly increases the rate of hydrocarbon degradation, it negatively impacts the structural and functional properties of the animal charcoal-polluted soil. It also revealed that intrinsic bioremediation of the polluted soil could be enhanced via addition of water and aeration. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-020-00089-9.
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Affiliation(s)
- Lateef Babatunde Salam
- Department of Biological Sciences, Microbiology unit, Summit University, Offa, Kwara, Nigeria.
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Hai Y, Wang WR, Hua Y, Guo WD, Song J, Han S, Zhang YG, Jiang XF, Zhang XH, Li ZJ, Li W, Liang XD, Han RL, Wei JC, Liu ZG. Changed epidemiology of anthrax and molecular characteristics of Bacillus anthracis in Inner Mongolia Autonomous Region, China. Transbound Emerg Dis 2020; 68:2250-2260. [PMID: 33048441 DOI: 10.1111/tbed.13877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/11/2020] [Accepted: 10/06/2020] [Indexed: 10/23/2022]
Abstract
Anthrax is a natural foci disease in Inner Mongolia, which poses a severe threat to public health. In this study, the incidence number, rate and constituent ratio were used to describe the epidemiological characteristics of anthrax in the region from 1956-2018. The molecular correlation and genetic characteristics of the strains were investigated using canonical single nucleotide polymorphisms (CanSNP), multiple-locus variable-number tandem repeat analysis (MLVA-15) and whole genome sequencing (WGS). The epidemiological characteristics of anthrax in Inner Mongolia have altered significantly. The incidence of anthrax has decreased annually without vaccination, and the regional distribution of anthrax gradually transferred from central and western regions to the eastern. Moreover, the occupation distribution evolved from multiple early occupations to predominated by farmers and herdsmen. This change is closely related to policy factors and to changes in the means of production and the living habits of the local population. This indicates that reformulating the control and prevention strategies is essential. Both A. Br. Ames and A. Br. 001/002 subgroups were the predominant CanSNP genotypes of Bacillus anthracis in Inner Mongolia. A total of 36 strains constituted six shared MLVA-15 genotypes, suggesting an epidemiological link between the strains of each shared genotype. The six shared genotypes ([GT1, 9, 11 and 15] and [GT8 and 12]) consisting of 2-7 strains confirmed the occurrence of multiple point outbreaks and cross-regional transmission caused by multiple common sources of infection. Phylogenetic analysis based on the WGS core genome showed that strains from this study formed an independent clade (C.V.), and they were positioned close to each other, suggesting a common origin. Further comparison analysis should be performed to ascertain the geographic origin of these strains.
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Affiliation(s)
- Yan Hai
- College of Veterinary Medicine, Inner Mongolia Agriculture University, Huhhot, China.,Inner Mongolia Autonomous Region Center for Comprehensive Disease Control and Prevention, Huhhot, China
| | - Wen-Rui Wang
- Inner Mongolia Autonomous Region Center for Comprehensive Disease Control and Prevention, Huhhot, China
| | - Yue Hua
- Inner Mongolia Autonomous Region Center for Comprehensive Disease Control and Prevention, Huhhot, China
| | - Wei-Dong Guo
- Inner Mongolia Autonomous Region Center for Comprehensive Disease Control and Prevention, Huhhot, China
| | - Jian Song
- Inner Mongolia Autonomous Region Center for Comprehensive Disease Control and Prevention, Huhhot, China
| | - Song Han
- Inner Mongolia Autonomous Region Center for Comprehensive Disease Control and Prevention, Huhhot, China
| | - Yu-Geng Zhang
- Inner Mongolia Autonomous Region Center for Comprehensive Disease Control and Prevention, Huhhot, China
| | - Xiao-Feng Jiang
- Inner Mongolia Autonomous Region Center for Comprehensive Disease Control and Prevention, Huhhot, China
| | - Xiu-Hong Zhang
- Inner Mongolia Autonomous Region Center for Comprehensive Disease Control and Prevention, Huhhot, China
| | - Zhen-Jun Li
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Wei Li
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Xu-Dong Liang
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Run-Lin Han
- College of Veterinary Medicine, Inner Mongolia Agriculture University, Huhhot, China
| | - Jian-Chun Wei
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Zhi-Guo Liu
- College of Veterinary Medicine, Inner Mongolia Agriculture University, Huhhot, China.,Inner Mongolia Autonomous Region Center for Comprehensive Disease Control and Prevention, Huhhot, China.,State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
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Sadeghpour SD, Karimi F, Alizadeh H. Predictive and fluorescent nanosensing experimental methods for evaluating anthrax protective antigen and lethal factor interactions for therapeutic applications. Int J Biol Macromol 2020; 160:1158-1167. [DOI: 10.1016/j.ijbiomac.2020.05.190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/22/2020] [Accepted: 05/22/2020] [Indexed: 10/24/2022]
