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Sun Kim B, Ko EJ, Choi J, Chang Y, Bai J. Isolation, characterization, and application of a lytic bacteriophage SSP49 to control Staphylococcus aureus contamination on baby spinach leaves. Food Res Int 2024; 192:114848. [PMID: 39147476 DOI: 10.1016/j.foodres.2024.114848] [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: 04/16/2024] [Revised: 07/22/2024] [Accepted: 07/26/2024] [Indexed: 08/17/2024]
Abstract
Staphylococcus aureus, a major foodborne pathogen, is frequently detected in fresh produce. It often causes food poisoning accompanied by abdominal pain, diarrhea, and vomiting. Additionally, the abuse of antibiotics to control S. aureus has resulted in the emergence of antibiotics-resistant bacteria, such as methicillin resistant S. aureus. Therefore, bacteriophage, a natural antimicrobial agent, has been suggested as an alternative to antibiotics. In this study, a lytic phage SSP49 that specifically infects S. aureus was isolated from a sewage sample, and its morphological, biological, and genetic characteristics were determined. We found that phage SSP49 belongs to the Straboviridae family (Caudoviricetes class) and maintained host growth inhibition for 30 h in vitro. In addition, it showed high host specificity and a broad host range against various S. aureus strains. Receptor analysis revealed that phage SSP49 utilized cell wall teichoic acid as a host receptor. Whole genome sequencing revealed that the genome size of SSP49 was 137,283 bp and it contained 191 open reading frames. The genome of phage SSP49 did not contain genes related to lysogen formation, bacterial toxicity, and antibiotic resistance, suggesting its safety in food application. The activity of phage SSP49 was considerably stable under various high temperature and pH conditions. Furthermore, phage SSP49 effectively inhibited S. aureus growth on baby spinach leaves both at 4 °C and 25 °C while maintaining the numbers of active phage during treatments (reductions of 1.2 and 2.1 log CFU/cm2, respectively). Thus, this study demonstrated the potential of phage SSP49 as an alternative natural biocontrol agent against S. aureus contamination in fresh produce.
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Affiliation(s)
- Bong Sun Kim
- Department of Food Science and Technology, Seoul Women's University, 621, Hwarangro, Nowon-gu, Seoul 01797, Republic of Korea
| | - Eun-Jin Ko
- Department of Food Science and Technology, Seoul Women's University, 621, Hwarangro, Nowon-gu, Seoul 01797, Republic of Korea
| | - Jieun Choi
- Department of Food and Nutrition, College of Science and Technology, Kookmin University, Seoul 02707, Republic of Korea
| | - Yoonjee Chang
- Department of Food and Nutrition, College of Science and Technology, Kookmin University, Seoul 02707, Republic of Korea
| | - Jaewoo Bai
- Department of Food Science and Technology, Seoul Women's University, 621, Hwarangro, Nowon-gu, Seoul 01797, Republic of Korea.
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2
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Hyde JR, Armond T, Herring JA, Hope S, Grose JH, Breakwell DP, Pickett BE. Diversity and conservation of the genome architecture of phages infecting the Alphaproteobacteria. Microbiol Spectr 2024; 12:e0282723. [PMID: 37991376 PMCID: PMC10783043 DOI: 10.1128/spectrum.02827-23] [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: 07/11/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE This study reports the results of the largest analysis of genome sequences from phages that infect the Alphaproteobacteria class of bacterial hosts. We analyzed over 100 whole genome sequences of phages to construct dotplots, categorize them into genetically distinct clusters, generate a bootstrapped phylogenetic tree, compute protein orthologs, and predict packaging strategies. We determined that the phage sequences primarily cluster by the bacterial host family, phage morphotype, and genome size. We expect that the findings reported in this seminal study will facilitate future analyses that will improve our knowledge of the phages that infect these hosts.
