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Ferreira RM, Dos Santos Silva DH, Silva KF, de Melo Monteiro J, Ferreira GF, Silva MRC, da Silva LCN, de Castro Oliveira L, Monteiro AS. Draft genome sequence of Staphylococcus aureus sequence type 5 SA01 isolated from bloodstream infection and comparative analysis with reference strains. Funct Integr Genomics 2023; 23:288. [PMID: 37653266 DOI: 10.1007/s10142-023-01204-y] [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: 06/19/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 09/02/2023]
Abstract
A Staphylococcus aureus isolate (SA01) obtained from bloodstream infection exhibited a remarkable drug resistance profile. In this study, we report the draft genome sequence of S. aureus ST 5 SA01, a multidrug-resistant isolate, and analyzed the genes associated with drug resistance and virulence. The genome sketch of S. aureus ST5 SA01 was sequenced with Illumina and annotated using the Prokka software. Rapid Annotation Subsystem Technology (RAST) was used to verify the gene functions in the genome subsystems. The Comprehensive Antibiotic Resistance Database (CARD) and Virulence Factor Database (VFDB) were used in the analysis. The RAST indicated a contribution of 25 proteins to host adenine, fibronectin-binding protein A (FnbA), and biofilm formation as an intercellular polysaccharide adhesive system (PIA). The MLST indicated that S. aureus ST 5 SA01 belongs to ST5 (CC5). In silico analyses also showed an extensive repertoire of genes associated with toxins, such as LukGH leukocidin, enterotoxins, and superantigen staphylococcal classes (SSL). The 11 genes for antimicrobial resistance in S. aureus ST 5 SA01 showed similarity and identity above ≥ 99% with nucleotide sequences deposited in GenBank. Although studies on ST5 clones in Brazil are scarce, monitoring the clone of S. aureus ST 5 SA01 is essential, as it has become a problem in pediatrics in several countries.
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Affiliation(s)
- Romulo Maia Ferreira
- Laboratório de Microbiologia Aplicada, Universidade CEUMA, São Luís, 65075-120, MA, Brasil
| | | | - Karinny Farias Silva
- Laboratório de Microbiologia Aplicada, Universidade CEUMA, São Luís, 65075-120, MA, Brasil
| | | | - Gabriella Freitas Ferreira
- Departamento de Farmácia, Universidade Federal de Juiz de Fora - Campus Governador Valadares, CEP 35010-180, Juiz de Fora, MG, Brasil
| | | | | | - Letícia de Castro Oliveira
- Departamento de Microbiologia, Universidade Federal Do Triângulo Mineiro, Imunologia E Parasitologia, 38025180, Uberaba, MG, Brasil
| | - Andrea Souza Monteiro
- Laboratório de Microbiologia Aplicada, Universidade CEUMA, São Luís, 65075-120, MA, Brasil
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Martínez-Seijas C, Mascarós P, Lizana V, Martí-Marco A, Arnau-Bonachera A, Chillida-Martínez E, Cardells J, Selva L, Viana D, Corpa JM. Genomic Characterization of Staphylococcus aureus in Wildlife. Animals (Basel) 2023; 13:ani13061064. [PMID: 36978605 PMCID: PMC10044652 DOI: 10.3390/ani13061064] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/09/2023] [Accepted: 03/11/2023] [Indexed: 03/17/2023] Open
Abstract
Staphylococcus aureus is an opportunistic multi-host pathogen that threatens both human and animal health. Animals can act as a reservoir of S. aureus for humans, but very little is known about wild animals’ epidemiological role. Therefore, in this study, we performed a genomic characterization of S. aureus isolates from wildlife, hunters, and their auxiliary hunting animals of Eastern Spain. Of 20 different species, 242 wild animals were examined, of which 28.1% were S. aureus carriers. The common genet, the Iberian ibex, and the European hedgehog were the species with the highest S. aureus carriage. We identified 30 different sequence types (STs), including lineages associated with wild animals such as ST49 and ST581, multispecies lineages such as ST130, ST398, and ST425, and lineages commonly isolated from humans, including ST1 and ST5. The hunters and the single positive ferret shared ST5, ST398, or ST425 with wild animals. In wildlife isolates, the highest resistance levels were found for penicillin (32.8%). For virulence factors, 26.2% of them carried superantigens, while 14.8% harbored the immune evasion cluster (IEC), which indicates probable human origin. Our findings suggest that wild animals are a reservoir of clinically relevant genes and lineages that could have the potential to be transmitted to humans. These data support the notion that wildlife surveillance is necessary to better understand the epidemiology of S. aureus as a pathogen that circulates among humans, animals, and the environment.
