1
|
Elek CKA, Brown TL, Le Viet T, Evans R, Baker DJ, Telatin A, Tiwari SK, Al-Khanaq H, Thilliez G, Kingsley RA, Hall LJ, Webber MA, Adriaenssens EM. A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses. Microb Genom 2023; 9:mgen001065. [PMID: 37463032 PMCID: PMC10438801 DOI: 10.1099/mgen.0.001065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/17/2023] [Indexed: 07/21/2023] Open
Abstract
Bacteriophages (phages) within the genus Przondovirus are T7-like podoviruses belonging to the subfamily Studiervirinae, within the family Autographiviridae, and have a highly conserved genome organisation. The genomes of these phages range from 37 to 42 kb in size, encode 50-60 genes and are characterised by the presence of direct terminal repeats (DTRs) flanking the linear chromosome. These DTRs are often deleted during short-read-only and hybrid assemblies. Moreover, long-read-only assemblies are often littered with sequencing and/or assembly errors and require additional curation. Here, we present the isolation and characterisation of ten novel przondoviruses targeting Klebsiella spp. We describe HYPPA, a HYbrid and Poly-polish Phage Assembly workflow, which utilises long-read assemblies in combination with short-read sequencing to resolve phage DTRs and correcting errors, negating the need for laborious primer walking and Sanger sequencing validation. Our assembly workflow utilised Oxford Nanopore Technologies for long-read sequencing for its accessibility, making it the more relevant long-read sequencing technology at this time, and Illumina DNA Prep for short-read sequencing, representing the most commonly used technologies globally. Our data demonstrate the importance of careful curation of phage assemblies before publication, and prior to using them for comparative genomics.
Collapse
Affiliation(s)
- Claire K. A. Elek
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
| | - Teagan L. Brown
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Thanh Le Viet
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Rhiannon Evans
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - David J. Baker
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Andrea Telatin
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Sumeet K. Tiwari
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Haider Al-Khanaq
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Gaëtan Thilliez
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Robert A. Kingsley
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
| | - Lindsay J. Hall
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
- Chair of Intestinal Microbiome, ZIEL—Institute for Food and Health, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mark A. Webber
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
| | | |
Collapse
|
2
|
Oliveira H, Santos S, Pires DP, Boeckaerts D, Pinto G, Domingues R, Otero J, Briers Y, Lavigne R, Schmelcher M, Dötsch A, Azeredo J. CkP1 bacteriophage, a S16-like myovirus that recognizes Citrobacter koseri lipopolysaccharide through its long tail fibers. Appl Microbiol Biotechnol 2023; 107:3621-3636. [PMID: 37133800 PMCID: PMC10175313 DOI: 10.1007/s00253-023-12547-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 04/11/2023] [Accepted: 04/17/2023] [Indexed: 05/04/2023]
Abstract
Citrobacter koseri is an emerging Gram-negative bacterial pathogen, which causes urinary tract infections. We isolated and characterized a novel S16-like myovirus CKP1 (vB_CkoM_CkP1), infecting C. koseri. CkP1 has a host range covering the whole C. koseri species, i.e., all strains that were tested, but does not infect other species. Its linear 168,463-bp genome contains 291 coding sequences, sharing sequence similarity with the Salmonella phage S16. Based on surface plasmon resonance and recombinant green florescence protein fusions, the tail fiber (gp267) was shown to decorate C. koseri cells, binding with a nanomolar affinity, without the need of accessory proteins. Both phage and the tail fiber specifically bind to bacterial cells by the lipopolysaccharide polymer. We further demonstrate that CkP1 is highly stable towards different environmental conditions of pH and temperatures and is able to control C. koseri cells in urine samples. Altogether, CkP1 features optimal in vitro characteristics to be used both as a control and detection agent towards drug-resistant C. koseri infections. KEY POINTS: • CkP1 infects all C. koseri strains tested • CkP1 recognizes C. koseri lipopolysaccharide through its long tail fiber • Both phage CkP1 and its tail fiber can be used to treat or detect C. koseri pathogens.
Collapse
Affiliation(s)
- Hugo Oliveira
- Centre of Biological Engineering, University of Minho, Braga, Portugal.