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Affiliation(s)
- Jonathan R. Hyde
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Thomas Armond
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Jacob A. Herring
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Sandra Hope
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Julianne H. Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Donald P. Breakwell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Brett E. Pickett
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
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Tian R, Xu S, Li P, Li M, Liu Y, Wang K, Liu G, Li Y, Dai L, Zhang W. Characterization of G-type Clostridium perfringens bacteriophages and their disinfection effect on chicken meat. Anaerobe 2023; 81:102736. [PMID: 37196842 DOI: 10.1016/j.anaerobe.2023.102736] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 04/27/2023] [Accepted: 05/01/2023] [Indexed: 05/19/2023]
Abstract
OBJECTIVE Clostridium perfringens is one of most important bacterial pathogens in the poultry industry and mainly causes necrotizing enteritis (NE). This pathogen and its toxins can cause foodborne diseases in humans through the food chain. In China, with the rise of antibiotic resistance and the banning of antibiotic growth promoters (AGPs) in poultry farming, food contamination and NE are becoming more prevalent. Bacteriophages are a viable technique to control C. perfringens as an alternative to antibiotics. We isolated Clostridium phage from the environment, providing a new method for the prevention of NE and C. perfringens contamination in meat. METHODS In this study, we selected C. perfringens strains from various regions and animal sources in China for phage isolation. The biological characteristics of Clostridium phage were studied in terms of host range, MOI, one-step curve, temperature and pH stability. We sequenced and annotated the genome of the Clostridium phage and performed phylogenetic and pangenomic analyses. Finally, we studied its antibacterial activity against bacterial culture and its disinfection effect against C. perfringens in meat. RESULTS A Clostridium phage, named ZWPH-P21 (P21), was isolated from chicken farm sewage in Jiangsu, China. P21 has been shown to specifically lyse C. perfringens type G. Further analysis of basic biological characteristics showed that P21 was stable under the conditions of pH 4-11 and temperature 4-60 °C, and the optimal multiple severity of infection (MOI) was 0.1. In addition, P21 could form a "halo" on agar plates, suggesting that the phage may encode depolymerase. Genome sequence analysis showed that P21 was the most closely related to Clostridium phage CPAS-15 belonging to the Myoviridae family, with a recognition rate of 97.24% and a query coverage rate of 98%. No virulence factors or drug resistance genes were found in P21. P21 showed promising antibacterial activity in vitro and in chicken disinfection experiments. In conclusion, P21 has the potential to be used for preventing and controlling C. perfringens in chicken food production.
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Affiliation(s)
- Rui Tian
- The Sanya Institute of Nanjing Agricultural University, Yabulun Industrial Park, Yazhou Bay Science and Technology City, Sanya, 572024, China; College of Veterinary Medicine, Nanjing Agricultural University, No.1 Weigang, Xuanwu District, Nanjing City, 210095, China
| | - Sixiang Xu
- The Sanya Institute of Nanjing Agricultural University, Yabulun Industrial Park, Yazhou Bay Science and Technology City, Sanya, 572024, China; College of Veterinary Medicine, Nanjing Agricultural University, No.1 Weigang, Xuanwu District, Nanjing City, 210095, China
| | - Pei Li
- The Sanya Institute of Nanjing Agricultural University, Yabulun Industrial Park, Yazhou Bay Science and Technology City, Sanya, 572024, China; College of Veterinary Medicine, Nanjing Agricultural University, No.1 Weigang, Xuanwu District, Nanjing City, 210095, China
| | - Mengxuan Li
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong Province, Jinan, 250100, China
| | - Yuqing Liu
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong Province, Jinan, 250100, China
| | - Kaicheng Wang
- China Animal Health and Epidemiology Center, 369 Nanjing Road, Qingdao, Shandong Province, China
| | - Guangjin Liu
- The Sanya Institute of Nanjing Agricultural University, Yabulun Industrial Park, Yazhou Bay Science and Technology City, Sanya, 572024, China; College of Veterinary Medicine, Nanjing Agricultural University, No.1 Weigang, Xuanwu District, Nanjing City, 210095, China
| | - Yubao Li
- Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China
| | - Lei Dai
- Hainan Animal Disease Prevention and Control Center, 16 Xingdan Road, Haikou, China.
| | - Wei Zhang
- The Sanya Institute of Nanjing Agricultural University, Yabulun Industrial Park, Yazhou Bay Science and Technology City, Sanya, 572024, China; College of Veterinary Medicine, Nanjing Agricultural University, No.1 Weigang, Xuanwu District, Nanjing City, 210095, China.