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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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Alameh S, Bartolo G, O’Brien S, Henderson EA, Gonzalez LO, Hartmann S, Klimko CP, Shoe JL, Cote CK, Grill LK, Levitin A, Martchenko Shilman M. Anthrax toxin component, Protective Antigen, protects insects from bacterial infections. PLoS Pathog 2020; 16:e1008836. [PMID: 32866212 PMCID: PMC7458312 DOI: 10.1371/journal.ppat.1008836] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 07/24/2020] [Indexed: 01/23/2023] Open
Abstract
Anthrax is a major zoonotic disease of wildlife, and in places like West Africa, it can be caused by Bacillus anthracis in arid nonsylvatic savannahs, and by B. cereus biovar anthracis (Bcbva) in sylvatic rainforests. Bcbva-caused anthrax has been implicated in as much as 38% of mortality in rainforest ecosystems, where insects can enhance the transmission of anthrax-causing bacteria. While anthrax is well-characterized in mammals, its transmission by insects points to an unidentified anthrax-resistance mechanism in its vectors. In mammals, a secreted anthrax toxin component, 83 kDa Protective Antigen (PA83), binds to cell-surface receptors and is cleaved by furin into an evolutionary-conserved PA20 and a pore-forming PA63 subunits. We show that PA20 increases the resistance of Drosophila flies and Culex mosquitoes to bacterial challenges, without directly affecting the bacterial growth. We further show that the PA83 loop known to be cleaved by furin to release PA20 from PA63 is, in part, responsible for the PA20-mediated protection. We found that PA20 binds directly to the Toll activating peptidoglycan-recognition protein-SA (PGRP-SA) and that the Toll/NF-κB pathway is necessary for the PA20-mediated protection of infected flies. This effect of PA20 on innate immunity may also exist in mammals: we show that PA20 binds to human PGRP-SA ortholog. Moreover, the constitutive activity of Imd/NF-κB pathway in MAPKK Dsor1 mutant flies is sufficient to confer the protection from bacterial infections in a manner that is independent of PA20 treatment. Lastly, Clostridium septicum alpha toxin protects flies from anthrax-causing bacteria, showing that other pathogens may help insects resist anthrax. The mechanism of anthrax resistance in insects has direct implications on insect-mediated anthrax transmission for wildlife management, and with potential for applications, such as reducing the sensitivity of pollinating insects to bacterial pathogens.
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Affiliation(s)
- Saleem Alameh
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, California, United States of America
| | - Gloria Bartolo
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, California, United States of America
| | - Summer O’Brien
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, California, United States of America
| | - Elizabeth A. Henderson
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, California, United States of America
| | - Leandra O. Gonzalez
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, California, United States of America
| | - Stella Hartmann
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, California, United States of America
| | - Christopher P. Klimko
- Bacteriology Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, United States of America
| | - Jennifer L. Shoe
- Bacteriology Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, United States of America
| | - Christopher K. Cote
- Bacteriology Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, United States of America
| | - Laurence K. Grill
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, California, United States of America
| | - Anastasia Levitin
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, California, United States of America
- * E-mail: (AL); (MMS)
| | - Mikhail Martchenko Shilman
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, California, United States of America
- * E-mail: (AL); (MMS)
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Rousset L, Alpha-Bazin B, Château A, Armengaud J, Clavel T, Berge O, Duport C. Groundwater promotes emergence of asporogenic mutants of emetic Bacillus cereus. Environ Microbiol 2020; 22:5248-5264. [PMID: 32815215 DOI: 10.1111/1462-2920.15203] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 01/15/2023]
Abstract
Bacillus cereus is a ubiquitous endospore-forming bacterium, which mainly affects humans as a food-borne pathogen. Bacillus cereus can contaminate groundwater used to irrigate food crops. Here, we examined the ability of the emetic strain B. cereus F4810/72 to survive abiotic conditions encountered in groundwater. Our results showed that vegetative B. cereus cells rapidly evolved in a mixed population composed of endospores and asporogenic variants bearing spo0A mutations. One asporogenic variant, VAR-F48, was isolated and characterized. VAR-F48 can survive in sterilized groundwater over a long period in a vegetative form and has a competitive advantage compared to its parental strain. Proteomics analysis allowed us to quantify changes to cellular and exoproteins after 24 and 72 h incubation in groundwater, for VAR-F48 compared to its parental strain. The results revealed a significant re-routing of the metabolism in the absence of Spo0A. We concluded that VAR-F48 maximizes its energy use to deal with oligotrophy, and the emergence of spo0A-mutated variants may contribute to the persistence of emetic B. cereus in natural oligotrophic environments.