- LABBELS -Associate Laboratory, Braga, Guimarães, Portugal.
| | - Sílvio Santos
- Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS -Associate Laboratory, Braga, Guimarães, Portugal
| | - Diana P Pires
- Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS -Associate Laboratory, Braga, Guimarães, Portugal
| | | | - Graça Pinto
- Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS -Associate Laboratory, Braga, Guimarães, Portugal
| | - Rita Domingues
- Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS -Associate Laboratory, Braga, Guimarães, Portugal
| | - Jennifer Otero
- Centre of Biological Engineering, University of Minho, Braga, Portugal
- Departament de Genètica I de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Yves Briers
- Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Louvain, Belgium
| | - Mathias Schmelcher
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Andreas Dötsch
- Max Rubner-Institute, Department of Physiology and Biochemistry of Nutrition, Karlsruhe, Germany
| | - Joana Azeredo
- Centre of Biological Engineering, University of Minho, Braga, Portugal.
- LABBELS -Associate Laboratory, Braga, Guimarães, Portugal.
| |
Collapse
|
3
|
Tang YJ, Yuan L, Chen CW, Tang AQ, Zhou WY, Yang ZQ. Isolation and characterization of the new isolated bacteriophage YZU-L1 against Citrobacter freundii from a package-swelling of meat product. Microb Pathog 2023; 179:106098. [PMID: 37028686 DOI: 10.1016/j.micpath.2023.106098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/02/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023]
Abstract
Citrobacter freundii is an important foodborne pathogen that can cause urethritis, bacteremia, necrotizing abscess, and meningitis in infants. In this study, a gas-producing isolate from vacuum-packed meat products was identified as C. freundii by 16S rDNA. In addition, a new virulent phage YZU-L1, which could specifically lyse C. freundii, was isolated from sewage samples in Yangzhou. Transmission electron microscopy showed that phage YZU-L1 had a polyhedral head of 73.51 nm in diameter and a long tail of 161.15 nm in length. According to phylogenetic analysis employing the terminase large subunit, phage YZU-L1 belonged to the Demerecviridae family and the Markadamsvirinae subfamily. The burst size was 96 PFU/cell after 30 min of latent period and 90 min of rising period. Phage YZU-L1 could maintain high activity at pH of 4-13, and resist 50 °C for up to 60 min. The complete genome of YZU-L1 was 115,014 bp double-stranded DNA with 39.94% G + C content, encoding 164 open reading frames (ORFs), without genes encoding for virulence, antibiotic resistance, or lysogenicity. Phage YZU-L1 treatment significantly reduced the viable bacterial count of C. freundii in a sterile fish juice model, which is expected to be a natural agent for the biocontrol of C. freundii in foods.
Collapse
|
4
|
Abstract
The mosquito microbiota has a profound impact on multiple biological processes ranging from reproduction to disease transmission. Interestingly, the adult mosquito microbiota is largely derived from the larval microbiota, which in turn is dependent on the microbiota of their water habitat. The larval microbiota not only plays a crucial role in larval development but also has a significant impact on the adult stage of the mosquito. By precisely engineering the larval microbiota, it is feasible to alter larval development and other life history traits of the mosquitoes. Bacteriophages, given their host specificity, can serve as a tool for modulating the microbiota. For this proof-of-principle study, we selected representative strains of five common Anopheles mosquito-associated bacterial genera, namely, Enterobacter, Serratia, Pseudomonas, Elizabethkingia, and Asaia. Our results with monoaxenic cultures showed that Anopheles larvae with Enterobacter and Pseudomonas displayed normal larval development with no significant mortality. However, monoaxenic Anopheles larvae with Elizabethkingia showed delayed larval development and higher mortality. Serratia and Asaia gnotobiotic larvae failed to develop past the first instar. We isolated and characterized three novel bacteriophages (EP1, SP1, and EKP1) targeting Enterobacter, Serratia, and Elizabethkingia, respectively, and utilized a previously characterized bacteriophage (GH1) targeting Pseudomonas to modulate larval water microbiota. Gnotobiotic Anopheles larvae with all five bacterial genera showed reduced survival and larval development with the addition of bacteriophages EP1 and GH1, targeting Enterobacter and Pseudomonas, respectively. The effect was synergistic when both EP1 and GH1 were added together. Our results demonstrate a novel application of bacteriophages for mosquito control. IMPORTANCE Mosquitoes are efficient vectors of multiple human and animal pathogens. The biology of mosquitoes is strongly affected by their associated microbiota. Because of the important role of the larval microbiota in mosquito biology, the microbiota can potentially serve as a target for altering mosquito life-history traits. Our study provides proof of principle that bacteriophages can be used as tools to modulate the mosquito larval habitat microbiota and can, in turn, affect larval development and survival. These results highlight the utility of bacteriophages in mosquito microbiota research and also provide a new potential mosquito control tool.