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4
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Węglewska M, Barylski J, Wojnarowski F, Nowicki G, Łukaszewicz M. Genome, biology and stability of the Thurquoise phage – A new virus from the Bastillevirinae subfamily. Front Microbiol 2023; 14:1120147. [PMID: 36998400 PMCID: PMC10043171 DOI: 10.3389/fmicb.2023.1120147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/17/2023] [Indexed: 03/18/2023] Open
Abstract
Bacteriophages from the Bastillevirinae subfamily (Herelleviridae family) have proven to be effective against bacteria from the Bacillus genus including organisms from the B. cereus group, which cause food poisoning and persistent contamination of industrial installations. However, successful application of these phages in biocontrol depends on understanding of their biology and stability in different environments. In this study, we isolated a novel virus from garden soil in Wrocław (Poland) and named it ‘Thurquoise’. The genome of that phage was sequenced and assembled into a single continuous contig with 226 predicted protein-coding genes and 18 tRNAs. The cryo-electron microscopy revealed that Thurquoise has complex virion structure typical for the Bastillevirinae family. Confirmed hosts include selected bacteria from the Bacillus cereus group–specifically B. thuringiensis (isolation host) and B. mycoides, but susceptible strains display different efficiency of plating (EOP). The eclipse and latent periods of Thurquoise in the isolation host last ~ 50 min and ~ 70 min, respectively. The phage remains viable for more than 8 weeks in variants of the SM buffer with magnesium, calcium, caesium, manganese or potassium and can withstand numerous freeze–thaw cycles if protected by the addition of 15% glycerol or, to a lesser extent, 2% gelatine. Thus, with proper buffer formulation, this virus can be safely stored in common freezers and refrigerators for a considerable time. The Thurquoise phage is the exemplar of a new candidate species within the Caeruleovirus genus in the Bastillevirinae subfamily of the Herelleviridae family with a genome, morphology and biology typical for these taxa.
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Affiliation(s)
- Martyna Węglewska
- Department of Molecular Virology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Jakub Barylski
- Department of Molecular Virology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
- *Correspondence: Jakub Barylski,
| | - Filip Wojnarowski
- Department of Molecular Virology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | | | - Marcin Łukaszewicz
- Department of Biotransformation, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
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5
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More's the Same-Multiple Hosts Do Not Select for Broader Host Range Phages. Viruses 2023; 15:v15020518. [PMID: 36851732 PMCID: PMC9960766 DOI: 10.3390/v15020518] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
Bacteriophage host range is a result of the interactions between phages and their hosts. For phage therapy, phages with a broader host range are desired so that a phage can infect and kill the broadest range of pathogen strains or related species possible. A common, but not well-tested, belief is that using multiple hosts during the phage isolation will make the isolation of broader host range phage more likely. Using a Bacillus cereus group system, we compared the host ranges of phages isolated on one or four hosts and found that there was no difference in the breadth of host ranges of the isolated phages. Both narrow and broader host range phage were also equally likely to be isolated from either isolation procedure. While there are methods that reliably isolate broader host range phages, such as sequential host isolation, and there are other reasons to use multiple hosts during isolation, multiple hosts are not a consistent way to obtain broader host range phages.
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6
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Abraha HB, Lee JW, Kim G, Ferdiansyah MK, Ramesha RM, Kim KP. Genomic diversity and comprehensive taxonomical classification of 61 Bacillus subtilis group member infecting bacteriophages, and the identification of ortholog taxonomic signature genes. BMC Genomics 2022; 23:835. [PMID: 36526963 PMCID: PMC9756591 DOI: 10.1186/s12864-022-09055-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Despite the applications of Bacillus subtilis group species in various sectors, limited information is available regarding their phages. Here, 61 B. subtilis group species-infecting phages (BSPs) were studied for their taxonomic classification considering the genome-size, genomic diversity, and the host, followed by the identification of orthologs taxonomic signature genes. RESULTS BSPs have widely ranging genome sizes that can be bunched into groups to demonstrate correlations to family and subfamily classifications. Comparative analysis re-confirmed the existing, BSPs-containing 14 genera and 21 species and displayed inter-genera similarities within existing subfamilies. Importantly, it also revealed the need for the creation of new taxonomic classifications, including 28 species, nine genera, and two subfamilies (New subfamily1 and New subfamily2) to accommodate inter-genera relatedness. Following pangenome analysis, no ortholog shared by all BSPs was identified, while orthologs, namely, the tail fibers/spike proteins and poly-gamma-glutamate hydrolase, that are shared by more than two-thirds of the BSPs were identified. More importantly, major capsid protein (MCP) type I, MCP type II, MCP type III and peptidoglycan binding proteins that are distinctive orthologs for Herelleviridae, Salasmaviridae, New subfamily1, and New subfamily2, respectively, were identified and analyzed which could serve as signatures to distinguish BSP members of the respective taxon. CONCLUSIONS In this study, we show the genomic diversity and propose a comprehensive classification of 61 BSPs, including the proposition for the creation of two new subfamilies, followed by the identification of orthologs taxonomic signature genes, potentially contributing to phage taxonomy.