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Affiliation(s)
- Carmen Martínez-Seijas
- Biomedical Research Institute, PASAPTA-Pathology Group, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
| | - Patricia Mascarós
- Biomedical Research Institute, PASAPTA-Pathology Group, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
| | - Víctor Lizana
- Servicio de Análisis, Investigación, Gestión de Animales Silvestres (SAIGAS), Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
- Wildlife Ecology & Health Group (WE&H), Universitat Autònoma de Barcelona (UAB), Edifici V, Travessera dels Turons, Bellaterra, 08193 Barcelona, Spain
| | - Alba Martí-Marco
- Servicio de Análisis, Investigación, Gestión de Animales Silvestres (SAIGAS), Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
- Wildlife Ecology & Health Group (WE&H), Universitat Autònoma de Barcelona (UAB), Edifici V, Travessera dels Turons, Bellaterra, 08193 Barcelona, Spain
| | - Alberto Arnau-Bonachera
- Biomedical Research Institute, PASAPTA-Pathology Group, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
| | - Eva Chillida-Martínez
- Servicio de Análisis, Investigación, Gestión de Animales Silvestres (SAIGAS), Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
| | - Jesús Cardells
- Servicio de Análisis, Investigación, Gestión de Animales Silvestres (SAIGAS), Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
- Wildlife Ecology & Health Group (WE&H), Universitat Autònoma de Barcelona (UAB), Edifici V, Travessera dels Turons, Bellaterra, 08193 Barcelona, Spain
| | - Laura Selva
- Biomedical Research Institute, PASAPTA-Pathology Group, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
| | - David Viana
- Biomedical Research Institute, PASAPTA-Pathology Group, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
- Correspondence: (D.V.); (J.M.C.); Tel.: +34-961-369-000 (D.V. & J.M.C.)
| | - Juan M. Corpa
- Biomedical Research Institute, PASAPTA-Pathology Group, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
- Correspondence: (D.V.); (J.M.C.); Tel.: +34-961-369-000 (D.V. & J.M.C.)
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Zhou W, Li Y, Xu X, Rao S, Wen H, Han Y, Deng A, Zhang Z, Yang Z, Zhu G. Whole-genome analysis showed the promotion of genetic diversity and coevolution in Staphylococcus aureus lytic bacteriophages and their hosts mediated by prophages via worldwide recombination events. Front Microbiol 2023; 14:1088125. [PMID: 36970693 PMCID: PMC10036374 DOI: 10.3389/fmicb.2023.1088125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/23/2023] [Indexed: 03/12/2023] Open
Abstract
Prophages as a part of Staphylococcus aureus genome contribute to the genetic diversity as well as survival strategies of their host. Some S. aureus prophages also have an imminent risk of host cell lysis and become a lytic phage. Nonetheless, interactions among S. aureus prophages, lytic phages, and their hosts, as well as the genetic diversity of S. aureus prophages, remain unclear. We identified 579 intact and 1,389 incomplete prophages in the genomes of 493 S. aureus isolates obtained from the NCBI database. The structural diversity and gene content of intact and incomplete prophages were investigated and compared with 188 lytic phages. Mosaic structure comparison, ortholog group clustering, phylogenetic analysis, and recombination network analysis were performed to estimate genetic relatedness among S. aureus intact prophages, incomplete prophages, and lytic phages. The intact and incomplete prophages harbored 148 and 522 distinct mosaic structures, respectively. The major difference between lytic phages and prophages was the lack of functional modules and genes. Compared to the lytic phages, both the S. aureus intact and incomplete prophages harbored multiple antimicrobial resistance (AMR) and virulence factor (VF) genes. Several functional modules of lytic phages 3_AJ_2017 and 23MRA shared more than 99% nucleotide sequence identity with S. aureus intact (ST20130943_p1 and UTSW_ MRSA_55_ip3) and incomplete prophages (SA3_LAU_ip3 and MRSA_FKTN_ip4); other modules showed little nucleotide sequence similarity. Ortholog and phylogenetic analyses revealed a common gene pool shared between the prophages and lytic Siphoviridae phages. Moreover, most shared sequences existed within intact (43428/137294, 31.6%) and incomplete prophages (41248/137294, 30.0%). Therefore, the maintenance or loss of functional modules in intact and incomplete prophages is key to balance the costs and benefits of large prophages harboring various AMR and VF genes in the bacterial host. The shared identical functional modules between S. aureus lytic phages and prophages are likely to result in the exchange, acquisition, and loss of functional modules, and therefore contribute to their genetic diversity. Moreover, constant recombination events within prophages globally were responsible for the coevolution of lytic phages and their bacterial hosts.