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Affiliation(s)
- Ludivine Rousset
- Avignon Université, INRAE, UMR SQPOV, Avignon, F-84914, France.,INRAE, Pathologie Végétale, Montfavet, F-84140, France
| | - Béatrice Alpha-Bazin
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France
| | - Alice Château
- Avignon Université, INRAE, UMR SQPOV, Avignon, F-84914, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France
| | - Thierry Clavel
- Avignon Université, INRAE, UMR SQPOV, Avignon, F-84914, France
| | - Odile Berge
- INRAE, Pathologie Végétale, Montfavet, F-84140, France
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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: 42] [Impact Index Per Article: 10.5] [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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33
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Roonie A, Majumder S, Kingston JJ, Parida M. Molecular characterization of B. anthracis isolates from the anthrax outbreak among cattle in Karnataka, India. BMC Microbiol 2020; 20:232. [PMID: 32736522 PMCID: PMC7394690 DOI: 10.1186/s12866-020-01917-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 07/21/2020] [Indexed: 12/02/2022] Open
Abstract
Background Anthrax, a zoonotic disease is caused by the Gram positive bacterium Bacillus anthracis. During January 2013, an anthrax outbreak among cattle was reported in Gundlupet Taluk, neighboring Bandipur National Park and tiger reserve, India. The present study aims at the molecular identification and characterization of 12 B. anthracis isolates from this outbreak by 16S rRNA gene sequencing, screening B. anthracis specific prophages and chromosomal markers, protective antigen (pag) gene and canonical single nucleotide polymorphism (canSNP) analysis to subtype the isolates into one of the twelve globally identified clonal sub-lineages of B. anthracis. Results These isolates had identical 16S rDNA nucleotide sequences with B. anthracis specific dual peaks showing mixed base pair R (G/A) at position 1139 with visual inspection while the automated basecaller software indicated a G. Alternatively the nucleotide A at 1146 position was indicative of the 16S rDNA type 7. Multiple sequence alignment with additional 170 (16S rDNA) sequences of B. cereus sensu lato group from GenBank database revealed 28 new 16S types in addition to eleven 16S types reported earlier. The twelve B. anthracis isolates were found to harbor the four B. anthracis specific prophages (lambdaBa01, lambdaBa02, lambdaBa03, and lambdaBa04) along with its four specific loci markers (dhp 61.183, dhp 77.002, dhp 73.019, and dhp 73.017). The pag gene sequencing identified the isolates as protective antigen (PA) genotype I with phenylalanine-proline-alanine phenotype (FPA phenotype). However, sequence clustering with additional 34 pag sequences from GenBank revealed two additional missense mutations at nucleotide positions 196 bp and 869 bp of the 2294 bp pag sequence among the 5 B. cereus strains with pXO1 like plasmids. The canSNP analysis showed that the isolates belong to A.Br.Aust94 sub-lineage that is distributed geographically in countries of Asia, Africa, Europe and Australia. Conclusions The analysis of 16S rDNA sequences reiterated the earlier findings that visual inspection of electropherogram for position 1139 having nucleotide R could be used for B. anthracis identification and not the consensus sequence from base caller. The canSNP results indicated that the anthrax outbreak among cattle was caused by B. anthracis of A.Br.Aust94 sub-lineage.
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Affiliation(s)
- Akanxa Roonie
- Microbiology Division, Defence Food Research Laboratory, Siddartha Nagar, Mysore, Karnataka, 570011, India
| | - Saugata Majumder
- Microbiology Division, Defence Food Research Laboratory, Siddartha Nagar, Mysore, Karnataka, 570011, India
| | - Joseph J Kingston
- Microbiology Division, Defence Food Research Laboratory, Siddartha Nagar, Mysore, Karnataka, 570011, India.
| | - Manmohan Parida
- Microbiology Division, Defence Food Research Laboratory, Siddartha Nagar, Mysore, Karnataka, 570011, India
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Zheng Z, Zhang Y, Liu Z, Dong Z, Xie C, Bravo A, Soberón M, Mahillon J, Sun M, Peng D. The CRISPR-Cas systems were selectively inactivated during evolution of Bacillus cereus group for adaptation to diverse environments. THE ISME JOURNAL 2020; 14:1479-1493. [PMID: 32132663 PMCID: PMC7242445 DOI: 10.1038/s41396-020-0623-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 02/16/2020] [Accepted: 02/19/2020] [Indexed: 12/27/2022]
Abstract
CRISPR-Cas systems are considered as barriers to horizontal gene transfer (HGT). However, the influence of such systems on HGT within species is unclear. Also, little is known about the impact of CRISPR-Cas systems on bacterial evolution at the population level. Here, using Bacillus cereus sensu lato as model, we investigate the interplay between CRISPR-Cas systems and HGT at the population scale. We found that only a small fraction of the strains have CRISPR-Cas systems (13.9% of 1871), and most of such systems are defective based on their gene content analysis. Comparative genomic analysis revealed that the CRISPR-Cas systems are barriers to HGT within this group, since strains harboring active systems contain less mobile genetic elements (MGEs), have lower fraction of unique genes and also display limited environmental distributions than strains without active CRISPR-Cas systems. The introduction of a functional CRISPR-Cas system into a strain lacking the system resulted in reduced adaptability to various stresses and decreased pathogenicity of the transformant strain, indicating that B. cereus group strains could benefit from inactivating such systems. Our work provides a large-scale case to support that the CRISPR-Cas systems are barriers to HGT within species, and that in the B. cereus group the inactivation of CRISPR-Cas systems correlated with acquisition of MGEs that could result in better adaptation to diverse environments.
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Affiliation(s)
- Ziqiang Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yulan Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhiyu Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhaoxia Dong
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Chuanshuai Xie
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Alejandra Bravo
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. postal 510-3, Cuernavaca, 62250, Morelos, Mexico
| | - Mario Soberón
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. postal 510-3, Cuernavaca, 62250, Morelos, Mexico
| | - 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
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Donghai Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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35
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Bruce SA, Schiraldi NJ, Kamath PL, Easterday WR, Turner WC. A classification framework for Bacillus anthracis defined by global genomic structure. Evol Appl 2020; 13:935-944. [PMID: 32431744 PMCID: PMC7232756 DOI: 10.1111/eva.12911] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/18/2019] [Accepted: 11/14/2019] [Indexed: 12/22/2022] Open
Abstract
Bacillus anthracis, the causative agent of anthrax, is a considerable global health threat affecting wildlife, livestock, and the general public. In this study, whole-genome sequence analysis of over 350 B. anthracis isolates was used to establish a new high-resolution global genotyping framework that is both biogeographically informative and compatible with multiple genomic assays. The data presented in this study shed new light on the diverse global dissemination of this species and indicate that many lineages may be uniquely suited to the geographic regions in which they are found. In addition, we demonstrate that plasmid genomic structure for this species is largely consistent with chromosomal population structure, suggesting vertical inheritance in this bacterium has contributed to its evolutionary persistence. This classification methodology is the first based on population genomic structure for this species and has potential use for local and broader institutions seeking to understand both disease outbreak origins and recent introductions. In addition, we provide access to a newly developed genotyping script as well as the full whole-genome sequence analyses output for this study, allowing future studies to rapidly employ and append their data in the context of this global collection. This framework may act as a powerful tool for public health agencies, wildlife disease laboratories, and researchers seeking to utilize and expand this classification scheme for further investigations into B. anthracis evolution.