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Affiliation(s)
- Haftom Baraki Abraha
- Department of Food Science and Technology, Jeonbuk National University, Jeonju, 54896, South Korea
| | - Jae-Won Lee
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, 54896, South Korea
| | - Gayeong Kim
- Department of Food Science and Technology, Jeonbuk National University, Jeonju, 54896, South Korea
| | | | | | - Kwang-Pyo Kim
- Department of Food Science and Technology, Jeonbuk National University, Jeonju, 54896, South Korea.
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, 54896, South Korea.
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Sozhamannan S, Hofmann ER. The State of the Art in Biodefense Related Bacterial Pathogen Detection Using Bacteriophages: How It Started and How It's Going. Viruses 2020; 12:v12121393. [PMID: 33291831 PMCID: PMC7762055 DOI: 10.3390/v12121393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/23/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
Accurate pathogen detection and diagnosis is paramount in clinical success of treating patients. There are two general paradigms in pathogen detection: molecular and immuno-based, and phage-based detection is a third emerging paradigm due to its sensitivity and selectivity. Molecular detection methods look for genetic material specific for a given pathogen in a sample usually by polymerase chain reaction (PCR). Immuno-methods look at the pathogen components (antigens) by antibodies raised against that pathogen specific antigens. There are different variations and products based on these two paradigms with advantages and disadvantages. The third paradigm at least for bacterial pathogen detection entails bacteriophages specific for a given bacterium. Sensitivity and specificity are the two key parameters in any pathogen detection system. By their very nature, bacteriophages afford the best sensitivity for bacterial detection. Bacteria and bacteriophages form the predator-prey pair in the evolutionary arms race and has coevolved over time to acquire the exquisite specificity of the pair, in some instances at the strain level. This specificity has been exploited for diagnostic purposes of various pathogens of concern in clinical and other settings. Many recent reviews focus on phage-based detection and sensor technologies. In this review, we focus on a very special group of pathogens that are of concern in biodefense because of their potential misuse in bioterrorism and their extremely virulent nature and as such fall under the Centers for Disease and Prevention (CDC) Category A pathogen list. We describe the currently available phage methods that are based on the usual modalities of detection from culture, to molecular and immuno- and fluorescent methods. We further highlight the gaps and the needs for more modern technologies and sensors drawing from technologies existing for detection and surveillance of other pathogens of clinical relevance.
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Affiliation(s)
- Shanmuga Sozhamannan
- National Security Science & Technology, Management Advisory Services, Logistics Management Institute, 7940 Jones Branch Drive, Tysons, VA 22102, USA;
- Defense Biological Product Assurance Office (DBPAO), Joint Program Executive Office (JPEO) for Chemical, Biological, Radiological and Nuclear Defense (CBRND) Joint Project Lead (JPL) CBRND Enabling Biotechnologies (EB), 110 Thomas Johnson Drive, Suite 250, Frederick, MD 21702, USA
| | - Edward R. Hofmann
- EXCET, Inc., 6225 Brandon Ave #360, Springfield, VA 22150, USA
- US Army Combat Capabilities Development Command, Chemical Biological Center, 8908 Guard St, E3831, Edgewood, MD 21010, USA
- Correspondence:
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Classifying the Unclassified: A Phage Classification Method. Viruses 2019; 11:v11020195. [PMID: 30813498 PMCID: PMC6409715 DOI: 10.3390/v11020195] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/06/2019] [Accepted: 02/20/2019] [Indexed: 01/21/2023] Open
Abstract
This work reports the method ClassiPhage to classify phage genomes using sequence derived taxonomic features. ClassiPhage uses a set of phage specific Hidden Markov Models (HMMs) generated from clusters of related proteins. The method was validated on all publicly available genomes of phages that are known to infect Vibrionaceae. The phages belong to the well-described phage families of Myoviridae, Podoviridae, Siphoviridae, and Inoviridae. The achieved classification is consistent with the assignments of the International Committee on Taxonomy of Viruses (ICTV), all tested phages were assigned to the corresponding group of the ICTV-database. In addition, 44 out of 58 genomes of Vibrio phages not yet classified could be assigned to a phage family. The remaining 14 genomes may represent phages of new families or subfamilies. Comparative genomics indicates that the ability of the approach to identify and classify phages is correlated to the conserved genomic organization. ClassiPhage classifies phages exclusively based on genome sequence data and can be applied on distinct phage genomes as well as on prophage regions within host genomes. Possible applications include (a) classifying phages from assembled metagenomes; and (b) the identification and classification of integrated prophages and the splitting of phage families into subfamilies.