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Affiliation(s)
- Wenyuan Zhou
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, China
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yajie Li
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xuechao Xu
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, China
| | - Shengqi Rao
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, China
| | - Hua Wen
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yeiling Han
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, China
| | - Aiping Deng
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhenwen Zhang
- Medical College, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhenquan Yang
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, China
- *Correspondence: Zhenquan Yang,
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Guoqiang Zhu,
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Zhou W, Wen H, Li Y, Gao Y, Zheng X, Yuan L, Zhu G, Yang Z. Whole-Genome Analysis Reveals That Bacteriophages Promote Environmental Adaptation of Staphylococcus aureus via Gene Exchange, Acquisition, and Loss. Viruses 2022; 14:v14061199. [PMID: 35746669 PMCID: PMC9230882 DOI: 10.3390/v14061199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 12/12/2022] Open
Abstract
The study of bacteriophages is experiencing a resurgence owing to their antibacterial efficacy, lack of side effects, and low production cost. Nonetheless, the interactions between Staphylococcus aureus bacteriophages and their hosts remain unexplored. In this study, whole-genome sequences of 188 S. aureus bacteriophages—20 Podoviridae, 56 Herelleviridae, and 112 Siphoviridae—were obtained from the National Center for Biotechnology Information (NCBI, USA) genome database. A phylogenetic tree was constructed to estimate their genetic relatedness using single-nucleotide polymorphism analysis. Comparative analysis was performed to investigate the structural diversity and ortholog groups in the subdividing clusters. Mosaic structures and gene content were compared in relation to phylogeny. Phylogenetic analysis revealed that the bacteriophages could be distinguished into three lineages (I–III), including nine subdividing clusters and seven singletons. The subdividing clusters shared similar mosaic structures and core ortholog clusters, including the genes involved in bacteriophage morphogenesis and DNA packaging. Notably, several functional modules of bacteriophages 187 and 2368A shared more than 95% nucleotide sequence identity with prophages in the S. aureus strain RJ1267 and the Staphylococcus pseudintermedius strain SP_11306_4, whereas other modules exhibited little nucleotide sequence similarity. Moreover, the cluster phages shared similar types of holins, lysins, and DNA packaging genes and harbored diverse genes associated with DNA replication and virulence. The data suggested that the genetic diversity of S. aureus bacteriophages was likely due to gene replacement, acquisition, and loss among staphylococcal phages, which may have crossed species barriers. Moreover, frequent module exchanges likely occurred exclusively among the subdividing cluster phages. We hypothesize that during evolution, the S. aureus phages enhanced their DNA replication in host cells and the adaptive environment of their host.
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Affiliation(s)
- Wenyuan Zhou
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225127, China; (W.Z.); (H.W.); (Y.L.); (Y.G.); (X.Z.); (L.Y.)
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225001, China;
| | - Hua Wen
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225127, China; (W.Z.); (H.W.); (Y.L.); (Y.G.); (X.Z.); (L.Y.)
| | - Yajie Li
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225127, China; (W.Z.); (H.W.); (Y.L.); (Y.G.); (X.Z.); (L.Y.)
| | - Yajun Gao
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225127, China; (W.Z.); (H.W.); (Y.L.); (Y.G.); (X.Z.); (L.Y.)
| | - Xiangfeng Zheng
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225127, China; (W.Z.); (H.W.); (Y.L.); (Y.G.); (X.Z.); (L.Y.)
| | - Lei Yuan
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225127, China; (W.Z.); (H.W.); (Y.L.); (Y.G.); (X.Z.); (L.Y.)
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225001, China;
| | - Zhenquan Yang
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225127, China; (W.Z.); (H.W.); (Y.L.); (Y.G.); (X.Z.); (L.Y.)
- Correspondence: ; Tel./Fax: +86-(514)-87978096
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5
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Khullar L, Harjai K, Chhibber S. Exploring the therapeutic potential of staphylococcal phage formulations: Current challenges and applications in phage therapy. J Appl Microbiol 2022; 132:3515-3532. [DOI: 10.1111/jam.15462] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/21/2021] [Accepted: 01/17/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Lavanya Khullar
- Department of Microbiology Panjab University Chandigarh India
| | - Kusum Harjai
- Department of Microbiology Panjab University Chandigarh India
| | - Sanjay Chhibber
- Department of Microbiology Panjab University Chandigarh India
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Göller PC, Elsener T, Lorgé D, Radulovic N, Bernardi V, Naumann A, Amri N, Khatchatourova E, Coutinho FH, Loessner MJ, Gómez-Sanz E. Multi-species host range of staphylococcal phages isolated from wastewater. Nat Commun 2021; 12:6965. [PMID: 34845206 PMCID: PMC8629997 DOI: 10.1038/s41467-021-27037-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/21/2021] [Indexed: 12/19/2022] Open
Abstract
The host range of bacteriophages defines their impact on bacterial communities and genome diversity. Here, we characterize 94 novel staphylococcal phages from wastewater and establish their host range on a diversified panel of 117 staphylococci from 29 species. Using this high-resolution phage-bacteria interaction matrix, we unveil a multi-species host range as a dominant trait of the isolated staphylococcal phages. Phage genome sequencing shows this pattern to prevail irrespective of taxonomy. Network analysis between phage-infected bacteria reveals that hosts from multiple species, ecosystems, and drug-resistance phenotypes share numerous phages. Lastly, we show that phages throughout this network can package foreign genetic material enclosing an antibiotic resistance marker at various frequencies. Our findings indicate a weak host specialism of the tested phages, and therefore their potential to promote horizontal gene transfer in this environment.
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Affiliation(s)
- Pauline C. Göller
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Tabea Elsener
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Dominic Lorgé
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Natasa Radulovic
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Viona Bernardi
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Annika Naumann
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Nesrine Amri
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Ekaterina Khatchatourova
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Felipe Hernandes Coutinho
- grid.26811.3c0000 0001 0586 4893Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain
| | - Martin J. Loessner
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Elena Gómez-Sanz
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Zurich, Switzerland. .,Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain.