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Affiliation(s)
- Spencer A. Bruce
- Department of Biological SciencesUniversity at Albany – State University of New YorkAlbanyNYUSA
| | - Nicholas J. Schiraldi
- Department of Information Technology ServicesUniversity at Albany – State University of New YorkAlbanyNYUSA
| | | | - W. Ryan Easterday
- Centre for Ecological and Evolutionary SynthesisDepartment of BiosciencesUniversity of OsloOsloNorway
| | - Wendy C. Turner
- Department of Biological SciencesUniversity at Albany – State University of New YorkAlbanyNYUSA
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36
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Tsimbalyuk S, Shornikov A, Thi Bich Le V, Kuhn ML, Forwood JK. SpeG polyamine acetyltransferase enzyme from Bacillus thuringiensis forms a dodecameric structure and exhibits high catalytic efficiency. J Struct Biol 2020; 210:107506. [PMID: 32283314 DOI: 10.1016/j.jsb.2020.107506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/24/2020] [Accepted: 04/08/2020] [Indexed: 11/30/2022]
Abstract
Polyamines are important for regulating biofilms and the exopolysaccharide of the biofilm matrix of Bacillus subtilis. Understanding how enzymes can regulate polyamine concentrations is critical for learning more about how these processes occur in diverse bacteria. Here, we describe the structure and function of another member of the spermidine/spermine acetyltransferases (SSAT) found in Bacilli. The SpeG enzyme from B. thuringiensis (BtSpeG) binds polyamines in its allosteric site and adopts a dodecameric oligomeric state similar to other SpeG enzymes from Gram-negative bacteria. Our kinetic results show the catalytic efficiency of BtSpeG was greater than any previously characterized SpeG to date, and in contrast to other SpeG proteins it exhibited very similar kinetic properties toward both spermine and spermidine. Similar to the SpeG enzyme from E. coli, BtSpeG was able to acetylate spermidine on the N1 and N8 positions. The turnover of BtSpeG toward spermine and spermidine was also two to three orders of magnitude greater than any other Bacilli SSAT enzyme that has been previously characterized. SpeG proteins from Bacilli, including B. cereus, B. thuringiensis and B. anthracis share nearly identical sequences and therefore our results likely provide insight into the structure/function relationship across multiple Bacillus species.
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Affiliation(s)
- Sofiya Tsimbalyuk
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Aleksander Shornikov
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Van Thi Bich Le
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA.
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia.
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Genotyping and population diversity of Bacillus anthracis in China based on MLVA and canSNP analysis. Microbiol Res 2020; 233:126414. [PMID: 31981903 DOI: 10.1016/j.micres.2020.126414] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/16/2019] [Accepted: 01/10/2020] [Indexed: 11/23/2022]
Abstract
In pastoral parts of China, anthrax still presents a major risk to livestock and threatens the health of local human populations. Currently, whole-genome-based molecular markers, such as single-nucleotide polymorphisms (SNPs) and variable number tandem repeats (VNTRs), are the most effective tools for genotyping Bacillus anthracis. In this study, 191 isolates were selected to assess the diversity of B. anthracis in China. Five isolates were confirmed not to be B. anthracis by clustered regularly interspaced short palindromic repeat analysis, while the remaining 186 isolates were typed using canonical SNP (canSNP) and VNTR analyses. Five sublineages/subgroups, A.Br.001/002, A.Br.Vollum, A.Br.Aust.94, A.Br.Ames, and A.Br.008/009, were detected based on 13 canSNP sites. The 186 isolates were further assigned 114 sequence types based on 27 VNTR loci, with major branches correlating with the canSNP analysis. We then used a simplified multiple-locus variable number tandem repeat analysis (MLVA) protocol (MLVAmin) based on eight high-resolution VNTR sites to analyze the Chinese isolates, with the resulting phylogeny again agreeing with the canSNP analysis. We also developed two schemes, MLVAc and MLVAp, using various numbers of VNTRs to analyze different canSNP sublineages to increase the typing resolution of the canSNP protocol. The results showed a highly imbalanced geographical distribution of the B. anthracis population, with four different sublineages observed in Xinjiang Province, while only one sublineage, A.Br.001/002, was found in the other six provinces, except for three A.Br.Ames strains isolated from Inner Mongolia. Based on the MLVA and canSNP analysis, the spread of B. anthracis appears to have occurred from west to east via three independent routes.