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Rahimi-Midani A, Kim KH, Lee SW, Jung SB, Choi TJ. Isolation and Characterization of a Bacteriophage Preying an Antifungal Bacterium. THE PLANT PATHOLOGY JOURNAL 2016; 32:584-588. [PMID: 27904467 PMCID: PMC5117869 DOI: 10.5423/ppj.nt.07.2016.0153] [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: 07/11/2016] [Revised: 08/01/2016] [Accepted: 08/04/2016] [Indexed: 06/06/2023]
Abstract
Several Bacillus species were isolated from rice field soils, and 16S rRNA gene sequence analysis showed that Bacillus cereus was the most abundant. A strain named BC1 showed antifungal activity against Rhizoctonia solani. Bacteriophages infecting strain BC1 were isolated from the same soil sample. The isolated phage PK16 had an icosahedral head of 100 ± 5 nm and tail of 200 ± 5 nm, indicating that it belonged to the family Myoviridae. Analysis of the complete linear dsDNA genome revealed a 158,127-bp genome with G + C content of 39.9% comprising 235 open reading frames as well as 19 tRNA genes (including 1 pseudogene). Blastp analysis showed that the proteins encoded by the PK16 genome had the closest hits to proteins of seven different bacteriophages. A neighbor-joining phylogenetic tree based on the major capsid protein showed a robust clustering of phage PK16 with phage JBP901 and BCP8-2 isolated from Korean fermented food.
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Affiliation(s)
| | - Kyoung-Ho Kim
- Department of Microbiology, Pukyong National University, Busan 48547,
Korea
| | - Seon-Woo Lee
- Department of Applied Biology, Dong-A University, Busan 49315,
Korea
| | - Sang Bong Jung
- Department of Clinical Laboratory Science, Dong-Eui Institute of Technology, Busan 47230,
Korea
| | - Tae-Jin Choi
- Department of Microbiology, Pukyong National University, Busan 48547,
Korea
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10
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Abstract
Bacillus cereus is an opportunistic foodborne pathogen. The phage vB_BceS-MY192 was isolated from B. cereus 192 in a cooked rice sample. The temperate phage belongs to the Siphoviridae family, Caudovirales order. Here we announce the phage genome sequence and its annotation, which may expand the understanding of B. cereus siphophages.
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11
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Genomic characterization and comparison of seven Myoviridae bacteriophage infecting Bacillus thuringiensis. Virology 2016; 489:243-51. [DOI: 10.1016/j.virol.2015.12.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 08/02/2015] [Accepted: 12/22/2015] [Indexed: 11/18/2022]
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12
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Asare PT, Jeong TY, Ryu S, Klumpp J, Loessner MJ, Merrill BD, Kim KP. Putative type 1 thymidylate synthase and dihydrofolate reductase as signature genes of a novel Bastille-like group of phages in the subfamily Spounavirinae. BMC Genomics 2015; 16:582. [PMID: 26250905 PMCID: PMC4528723 DOI: 10.1186/s12864-015-1757-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 07/07/2015] [Indexed: 12/12/2022] Open
Abstract
Background Spounavirinae viruses have received an increasing interest as tools for the control of harmful bacteria due to their relatively broad host range and strictly virulent phenotype. Results In this study, we collected and analyzed the complete genome sequences of 61 published phages, either ICTV-classified or candidate members of the Spounavirinae subfamily of the Myoviridae. A set of comparative analyses identified a distinct, recently proposed Bastille-like phage group within the Spounavirinae. More importantly, type 1 thymidylate synthase (TS1) and dihydrofolate reductase (DHFR) genes were shown to be unique for the members of the proposed Bastille-like phage group, and are suitable as molecular markers. We also show that the members of this group encode beta-lactamase and/or sporulation-related SpoIIIE homologs, possibly questioning their suitability as biocontrol agents. Conclusions We confirm the creation of a new genus—the “Bastille-like group”—in Spounavirinae, and propose that the presence of TS1- and DHFR-encoding genes could serve as signatures for the new Bastille-like group. In addition, the presence of metallo-beta-lactamase and/or SpoIIIE homologs in all members of Bastille-like group phages makes questionable their suitability for use in biocontrol. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1757-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paul Tetteh Asare
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea.