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7
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Humphrey S, Fillol-Salom A, Quiles-Puchalt N, Ibarra-Chávez R, Haag AF, Chen J, Penadés JR. Bacterial chromosomal mobility via lateral transduction exceeds that of classical mobile genetic elements. Nat Commun 2021; 12:6509. [PMID: 34750368 PMCID: PMC8575950 DOI: 10.1038/s41467-021-26004-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 09/03/2021] [Indexed: 12/02/2022] Open
Abstract
It is commonly assumed that the horizontal transfer of most bacterial chromosomal genes is limited, in contrast to the frequent transfer observed for typical mobile genetic elements. However, this view has been recently challenged by the discovery of lateral transduction in Staphylococcus aureus, where temperate phages can drive the transfer of large chromosomal regions at extremely high frequencies. Here, we analyse previously published as well as new datasets to compare horizontal gene transfer rates mediated by different mechanisms in S. aureus and Salmonella enterica. We find that the horizontal transfer of core chromosomal genes via lateral transduction can be more efficient than the transfer of classical mobile genetic elements via conjugation or generalized transduction. These results raise questions about our definition of mobile genetic elements, and the potential roles played by lateral transduction in bacterial evolution.
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Affiliation(s)
- Suzanne Humphrey
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - Alfred Fillol-Salom
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Nuria Quiles-Puchalt
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Rodrigo Ibarra-Chávez
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
- Department of Biology, Section of Microbiology, University of Copenhagen, Universitetsparken 15, Bldg. 1, DK2100, Copenhagen, Denmark
| | - Andreas F Haag
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - John Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore, Singapore
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK.
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK.
- Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad CEU Cardenal Herrera, Valencia, 46113, Spain.
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Genomic Analysis of Pasteurella atlantica Provides Insight on Its Virulence Factors and Phylogeny and Highlights the Potential of Reverse Vaccinology in Aquaculture. Microorganisms 2021; 9:microorganisms9061215. [PMID: 34199775 PMCID: PMC8226905 DOI: 10.3390/microorganisms9061215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/21/2021] [Accepted: 06/01/2021] [Indexed: 12/20/2022] Open
Abstract
Pasteurellosis in farmed lumpsuckers, Cyclopterus lumpus, has emerged as a serious disease in Norwegian aquaculture in recent years. Genomic characterization of the causative agent is essential in understanding the biology of the bacteria involved and in devising an efficient preventive strategy. The genomes of two clinical Pasteurella atlantica isolates were sequenced (≈2.3 Mbp), and phylogenetic analysis confirmed their position as a novel species within the Pasteurellaceae. In silico analyses revealed 11 genomic islands and 5 prophages, highlighting the potential of mobile elements as driving forces in the evolution of this species. The previously documented pathogenicity of P. atlantica is strongly supported by the current study, and 17 target genes were recognized as putative primary drivers of pathogenicity. The expression level of a predicted vaccine target, an uncharacterized adhesin protein, was significantly increased in both broth culture and following the exposure of P. atlantica to lumpsucker head kidney leucocytes. Based on in silico and functional analyses, the strongest gene target candidates will be prioritized in future vaccine development efforts to prevent future pasteurellosis outbreaks.
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Sklyar T, Kurahina N, Lavrentieva K, Burlaka V, Lykholat T, Lykholat O. Autonomic (Mobile) Genetic Elements of Bacteria and Their Hierarchy. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721030099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Park DW, Lee YD, Park JH. Characteristics for phage-encoded cell wall hydrolase of LysSAP27 to reduce staphylococcal food poisoning. Food Sci Biotechnol 2021; 30:745-753. [PMID: 34123470 PMCID: PMC8144258 DOI: 10.1007/s10068-021-00910-2] [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: 02/18/2021] [Revised: 03/17/2021] [Accepted: 03/30/2021] [Indexed: 10/21/2022] Open
Abstract
To reduce staphylococcal food poisoning (SFP), a phage-encoded cell wall hydrolase called endolysin has emerged as an attractive antibacterial agent. In this study, the Staphylococcus aureus infecting phage vB_SauS-SAP27 (ϕSAP27) was isolated from sewage and characterized morphologically and genetically. ϕSAP27 was identified as Siphoviridae temperate phage, with a genome of 43 kbp. A ϕSAP27 endolysin named LysSAP27 was produced recombinantly in Escherichia coli. LysSAP27 exhibited the highest activity at neutral pH and a temperature of 30 °C, and its lytic activity was upregulated by calcium ions. Following optimization of the enzymatic conditions, LysSAP27 was applied to S. aureus-contaminated milk. Treatment with 2 μM LysSAP27 led to a significant bactericidal effect, corresponding to a reduction in bacterial titer by 2.8 log CFU/mL within 1 h and 3.4 log CFU/mL within 2 h. Therefore, LysSAP27 could be used as an effective antimicrobial agent to prevent SFP in food. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10068-021-00910-2.