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38
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Kindle P, Etter D, Stephan R, Johler S. Population structure and toxin gene profiles of Bacillus cereus sensu lato isolated from flour products. FEMS Microbiol Lett 2019; 366:5643888. [DOI: 10.1093/femsle/fnz240] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/22/2019] [Indexed: 12/23/2022] Open
Abstract
ABSTRACTData on the occurrence, population structure and toxinogenic potential of Bacillus cereus sensu lato isolated from flour is essential to enable improved risk assessment. We aimed to provide data on the occurrence of B. cereus sensu lato in flour products at retail level. In addition, we screened the isolates for Bacillus thuringiensis and Bacillus cytotoxicus and determined population structure and toxin gene profiles. We screened 89 flour products for presence of B. cereus sensu lato, resulting in 75 positive samples (84%). We were able to show that the population structure of members of the B. cereus group isolated from flour is highly diverse. Isolates were assigned to panC types II (4%), III (21%), IV (39%) and V (36%). Production of parasporal crystals characteristic for Bacillus thuringiensis was detected in seven isolates assigned to panC type III, IV and V. No B. cytotoxicus were detected. Two of the isolates harbored ces encoding cereulide, which causes the emetic syndrome. Various enterotoxin genes were found, with all isolates harboring nhe, 75% of isolates harboring hbl and 51% of the isolates harboring cytK-2. Our findings suggest that toxinogenic B. cereus sensu lato are common in flour products at retail level.
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Affiliation(s)
- Patrick Kindle
- Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zurich, Winterthurerstrasse 272, 8057 Zurich, Switzerland
| | - Danai Etter
- Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zurich, Winterthurerstrasse 272, 8057 Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zurich, Winterthurerstrasse 272, 8057 Zurich, Switzerland
| | - Sophia Johler
- Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zurich, Winterthurerstrasse 272, 8057 Zurich, Switzerland
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39
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Baek I, Lee K, Goodfellow M, Chun J. Comparative Genomic and Phylogenomic Analyses Clarify Relationships Within and Between Bacillus cereus and Bacillus thuringiensis: Proposal for the Recognition of Two Bacillus thuringiensis Genomovars. Front Microbiol 2019; 10:1978. [PMID: 31507580 PMCID: PMC6716467 DOI: 10.3389/fmicb.2019.01978] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 08/12/2019] [Indexed: 01/03/2023] Open
Abstract
The present study was designed to clarify the taxonomic status of two species classified as Bacillus cereus sensu lato, namely B. cereus sensu stricto and Bacillus thuringiensis. To this end, nearly 900 whole genome sequences of strains assigned to these taxa were the subject of comparative genomic and phylogenomic analyses. A phylogenomic tree based on core gene sequences showed that the type strains of B. cereus and B. thuringiensis formed a well-supported monophyletic clade that was clearly separated from corresponding clades composed of the remaining validly published species classified as B. cereus sensu lato. However, since average nucleotide identity and digital DNA-DNA hybridization similarities between the two types of Bacillus were slightly higher than the thresholds used to distinguish between closely related species we conclude that B. cereus and B. thuringiensis should continue to be recognized as validly published species. The B. thuringiensis strains were assigned to two genomically distinct groups, we propose that these taxa be recognized as genomovars, that is, as B. thuringiensis gv. thuringiensis and B. thuringiensis gv. cytolyticus. The extensive comparative genomic data clearly show that the distribution of pesticidal genes is irregular as strains identified as B. thuringiensis were assigned to several polyphyletic groups/subclades within the B. cereus-B. thuringiensis clade. Consequently, we recommend that genomic or equivalent molecular systematic features should be used to identify B. thuringiensis strains as the presence of pesticidal genes cannot be used as a diagnostic marker for this species. Comparative taxonomic studies are needed to find phenotypic properties that can be used to distinguish between the B. thuringiensis genomovars and between them and B. cereus.
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Affiliation(s)
- Inwoo Baek
- School of Biological Sciences, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Kihyun Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jongsik Chun
- School of Biological Sciences, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
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40
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Cardoso PDF, Perchat S, Vilas-Boas LA, Lereclus D, Vilas-Bôas GT. Diversity of the Rap-Phr quorum-sensing systems in the Bacillus cereus group. Curr Genet 2019; 65:1367-1381. [PMID: 31104082 DOI: 10.1007/s00294-019-00993-9] [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] [Received: 12/07/2018] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 12/20/2022]
Abstract
Bacteria of the Bacillus cereus group colonize several ecological niches and infect different hosts. Bacillus cereus, a ubiquitous species causing food poisoning, Bacillus thuringiensis, an entomopathogen, and Bacillus anthracis, which is highly pathogenic to mammals, are the most important species of this group. These species are closely related genetically, and their specific toxins are encoded by plasmids. The infectious cycle of B. thuringiensis in its insect host is regulated by quorum-sensing systems from the RNPP family. Among them, the Rap-Phr systems, which are well-described in Bacillus subtilis, regulate essential processes, such as sporulation. Given the importance of these systems, we performed a global in silico analysis to investigate their prevalence, distribution, diversity and their role in sporulation in B. cereus group species. The rap-phr genes were identified in all selected strains with 30% located on plasmids, predominantly in B. thuringiensis. Despite a high variability in their sequences, there is a remarkable association between closely related strains and their Rap-Phr profile. Based on the key residues involved in RapH phosphatase activity, we predicted that 32% of the Rap proteins could regulate sporulation by preventing the phosphorylation of Spo0F. These Rap are preferentially located on plasmids and mostly related to B. thuringiensis. The predictions were partially validated by in vivo sporulation experiments suggesting that the residues linked to the phosphatase function are necessary but not sufficient to predict this activity. The wide distribution and diversity of Rap-Phr systems could strictly control the commitment to sporulation and then improve the adaptation capacities of the bacteria to environmental changes.