| | - Tae-Yong Jeong
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea.
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, Korea. .,Department of Agricultural Biotechnology, Center for Agricultural Biomaterials, Seoul National University, Seoul, Korea. .,Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Korea.
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland.
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland.
| | - Bryan D Merrill
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA.
| | - Kwang-Pyo Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea.
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13
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Asare PT, Bandara N, Jeong TY, Ryu S, Klumpp J, Kim KP. Complete genome sequence analysis and identification of putative metallo-beta-lactamase and SpoIIIE homologs in Bacillus cereus group phage BCP8-2, a new member of the proposed Bastille-like group. Arch Virol 2015; 160:2647-50. [PMID: 26234184 DOI: 10.1007/s00705-015-2548-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 07/20/2015] [Indexed: 11/25/2022]
Abstract
Bacillus cereus group-specific bacteriophage BCP8-2 exhibits a broad lysis spectrum among food and human isolates (330/364) of B. cereus while not infecting B. subtilis (50) or B. licheniformis (12) strains. Its genome is 159,071 bp long with 220 open reading frames, including genes for putative methyltransferases, metallo-beta-lactamase, and a sporulation-related SpoIIIE homolog, as wells as 18 tRNAs. Comparative genome analysis showed that BCP8-2 is related to the recently proposed Bastille-like phages, but not with either SPO1-like or Twort-like phages of the subfamily Spounavirinae.
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Affiliation(s)
- Paul Tetteh Asare
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea
| | - Nadeeka Bandara
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea
| | - Tae-Yong Jeong
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Center for Agricultural Biomaterials, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Korea.,Department of Agricultural Biotechnology, Center for Agricultural Biomaterials, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Kwang-Pyo Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea.
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Pope WH, Bowman CA, Russell DA, Jacobs-Sera D, Asai DJ, Cresawn SG, Jacobs WR, Hendrix RW, Lawrence JG, Hatfull GF. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. eLife 2015; 4:e06416. [PMID: 25919952 PMCID: PMC4408529 DOI: 10.7554/elife.06416] [Citation(s) in RCA: 247] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 03/19/2015] [Indexed: 01/21/2023] Open
Abstract
The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery. DOI:http://dx.doi.org/10.7554/eLife.06416.001 Viruses are unable to replicate independently. To generate copies of itself, a virus must instead invade a target cell and commandeer that cell's replication machinery. Different viruses are able to invade different types of cell, and a group of viruses known as bacteriophages (or phages for short) replicate within bacteria. The enormous number and diversity of phages in the world means that they play an important role in virtually every ecosystem. Despite their importance, relatively little is known about how different phage populations are related to each other and how they evolved. Many phages contain their genetic information in the form of strands of DNA. Using genetic sequencing to find out where and how different genes are encoded in the DNA can reveal information about how different viruses are related to each other. These relationships are particularly complicated in phages, as they can exchange genes with other viruses and microbes. Previous studies comparing the genomes—the complete DNA sequence—of reasonably small numbers of phages that infect the Mycobacterium group of bacteria have found that the phages can be sorted into ‘clusters’ based on similarities in their genes and where these are encoded in their DNA. However, the number of phages investigated so far has been too small to conclude how different clusters are related. Are the clusters separate, or do they form a ‘continuum’ with different genes and DNA sequences shared between different clusters? Here, Pope, Bowman, Russell et al. compare the individual genomes of 627 bacteriophages that infect the bacterial species Mycobacterium smegmatis. This is by far the largest number of phage genomes analyzed from a single host species. The large number of genomes analyzed allowed a much clearer understanding of the complexity and diversity of these phages to be obtained. The isolation, sequencing and analysis of the hundreds of M. smegmatis bacteriophage genomes was performed by an integrated research and education program, called the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program. This enabled thousands of undergraduate students from different institutions to contribute to the phage discovery and sequencing project, and co-author the report. SEA-PHAGES therefore shows that it is possible to successfully incorporate genuine scientific research into an undergraduate course, and that doing so can benefit both the students and researchers involved. The results show that while the genomes could be categorized into 28 clusters, the genomes are not completely unrelated. Instead, a spread of diversity is seen, as genes and groups of genes are shared between different clusters. Pope, Bowman, Russell et al. further reveal that the phage population is in a constant state of change, and continuously acquires genes from other microorganisms and viruses. DOI:http://dx.doi.org/10.7554/eLife.06416.002