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Affiliation(s)
- Do-won Park
- Department of Food Science and Biotechnology, College of Bionano Technology, Gachon University, Seongnam, 13120 Republic of Korea
| | - Young-Duck Lee
- Department of Food Science and Engineering, Seowon University, Cheongju, 28674 Republic of Korea
| | - Jong-Hyun Park
- Department of Food Science and Biotechnology, College of Bionano Technology, Gachon University, Seongnam, 13120 Republic of Korea
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Genomic islands and the evolution of livestock-associated Staphylococcus aureus genomes. Biosci Rep 2021; 40:226941. [PMID: 33185245 PMCID: PMC7689654 DOI: 10.1042/bsr20202287] [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: 07/21/2020] [Revised: 09/23/2020] [Accepted: 10/07/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Genomic Islands (GIs) are commonly believed to be relics of horizontal transfer and associated with specific metabolic capacities, including virulence of the strain. Horizontal gene transfer (HGT) plays a vital role in the acquisition of GIs and the evolution and adaptation of bacterial genomes. OBJECTIVE The present study was designed to predict the GIs and role of HGT in evolution of livestock-associated Staphylococcus aureus (LA-SA). METHODS GIs were predicted with two methods namely, Ensemble algorithm for Genomic Island Detection (EGID) tool, and Seq word Sniffer script. Functional characterization of GI elements was performed with clustering of orthologs. The putative donor predictions of GIs was done with the aid of the pre_GI database. RESULTS The present study predicted a pan of 46 GIs across the LA-SA genomes. Functional characterization of GI sequences revealed few unique results like the presence of metabolic operons like leuABCD and folPK genes in GIs and showed the importance of GIs in the adaptation to the host niche. The developed framework for GI donor prediction results revealed Rickettsia and Mycoplasma as the major donors of GI elements. CONCLUSIONS The role of GIs during the evolutionary race of LA-SA could be concluded from the present study. Niche adaptation of LA-SA enhanced presumably due to these GIs. Future studies could focus on the evolutionary relationships between Rickettsia and Mycoplasma sp. with S. aureus and also the evolution of Leucine/Isoleucine mosaic operon (leuABCD).
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Ko DS, Kim D, Kim EK, Kim JH, Kwon HJ. Evolution of a major bovine mastitic genotype (rpoB sequence type 10-2) of Staphylococcus aureus in cows. J Microbiol 2019; 57:587-596. [PMID: 30982119 DOI: 10.1007/s12275-019-8699-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 01/31/2019] [Accepted: 02/11/2019] [Indexed: 01/21/2023]
Abstract
Staphylococcus aureus is the major pathogen leading to bovine mastitis globally while livestock-associated methicillin resistant S. aureus (LA-MRSA) has become a potential threat to public health. MRSA from bovine mastitis is not common but a methicillin susceptible S. aureus (MSSA) genotype, rpoB sequence type (RST)10-2 (RST10-2), is prevalent in Korea. To date, many genomic sequences from S. aureus have been elucidated, but the complete genome sequences of RST10-2 MSSA from bovine mastitis has never been reported. In this study, we determined the complete genome sequence of two RST10-2 MSSA that differ from each other in staphylococcal protein A and molecular prophage types [PMB64-1 (t2489/ mPPT0) and PMB81-4 (t127/mPPT1-2-3)] and conducted a comparative genomics study. The genomic sequences of PMB64-1 and PMB81-4 were more homologous to the representative human RST10-2 strains (MSSA476, MW2 etc.) compared to other RSTs. Most of them shared five common pseudogenes, along with high amino acid identity of four variable virulence genes that were identified in this study. However, PMB64-1 and PMB81-4 acquired different strainspecific pseudogenes and mobile genetic elements than the human strains. The unique pseudogene profile and high identity of the virulence genes were verified in RST10-2 field strains from bovine mastitis. Thus, bovine mastitic RST10-2 MSSA may have an evolutionary relationship with the human RST10-2 community-associated (CA) MSSA and CA-MRSA strains but may have adapted to cows.
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Affiliation(s)
- Dae-Sung Ko
- Department of Farm Animal Medicine, Seoul National University, Seoul, 08826, Republic of Korea.,Laboratory of Avian Diseases, Seoul National University, Seoul, 08826, Republic of Korea
| | - Danil Kim
- Department of Farm Animal Medicine, Seoul National University, Seoul, 08826, Republic of Korea
| | - Eun-Kyung Kim
- Department of Farm Animal Medicine, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae-Hong Kim
- Laboratory of Avian Diseases, Seoul National University, Seoul, 08826, Republic of Korea.,The Research Institute for Veterinary Science, College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyuk-Joon Kwon
- Department of Farm Animal Medicine, Seoul National University, Seoul, 08826, Republic of Korea. .,The Research Institute for Veterinary Science, College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea.
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14
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Zhou W, Li X, Osmundson T, Shi L, Ren J, Yan H. WGS analysis of ST9-MRSA-XII isolates from live pigs in China provides insights into transmission among porcine, human and bovine hosts. J Antimicrob Chemother 2018; 73:2652-2661. [DOI: 10.1093/jac/dky245] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/27/2018] [Indexed: 12/21/2022] Open
Affiliation(s)
- Wenyuan Zhou
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Xinhui Li
- Department of Microbiology, University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI, USA
| | - Todd Osmundson
- Department of Biology, University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI, USA
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China
- State Key Laboratory of Food Safely Technology for Meat Products, Xiamen, Fujian, China
| | - Jiaoyan Ren
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - He Yan
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- State Key Laboratory of Food Safely Technology for Meat Products, Xiamen, Fujian, China
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15
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Górski A, Międzybrodzki R, Łobocka M, Głowacka-Rutkowska A, Bednarek A, Borysowski J, Jończyk-Matysiak E, Łusiak-Szelachowska M, Weber-Dąbrowska B, Bagińska N, Letkiewicz S, Dąbrowska K, Scheres J. Phage Therapy: What Have We Learned? Viruses 2018; 10:E288. [PMID: 29843391 PMCID: PMC6024844 DOI: 10.3390/v10060288] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/11/2018] [Accepted: 05/22/2018] [Indexed: 02/07/2023] Open
Abstract
In this article we explain how current events in the field of phage therapy may positively influence its future development. We discuss the shift in position of the authorities, academia, media, non-governmental organizations, regulatory agencies, patients, and doctors which could enable further advances in the research and application of the therapy. In addition, we discuss methods to obtain optimal phage preparations and suggest the potential of novel applications of phage therapy extending beyond its anti-bacterial action.