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Affiliation(s)
- Priscilla de F Cardoso
- Depto. Biologia Geral, Universidade Estadual de Londrina, Londrina, Brazil.,Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Stéphane Perchat
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | | | - Didier Lereclus
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
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41
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Buisson C, Gohar M, Huillet E, Nielsen-LeRoux C. Bacillus thuringiensis Spores and Vegetative Bacteria: Infection Capacity and Role of the Virulence Regulon PlcR Following Intrahaemocoel Injection of Galleria mellonella. INSECTS 2019; 10:insects10050129. [PMID: 31060274 PMCID: PMC6571593 DOI: 10.3390/insects10050129] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/19/2019] [Accepted: 04/30/2019] [Indexed: 11/16/2022]
Abstract
Bacillus thuringiensis is an invertebrate pathogen that produces insecticidal crystal toxins acting on the intestinal barrier. In the Galleria mellonella larvae infection model, toxins from the PlcR virulence regulon contribute to pathogenicity by the oral route. While B. thuringiensis is principally an oral pathogen, bacteria may also reach the insect haemocoel following injury of the cuticle. Here, we address the question of spore virulence as compared to vegetative cells when the wild-type Bt407cry- strain and its isogenic ∆plcR mutant are inoculated directly into G. mellonella haemocoel. Mortality dose-response curves were constructed at 25 and 37 °C using spores or vegetative cell inocula, and the 50% lethal dose (LD50) in all infection conditions was determined after 48 h of infection. Our findings show that (i) the LD50 is lower for spores than for vegetative cells for both strains, while the temperature has no significant influence, and (ii) the ∆plcR mutant is four to six times less virulent than the wild-type strain in all infection conditions. Our results suggest that the environmental resistant spores are the most infecting form in haemocoel and that the PlcR virulence regulon plays an important role in toxicity when reaching the haemocoel from the cuticle and not only following ingestion.
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Affiliation(s)
- Christophe Buisson
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Michel Gohar
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Eugénie Huillet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
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42
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Phylogenetic diversity of aerobic spore-forming Bacillalles isolated from Brazilian soils. Int Microbiol 2019; 22:511-520. [PMID: 31049768 DOI: 10.1007/s10123-019-00080-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 03/20/2019] [Accepted: 04/15/2019] [Indexed: 10/26/2022]
Abstract
The phylum Firmicutes comprises seven classes where most species are either aerobic or anaerobic endospore former. Inside Firmicutes, species allocated in the genus Bacillus and related genera are collectively named aerobic endospore-forming bacteria (AEFB), and the soil is their major reservoir. AEFB have great importance in health, agriculture, and biotechnology although the more studied species are Bacillus subtilis and the human pathogens Bacillus cereus and Bacillus anthracis. AEFB have great importance in health, agriculture, and biotechnology; although the knowledge about these organisms is based on few species, notably, Bacillus subtilis, Bacillus cereus, and Bacillus anthracis. In this work, we generated partial 16S rRNA gene sequences of both strands of 192 AEFB strains isolated from soils of Distrito Federal, Brazil (SDF strains). The resulting consensus sequences were used to obtain taxonomic assignment and establish the phylogenetic relationships among these strains. Through this approach, we could observe that classified SDF strains were distributed among genera Bacillus (169 strains; 88.02%), Paenibacillus (11; 5.73%), Lysinibacillus (6; 3.13%), Brevibacillus (4; 2.08%), Terribacillus (1; 0.52%), and Rummeliibacillus (1; 0.52%). Phylogenetic trees revealed these 192 SDF strains can be segregated into eight groups spanning families Bacillaceae and Paenibacillaceae belonging to the order Bacillales. To expand the knowledge about the diversity of these SDF strains, further studies regarding characterization with different methodologies are underway.
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Ehling-Schulz M, Lereclus D, Koehler TM. The Bacillus cereus Group: Bacillus Species with Pathogenic Potential. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0032-2018. [PMID: 31111815 PMCID: PMC6530592 DOI: 10.1128/microbiolspec.gpp3-0032-2018] [Citation(s) in RCA: 235] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Indexed: 12/17/2022] Open
Abstract
The Bacillus cereus group includes several Bacillus species with closely related phylogeny. The most well-studied members of the group, B. anthracis, B. cereus, and B. thuringiensis, are known for their pathogenic potential. Here, we present the historical rationale for speciation and discuss shared and unique features of these bacteria. Aspects of cell morphology and physiology, and genome sequence similarity and gene synteny support close evolutionary relationships for these three species. For many strains, distinct differences in virulence factor synthesis provide facile means for species assignment. B. anthracis is the causative agent of anthrax. Some B. cereus strains are commonly recognized as food poisoning agents, but strains can also cause localized wound and eye infections as well as systemic disease. Certain B. thuringiensis strains are entomopathogens and have been commercialized for use as biopesticides, while some strains have been reported to cause infection in immunocompromised individuals. In this article we compare and contrast B. anthracis, B. cereus, and B. thuringiensis, including ecology, cell structure and development, virulence attributes, gene regulation and genetic exchange systems, and experimental models of disease.