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Affiliation(s)
- Welkin H Pope
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
| | - Charles A Bowman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
| | - David J Asai
- Howard Hughes Medical Institute, Chevy Chase, United States
| | - Steven G Cresawn
- Department of Biology, James Madison University, Harrisonburg, United States
| | - William R Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, United States
| | - Roger W Hendrix
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
| | - Jeffrey G Lawrence
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
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Grose JH, Jensen GL, Burnett SH, Breakwell DP. Correction: genomic comparison of 93 Bacillus phages reveals 12 clusters, 14 singletons and remarkable diversity. BMC Genomics 2014; 15:1184. [PMID: 25547158 PMCID: PMC4464726 DOI: 10.1186/1471-2164-15-1184] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 12/04/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The Bacillus genus of Firmicutes bacteria is ubiquitous in nature and includes one of the best characterized model organisms, B. subtilis, as well as medically significant human pathogens, the most notorious being B. anthracis and B. cereus. As the most abundant living entities on the planet, bacteriophages are known to heavily influence the ecology and evolution of their hosts, including providing virulence factors. Thus, the identification and analysis of Bacillus phages is critical to understanding the evolution of Bacillus species, including pathogenic strains. RESULTS Whole genome nucleotide and proteome comparison of the 83 extant, fully sequenced Bacillus phages revealed 10 distinct clusters, 24 subclusters and 15 singleton phages. Host analysis of these clusters supports host boundaries at the subcluster level and suggests phages as vectors for genetic transfer within the Bacillus cereus group, with B. anthracis as a distant member. Analysis of the proteins conserved among these phages reveals enormous diversity and the uncharacterized nature of these phages, with a total of 4,442 protein families (phams) of which only 894 (20%) had a predicted function. In addition, 2,583 (58%) of phams were orphams (phams containing a single member). The most populated phams were those encoding proteins involved in DNA metabolism, virion structure and assembly, cell lysis, or host function. These included several genes that may contribute to the pathogenicity of Bacillus strains. CONCLUSIONS This analysis provides a basis for understanding and characterizing Bacillus and other related phages as well as their contributions to the evolution and pathogenicity of Bacillus cereus group bacteria. The presence of sparsely populated clusters, the high ratio of singletons to clusters, and the large number of uncharacterized, conserved proteins confirms the need for more Bacillus phage isolation in order to understand the full extent of their diversity as well as their impact on host evolution.
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Affiliation(s)
- Julianne H Grose
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, UT, USA.
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Jończyk-Matysiak E, Kłak M, Weber-Dąbrowska B, Borysowski J, Górski A. Possible use of bacteriophages active against Bacillus anthracis and other B. cereus group members in the face of a bioterrorism threat. BIOMED RESEARCH INTERNATIONAL 2014; 2014:735413. [PMID: 25247187 PMCID: PMC4163355 DOI: 10.1155/2014/735413] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/25/2014] [Accepted: 07/25/2014] [Indexed: 12/14/2022]
Abstract
Anthrax is an infectious fatal disease with epidemic potential. Nowadays, bioterrorism using Bacillus anthracis is a real possibility, and thus society needs an effective weapon to neutralize this threat. The pathogen may be easily transmitted to human populations. It is easy to store, transport, and disseminate and may survive for many decades. Recent data strongly support the effectiveness of bacteriophage in treating bacterial diseases. Moreover, it is clear that bacteriophages should be considered a potential incapacitative agent against bioterrorism using bacteria belonging to B. cereus group, especially B. anthracis. Therefore, we have reviewed the possibility of using bacteriophages active against Bacillus anthracis and other species of the B. cereus group in the face of a bioterrorism threat.