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Affiliation(s)
- Andrzej Górski
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
- Department of Clinical Immunology, Transplantation Institute, Medical University of Warsaw, Nowogrodzka Street 59, 02-006 Warsaw, Poland.
| | - Ryszard Międzybrodzki
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
- Department of Clinical Immunology, Transplantation Institute, Medical University of Warsaw, Nowogrodzka Street 59, 02-006 Warsaw, Poland.
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego Street 5 A, 02-106 Warsaw, Poland.
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Nowoursynowska Street 159, 02-776 Warsaw, Poland.
| | - Aleksandra Głowacka-Rutkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego Street 5 A, 02-106 Warsaw, Poland.
| | - Agnieszka Bednarek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego Street 5 A, 02-106 Warsaw, Poland.
| | - Jan Borysowski
- Department of Clinical Immunology, Transplantation Institute, Medical University of Warsaw, Nowogrodzka Street 59, 02-006 Warsaw, Poland.
| | - Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
| | - Marzanna Łusiak-Szelachowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
| | - Beata Weber-Dąbrowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
| | - Natalia Bagińska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
| | - Sławomir Letkiewicz
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
- Medical Sciences Institute, Katowice School of Economics, Harcerzy Września Street 3, 40-659 Katowice, Poland.
| | - Krystyna Dąbrowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
- Research and Development Center, Regional Specialized Hospital, Kamieńskiego 73a, 51-124 Wrocław, Poland.
| | - Jacques Scheres
- National Institute of Public Health NIZP, Chocimska Street 24, 00-971 Warsaw, Poland.
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16
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Lee J, Park N, Park JY, Kaplan BLF, Pruett SB, Park JW, Park YH, Seo KS. Induction of Immunosuppressive CD8 +CD25 +FOXP3 + Regulatory T Cells by Suboptimal Stimulation with Staphylococcal Enterotoxin C1. THE JOURNAL OF IMMUNOLOGY 2017; 200:669-680. [PMID: 29237775 DOI: 10.4049/jimmunol.1602109] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 11/13/2017] [Indexed: 12/17/2022]
Abstract
Superantigens (SAgs) produced by Staphylococcus aureus at high concentrations induce proliferation of T cells bearing specific TCR Vβ sequences and massive cytokinemia that cause toxic shock syndrome. However, the biological relevance of SAgs produced at very low concentrations during asymptomatic colonization or chronic infections is not understood. In this study, we demonstrate that suboptimal stimulation of human PBMCs with a low concentration (1 ng/ml) of staphylococcal enterotoxin C1, at which half-maximal T cell proliferation was observed, induced CD8+CD25+ T cells expressing markers related to regulatory T cells (Tregs), such as IFN-γ, IL-10, TGF-β, FOXP3, CD28, CTLA4, TNFR2, CD45RO, and HLA-DR. Importantly, these CD8+CD25+ T cells suppressed responder cell proliferation mediated in contact-dependent and soluble factor-dependent manners, involving galectin-1 and granzymes, respectively. In contrast, optimal stimulation of human PBMCs with a high concentration (1 μg/ml) of staphylococcal enterotoxin C1, at which maximal T cell proliferation was observed, also induced similar expression of markers related to Tregs, including FOXP3 in CD8+CD25+ cells, but these T cells were not functionally immunosuppressive. We further demonstrated that SAg-induced TCR Vβ-restricted and MHC class II-restricted expansion of immunosuppressive CD8+CD25+ T cells is independent of CD4+ T cells. Our results suggest that the concentration of SAg strongly affects the functional characteristics of activated T cells, and low concentrations of SAg produced during asymptomatic colonization or chronic S. aureus infection induce immunosuppressive CD8+ Tregs, potentially promoting colonization, propagation, and invasion of S. aureus in the host.