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Affiliation(s)
- Monika Ehling-Schulz
- Institute of Microbiology, Department of Pathology, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Didier Lereclus
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Theresa M Koehler
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center - Houston, Houston, TX 77030
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Bağcıoğlu M, Fricker M, Johler S, Ehling-Schulz M. Detection and Identification of Bacillus cereus, Bacillus cytotoxicus, Bacillus thuringiensis, Bacillus mycoides and Bacillus weihenstephanensis via Machine Learning Based FTIR Spectroscopy. Front Microbiol 2019; 10:902. [PMID: 31105681 PMCID: PMC6498184 DOI: 10.3389/fmicb.2019.00902] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 04/09/2019] [Indexed: 12/04/2022] Open
Abstract
The Bacillus cereus group comprises genetical closely related species with variable toxigenic characteristics. However, detection and differentiation of the B. cereus group species in routine diagnostics can be difficult, expensive and laborious since current species designation is linked to specific phenotypic characteristic or the presence of species-specific genes. Especially the differentiation of Bacillus cereus and Bacillus thuringiensis, the identification of psychrotolerant Bacillus mycoides and Bacillus weihenstephanensis, as well as the identification of emetic B. cereus and Bacillus cytotoxicus, which are both producing highly potent toxins, is of high importance in food microbiology. Thus, we investigated the use of a machine learning approach, based on artificial neural network (ANN) assisted Fourier transform infrared (FTIR) spectroscopy, for discrimination of B. cereus group members. The deep learning tool box of Matlab was employed to construct a one-level ANN, allowing the discrimination of the aforementioned B. cereus group members. This model resulted in 100% correct identification for the training set and 99.5% correct identification overall. The established ANN was applied to investigate the composition of B. cereus group members in soil, as a natural habitat of B. cereus, and in food samples originating from foodborne outbreaks. These analyses revealed a high complexity of B. cereus group populations, not only in soil samples but also in the samples from the foodborne outbreaks, highlighting the importance of taking multiple isolates from samples implicated in food poisonings. Notable, in contrast to the soil samples, no bacteria belonging to the psychrotolerant B. cereus group members were detected in the food samples linked to foodborne outbreaks, while the overall abundancy of B. thuringiensis did not significantly differ between the sample categories. None of the isolates was classified as B. cytotoxicus, fostering the hypothesis that the latter species is linked to very specific ecological niches. Overall, our work shows that machine learning assisted (FTIR) spectroscopy is suitable for identification of B. cereus group members in routine diagnostics and outbreak investigations. In addition, it is a promising tool to explore the natural habitats of B. cereus group, such as soil.
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Affiliation(s)
- Murat Bağcıoğlu
- Functional Microbiology, Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Martina Fricker
- Functional Microbiology, Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Sophia Johler
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Monika Ehling-Schulz
- Functional Microbiology, Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
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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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Parulekar RS, Sonawane KD. Insights into the antibiotic resistance and inhibition mechanism of aminoglycoside phosphotransferase from
Bacillus cereus
: In silico and in vitro perspective. J Cell Biochem 2018; 119:9444-9461. [DOI: 10.1002/jcb.27261] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/22/2018] [Indexed: 01/13/2023]
Affiliation(s)
| | - Kailas Dashrath Sonawane
- Department of Microbiology Shivaji University Kolhapur Maharashtra India
- Structural Bioinformatics Unit, Department of Biochemistry Shivaji University Kolhapur Maharashtra India
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Andreou A, Giastas P, Christoforides E, Eliopoulos EE. Structural and Evolutionary Insights within the Polysaccharide Deacetylase Gene Family of Bacillus anthracis and Bacillus cereus. Genes (Basel) 2018; 9:E386. [PMID: 30065210 PMCID: PMC6115787 DOI: 10.3390/genes9080386] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 02/06/2023] Open
Abstract
Functional and folding constraints impose interdependence between interacting sites along the protein chain that are envisaged through protein sequence evolution. Studying the influence of structure in phylogenetic models requires detailed and reliable structural models. Polysaccharide deacetylases (PDAs), members of the carbohydrate esterase family 4, perform mainly metal-dependent deacetylation of O- or N-acetylated polysaccharides such as peptidoglycan, chitin and acetylxylan through a conserved catalytic core termed the NodB homology domain. Genomes of Bacillus anthracis and its relative Bacillus cereus contain multiple genes of putative or known PDAs. A comparison of the functional domains of the recently determined PDAs from B. anthracis and B. cereus and multiple amino acid and nucleotide sequence alignments and phylogenetic analysis performed on these closely related species showed that there were distinct differences in binding site formation, despite the high conservation on the protein sequence, the folding level and the active site assembly. This may indicate that, subject to biochemical verification, the binding site-forming sequence fragments are under functionally driven evolutionary pressure to accommodate and recognize distinct polysaccharide residues according to cell location, use, or environment. Finally, we discuss the suggestion of the paralogous nature of at least two genes of B. anthracis, ba0330 and ba0331, via specific differences in gene sequence, protein structure, selection pressure and available localization patterns. This study may contribute to understanding the mechanisms under which sequences evolve in their structures and how evolutionary processes enable structural variations.