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Affiliation(s)
- Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
| | - Marlena Kłak
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
| | - Beata Weber-Dąbrowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
| | - Jan Borysowski
- Department of Clinical Immunology, Transplantation Institute, The Medical University of Warsaw, Nowogrodzka 59, 02-006 Warsaw, Poland
| | - Andrzej Górski
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
- Department of Clinical Immunology, Transplantation Institute, The Medical University of Warsaw, Nowogrodzka 59, 02-006 Warsaw, Poland
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17
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The odd one out: Bacillus ACT bacteriophage CP-51 exhibits unusual properties compared to related Spounavirinae W.Ph. and Bastille. Virology 2014; 462-463:299-308. [DOI: 10.1016/j.virol.2014.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 05/23/2014] [Accepted: 06/11/2014] [Indexed: 11/19/2022]
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Gillis A, Mahillon J. Phages preying on Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis: past, present and future. Viruses 2014; 6:2623-72. [PMID: 25010767 PMCID: PMC4113786 DOI: 10.3390/v6072623] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/19/2014] [Accepted: 06/18/2014] [Indexed: 01/18/2023] Open
Abstract
Many bacteriophages (phages) have been widely studied due to their major role in virulence evolution of bacterial pathogens. However, less attention has been paid to phages preying on bacteria from the Bacillus cereus group and their contribution to the bacterial genetic pool has been disregarded. Therefore, this review brings together the main information for the B. cereus group phages, from their discovery to their modern biotechnological applications. A special focus is given to phages infecting Bacillus anthracis, B. cereus and Bacillus thuringiensis. These phages belong to the Myoviridae, Siphoviridae, Podoviridae and Tectiviridae families. For the sake of clarity, several phage categories have been made according to significant characteristics such as lifestyles and lysogenic states. The main categories comprise the transducing phages, phages with a chromosomal or plasmidial prophage state, γ-like phages and jumbo-phages. The current genomic characterization of some of these phages is also addressed throughout this work and some promising applications are discussed here.
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Affiliation(s)
- Annika Gillis
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, Croix du Sud 2, L7.05.12, B-1348 Louvain-la-Neuve, Belgium.
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, Croix du Sud 2, L7.05.12, B-1348 Louvain-la-Neuve, Belgium.
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Gillis A, Mahillon J. Prevalence, genetic diversity, and host range of tectiviruses among members of the Bacillus cereus group. Appl Environ Microbiol 2014; 80:4138-52. [PMID: 24795369 PMCID: PMC4068676 DOI: 10.1128/aem.00912-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 04/25/2014] [Indexed: 11/20/2022] Open
Abstract
GIL01, Bam35, GIL16, AP50, and Wip1 are tectiviruses preying on the Bacillus cereus group. Despite the significant contributions of phages in different biological processes, little is known about the dealings taking place between tectiviruses and their Gram-positive bacterial hosts. Therefore, this work focuses on characterizing the interactions between tectiviruses and the B. cereus group by assessing their occurrence and genetic diversity and evaluating their host range. To study the occurrence of tectiviruses in the B. cereus group, 2,000 isolates were evaluated using primers designed to be specific to two variable regions detected in previously described elements. PCR and propagation tests revealed that tectivirus-like elements occurred in less than 3% of the isolates. Regardless of this limited distribution, several novel tectiviruses were found, and partial DNA sequencing indicated that a greater diversity exists within the family Tectiviridae. Analyses of the selected variable regions, along with their host range, showed that tectiviruses in the B. cereus group can be clustered mainly into two different groups: the ones infecting B. anthracis and those isolated from other B. cereus group members. In order to address the host range of some novel tectiviruses, 120 strains were tested for sensitivity. The results showed that all the tested tectiviruses produced lysis in at least one B. cereus sensu lato strain. Moreover, no simple relationship between the infection patterns of the tectiviruses and their diversity was found.
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Affiliation(s)
- Annika Gillis
- Laboratory of Food and Environmental Microbiology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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