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Affiliation(s)
- Juyeun Lee
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762
| | - Nogi Park
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762
| | - Joo Youn Park
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762
| | - Barbara L F Kaplan
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762
| | - Stephen B Pruett
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762
| | - Juw Won Park
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292; and
| | - Yong Ho Park
- Department of Microbiology, BK21 Program for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 151-742, South Korea
| | - Keun Seok Seo
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762;
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Sansevere EA, Robinson DA. Staphylococci on ICE: Overlooked agents of horizontal gene transfer. Mob Genet Elements 2017; 7:1-10. [PMID: 28932624 DOI: 10.1080/2159256x.2017.1368433] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/08/2017] [Accepted: 08/14/2017] [Indexed: 10/19/2022] Open
Abstract
Horizontal gene transfer plays a significant role in spreading antimicrobial resistance and virulence genes throughout the genus Staphylococcus, which includes species of clinical relevance to humans and animals. While phages and plasmids are the most well-studied agents of horizontal gene transfer in staphylococci, the contribution of integrative conjugative elements (ICEs) has been mostly overlooked. Experimental work demonstrating the activity of ICEs in staphylococci remained frozen for years after initial work in the 1980s that showed Tn916 was capable of transfer from Enterococcus to Staphylococcus. However, recent work has begun to thaw this field. To date, 2 families of ICEs have been identified among staphylococci - Tn916 that includes the Tn5801 subfamily, and ICE6013 that includes at least 7 subfamilies. Both Tn5801 and ICE6013 commonly occur in clinical strains of S. aureus. Tn5801 is the most studied of the Tn916 family elements in staphylococci and encodes tetracycline resistance and a protein that, when expressed in Escherichia coli, inhibits restriction barriers to incoming DNA. ICE6013 is among the shortest known ICEs, but it still includes many uncharacterized open reading frames. This element uses an IS30-like transposase as its recombinase, providing some versatility in integration sites. ICE6013 also conjugatively transfers among receptive S. aureus strains at relatively higher frequency than Tn5801. Continued study of these mobile genetic elements may reveal the full extent to which ICEs impact horizontal gene transfer and the evolution of staphylococci.
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Affiliation(s)
- Emily A Sansevere
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, USA
| | - D Ashley Robinson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, USA
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18
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Recent advances in therapeutic delivery systems of bacteriophage and bacteriophage-encoded endolysins. Ther Deliv 2017. [DOI: 10.4155/tde-2017-0040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Antibiotics have been the cornerstone of clinical management of bacterial infection since their discovery in the early 20th century. However, their widespread and often indiscriminate use has now led to reports of multidrug resistance becoming globally commonplace. Bacteriophage therapy has undergone a recent revival in battle against pathogenic bacteria, as the self-replicating and co-evolutionary features of these predatory virions offer several advantages over conventional therapeutic agents. In particular, the use of targeted bacteriophage therapy from specialized delivery platforms has shown particular promise owing to the control of delivery location, administration conditions and dosage of the therapeutic cargo. This review presents an overview of the recent formulations and applications of such delivery vehicles as an innovative and elegant tool for bacterial control.
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19
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Vázquez-Rosas-Landa M, Ponce-Soto GY, Eguiarte LE, Souza V. Comparative genomics of free-living Gammaproteobacteria: pathogenesis-related genes or interaction-related genes? Pathog Dis 2017; 75:3861975. [DOI: 10.1093/femspd/ftx059] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/02/2017] [Indexed: 12/25/2022] Open
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20
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Transposase-Mediated Excision, Conjugative Transfer, and Diversity of ICE 6013 Elements in Staphylococcus aureus. J Bacteriol 2017; 199:JB.00629-16. [PMID: 28138100 DOI: 10.1128/jb.00629-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 01/25/2017] [Indexed: 01/04/2023] Open
Abstract
ICE6013 represents one of two families of integrative conjugative elements (ICEs) identified in the pan-genome of the human and animal pathogen Staphylococcus aureus Here we investigated the excision and conjugation functions of ICE6013 and further characterized the diversity of this element. ICE6013 excision was not significantly affected by growth, temperature, pH, or UV exposure and did not depend on recA The IS30-like DDE transposase (Tpase; encoded by orf1 and orf2) of ICE6013 must be uninterrupted for excision to occur, whereas disrupting three of the other open reading frames (ORFs) on the element significantly affects the level of excision. We demonstrate that ICE6013 conjugatively transfers to different S. aureus backgrounds at frequencies approaching that of the conjugative plasmid pGO1. We found that excision is required for conjugation, that not all S. aureus backgrounds are successful recipients, and that transconjugants acquire the ability to transfer ICE6013 Sequencing of chromosomal integration sites in serially passaged transconjugants revealed a significant integration site preference for a 15-bp AT-rich palindromic consensus sequence, which surrounds the 3-bp target site that is duplicated upon integration. A sequence analysis of ICE6013 from different host strains of S. aureus and from eight other species of staphylococci identified seven divergent subfamilies of ICE6013 that include sequences previously classified as a transposon, a plasmid, and various ICEs. In summary, these results indicate that the IS30-like Tpase functions as the ICE6013 recombinase and that ICE6013 represents a diverse family of mobile genetic elements that mediate conjugation in staphylococci.IMPORTANCE Integrative conjugative elements (ICEs) encode the abilities to integrate into and excise from bacterial chromosomes and plasmids and mediate conjugation between bacteria. As agents of horizontal gene transfer, ICEs may affect bacterial evolution. ICE6013 represents one of two known families of ICEs in the pathogen Staphylococcus aureus, but its core functions of excision and conjugation are not well studied. Here, we show that ICE6013 depends on its IS30-like DDE transposase for excision, which is unique among ICEs, and we demonstrate the conjugative transfer and integration site preference of ICE6013 A sequence analysis revealed that ICE6013 has diverged into seven subfamilies that are dispersed among staphylococci.