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Affiliation(s)
- Athena Andreou
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
| | - Petros Giastas
- Department of Neurobiology, Hellenic Pasteur Institute, Vasilissis Sofias 127, 11521 Athens, Greece.
| | - Elias Christoforides
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
| | - Elias E Eliopoulos
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
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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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Abstract
Bacillus anthracis, the anthrax agent, is a member of the Bacillus cereus sensu lato group, which includes invasive pathogens of mammals or insects as well as nonpathogenic environmental strains. The genes for anthrax pathogenesis are located on two large virulence plasmids. Similar virulence plasmids have been acquired by other B. cereus strains and enable the pathogenesis of anthrax-like diseases. Among the virulence factors of B. anthracis is the S-layer-associated protein BslA, which endows bacilli with invasive attributes for mammalian hosts. BslA surface display and function are dependent on the bacterial S-layer, whose constituents assemble by binding to the secondary cell wall polysaccharide (SCWP) via S-layer homology (SLH) domains. B. anthracis and other pathogenic B. cereus isolates harbor genes for the secretion of S-layer proteins, for S-layer assembly, and for synthesis of the SCWP. We review here recent insights into the assembly and function of the S-layer and the SCWP.
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Affiliation(s)
- Dominique Missiakas
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois 60649.,Department of Microbiology, University of Chicago, Chicago, Illinois 60637;
| | - Olaf Schneewind
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois 60649.,Department of Microbiology, University of Chicago, Chicago, Illinois 60637;
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Carlson CJ, Getz WM, Kausrud KL, Cizauskas CA, Blackburn JK, Bustos Carrillo FA, Colwell R, Easterday WR, Ganz HH, Kamath PL, Økstad OA, Turner WC, Kolstø AB, Stenseth NC. Spores and soil from six sides: interdisciplinarity and the environmental biology of anthrax (Bacillus anthracis). Biol Rev Camb Philos Soc 2018; 93:1813-1831. [PMID: 29732670 DOI: 10.1111/brv.12420] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 03/27/2018] [Accepted: 04/03/2018] [Indexed: 12/11/2022]
Abstract
Environmentally transmitted diseases are comparatively poorly understood and managed, and their ecology is particularly understudied. Here we identify challenges of studying environmental transmission and persistence with a six-sided interdisciplinary review of the biology of anthrax (Bacillus anthracis). Anthrax is a zoonotic disease capable of maintaining infectious spore banks in soil for decades (or even potentially centuries), and the mechanisms of its environmental persistence have been the topic of significant research and controversy. Where anthrax is endemic, it plays an important ecological role, shaping the dynamics of entire herbivore communities. The complex eco-epidemiology of anthrax, and the mysterious biology of Bacillus anthracis during its environmental stage, have necessitated an interdisciplinary approach to pathogen research. Here, we illustrate different disciplinary perspectives through key advances made by researchers working in Etosha National Park, a long-term ecological research site in Namibia that has exemplified the complexities of the enzootic process of anthrax over decades of surveillance. In Etosha, the role of scavengers and alternative routes (waterborne transmission and flies) has proved unimportant relative to the long-term persistence of anthrax spores in soil and their infection of herbivore hosts. Carcass deposition facilitates green-ups of vegetation to attract herbivores, potentially facilitated by the role of anthrax spores in the rhizosphere. The underlying seasonal pattern of vegetation, and herbivores' immune and behavioural responses to anthrax risk, interact to produce regular 'anthrax seasons' that appear to be a stable feature of the Etosha ecosystem. Through the lens of microbiologists, geneticists, immunologists, ecologists, epidemiologists, and clinicians, we discuss how anthrax dynamics are shaped at the smallest scale by population genetics and interactions within the bacterial communities up to the broadest scales of ecosystem structure. We illustrate the benefits and challenges of this interdisciplinary approach to disease ecology, and suggest ways anthrax might offer insights into the biology of other important pathogens. Bacillus anthracis, and the more recently emerged Bacillus cereus biovar anthracis, share key features with other environmentally transmitted pathogens, including several zoonoses and panzootics of special interest for global health and conservation efforts. Understanding the dynamics of anthrax, and developing interdisciplinary research programs that explore environmental persistence, is a critical step forward for understanding these emerging threats.
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Affiliation(s)
- Colin J Carlson
- National Socio-Environmental Synthesis Center (SESYNC), University of Maryland, Annapolis, MD 21401, U.S.A.,Department of Biology, Georgetown University, Washington, DC 20057, U.S.A
| | - Wayne M Getz
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, U.S.A.,School of Mathematical Sciences, University of KwaZulu-Natal, PB X 54001, Durban 4000, South Africa
| | - Kyrre L Kausrud
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316, Oslo, Norway
| | - Carrie A Cizauskas
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, U.S.A
| | - Jason K Blackburn
- Spatial Epidemiology & Ecology Research Lab, Department of Geography, University of Florida, Gainesville, FL 32611, U.S.A.,Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
| | - Fausto A Bustos Carrillo
- Department of Epidemiology & Department of Biostatistics, School of Public Health, University of California, Berkeley, CA 94720-7360, U.S.A
| | - Rita Colwell
- CosmosID Inc., Rockville, MD 20850, U.S.A.,Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, U.S.A.,Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, U.S.A
| | - W Ryan Easterday
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316, Oslo, Norway
| | - Holly H Ganz
- UC Davis Genome Center, University of California, Davis, CA 95616, U.S.A
| | - Pauline L Kamath
- School of Food and Agriculture, University of Maine, Orono, ME 04469, U.S.A
| | - Ole A Økstad
- Centre for Integrative Microbial Evolution and Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, PO Box 1068 Blindern, N-0316, Oslo, Norway
| | - Wendy C Turner
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, U.S.A
| | - Anne-Brit Kolstø
- Centre for Integrative Microbial Evolution and Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, PO Box 1068 Blindern, N-0316, Oslo, Norway
| | - Nils C Stenseth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316, Oslo, Norway
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