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Genetic engineering of a temperate phage-based delivery system for CRISPR/Cas9 antimicrobials against Staphylococcus aureus. Sci Rep 2017; 7:44929. [PMID: 28322317 PMCID: PMC5359561 DOI: 10.1038/srep44929] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 02/16/2017] [Indexed: 12/29/2022] Open
Abstract
Discovery of clustered, regularly interspaced, short palindromic repeats and the Cas9 RNA-guided nuclease (CRISPR/Cas9) system provides a new opportunity to create programmable gene-specific antimicrobials that are far less likely to drive resistance than conventional antibiotics. However, the practical therapeutic use of CRISPR/Cas9 is still questionable due to current shortcomings in phage-based delivery systems such as inefficient delivery, narrow host range, and potential transfer of virulence genes by generalized transduction. In this study, we demonstrate genetic engineering strategies to overcome these shortcomings by integrating CRISPR/Cas9 system into a temperate phage genome, removing major virulence genes from the host chromosome, and expanding host specificity of the phage by complementing tail fiber protein. This significantly improved the efficacy and safety of CRISPR/Cas9 antimicrobials to therapeutic levels in both in vitro and in vivo assays. The genetic engineering tools and resources established in this study are expected to provide an efficacious and safe CRISPR/Cas9 antimicrobial, broadly applicable to Staphylococcus aureus.
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Comparative Genome Analyses of Vibrio anguillarum Strains Reveal a Link with Pathogenicity Traits. mSystems 2017; 2:mSystems00001-17. [PMID: 28293680 PMCID: PMC5347184 DOI: 10.1128/msystems.00001-17] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/30/2017] [Indexed: 01/30/2023] Open
Abstract
Comparative genome analysis of strains of a pathogenic bacterial species can be a powerful tool to discover acquisition of mobile genetic elements related to virulence. Here, we compared 28 V. anguillarum strains that differed in virulence in fish larval models. By pan-genome analyses, we found that six of nine highly virulent strains had a unique core and accessory genome. In contrast, V. anguillarum strains that were medium to nonvirulent had low genomic diversity. Integration of genomic and phenotypic features provides insights into the evolution of V. anguillarum and can also be important for survey and diagnostic purposes. Vibrio anguillarum is a marine bacterium that can cause vibriosis in many fish and shellfish species, leading to high mortalities and economic losses in aquaculture. Although putative virulence factors have been identified, the mechanism of pathogenesis of V. anguillarum is not fully understood. Here, we analyzed whole-genome sequences of a collection of V. anguillarum strains and compared them to virulence of the strains as determined in larval challenge assays. Previously identified virulence factors were globally distributed among the strains, with some genetic diversity. However, the pan-genome revealed that six out of nine high-virulence strains possessed a unique accessory genome that was attributed to pathogenic genomic islands, prophage-like elements, virulence factors, and a new set of gene clusters involved in biosynthesis, modification, and transport of polysaccharides. In contrast, V. anguillarum strains that were medium to nonvirulent had a high degree of genomic homogeneity. Finally, we found that a phylogeny based on the core genomes clustered the strains with moderate to no virulence, while six out of nine high-virulence strains represented phylogenetically separate clusters. Hence, we suggest a link between genotype and virulence characteristics of Vibrio anguillarum, which can be used to unravel the molecular evolution of V. anguillarum and can also be important from survey and diagnostic perspectives. IMPORTANCE Comparative genome analysis of strains of a pathogenic bacterial species can be a powerful tool to discover acquisition of mobile genetic elements related to virulence. Here, we compared 28 V. anguillarum strains that differed in virulence in fish larval models. By pan-genome analyses, we found that six of nine highly virulent strains had a unique core and accessory genome. In contrast, V. anguillarum strains that were medium to nonvirulent had low genomic diversity. Integration of genomic and phenotypic features provides insights into the evolution of V. anguillarum and can also be important for survey and diagnostic purposes.
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Pourcel C, Midoux C, Hauck Y, Vergnaud G, Latino L. Large Preferred Region for Packaging of Bacterial DNA by phiC725A, a Novel Pseudomonas aeruginosa F116-Like Bacteriophage. PLoS One 2017; 12:e0169684. [PMID: 28060939 PMCID: PMC5217972 DOI: 10.1371/journal.pone.0169684] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/20/2016] [Indexed: 11/24/2022] Open
Abstract
Bacteriophage vB_PaeP_PAO1_phiC725A (short name phiC725A) was isolated following mitomycin C induction of C7-25, a clinical Pseudomonas aeruginosa strain carrying phiC725A as a prophage. The phiC725A genome sequence shows similarity to F116, a P. aeruginosa podovirus capable of generalized transduction. Likewise, phiC725A is a podovirus with long tail fibers. PhiC725A was able to lysogenize two additional P. aeruginosa strains in which it was maintained both as a prophage and in an episomal state. Investigation by deep sequencing showed that bacterial DNA carried inside phage particles originated predominantly from a 700-800kb region, immediately flanking the attL prophage insertion site, whether the phages were induced from a lysogen or recovered after infection. This indicates that during productive replication, recombination of phage genomes with the bacterial chromosome at the att site occurs occasionally, allowing packaging of adjacent bacterial DNA.
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Affiliation(s)
- Christine Pourcel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
- * E-mail:
| | - Cédric Midoux
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Yolande Hauck
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Libera Latino
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
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