Collapse
|
5
|
Chancharoenthana W, Sutnu N, Visitchanakun P, Sawaswong V, Chitcharoen S, Payungporn S, Schuetz A, Schultz MJ, Leelahavanichkul A. Critical roles of sepsis-reshaped fecal virota in attenuating sepsis severity. Front Immunol 2022; 13:940935. [PMID: 35983067 PMCID: PMC9380439 DOI: 10.3389/fimmu.2022.940935] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Because studies on all fecal organisms (bacteria, fungi, and viruses) in sepsis are rare and bacteriophages during sepsis might have adapted against gut bacteria with possible pathogenicity, cecal ligation and puncture (CLP; a sepsis mouse model) was evaluated. In fecal bacteriome, sepsis increased Bacteroides and Proteobacteria but decreased Firmicutes, while fecal virome demonstrated increased Podoviridae when compared with sham feces. There was no difference in the fungal microbiome (predominant Ascomycota in both sham and CLP mice) and the abundance of all organisms between sepsis and control groups. Interestingly, the transfers of feces from CLP mice worsened sepsis severity when compared with sham fecal transplantation, as evaluated by mortality, renal injury (serum creatinine and histology), liver damage (liver enzyme and histology), spleen apoptosis, serum cytokines, endotoxemia, and bacteremia. In contrast, the transfers of fecal viral particles from sepsis mice, but not from sham mice, attenuated inflammation in CLP sepsis possibly through the decrease in several fecal pathogenic bacteria (such as Proteobacteria, Gammaproteobacteria, and Prevotellaceae) as evaluated by fecal microbiome analysis. Perhaps the isolation of favorable bacteriophages in sepsis feces and increased abundance ex vivo before oral treatment in a high concentration are beneficial.
Collapse
Affiliation(s)
- Wiwat Chancharoenthana
- Tropical Nephrology Research Unit, Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Tropical Immunology and Translational Research Unit, Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- *Correspondence: Wiwat Chancharoenthana, ; Asada Leelahavanichkul,
| | - Nattawut Sutnu
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence on Translational Research in Inflammatory and Immunology (CETRII), Department of Microbiology, Chulalongkorn University, Bangkok, Thailand
| | - Peerapat Visitchanakun
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence on Translational Research in Inflammatory and Immunology (CETRII), Department of Microbiology, Chulalongkorn University, Bangkok, Thailand
| | - Vorthon Sawaswong
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Suwalak Chitcharoen
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sunchai Payungporn
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Alexandra Schuetz
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda , MD, United States
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences-United States Component, Bangkok, Thailand
| | - Marcus J. Schultz
- Mahidol–Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Intensive Care & Laboratory of Experimental Intensive Care and Anesthesiology (L.E.I.C.A), Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Asada Leelahavanichkul
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence on Translational Research in Inflammatory and Immunology (CETRII), Department of Microbiology, Chulalongkorn University, Bangkok, Thailand
- *Correspondence: Wiwat Chancharoenthana, ; Asada Leelahavanichkul,
| |
Collapse
|
6
|
Yuanyuan N, Xiaobo Y, Shang W, Yutong Y, Hongrui Z, Chenyu L, Bin X, Xi Z, Chen Z, Zhiqiang S, Jingfeng W, Yun L, Pingfeng Y, Zhigang Q. Isolation and characterization of two homolog phages infecting Pseudomonas aeruginosa. Front Microbiol 2022; 13:946251. [PMID: 35935197 PMCID: PMC9348578 DOI: 10.3389/fmicb.2022.946251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/24/2022] [Indexed: 12/02/2022] Open
Abstract
Bacteriophages (phages) are capable of infecting specific bacteria, and therefore can be used as a biological control agent to control bacteria-induced animal, plant, and human diseases. In this study, two homolog phages (named PPAY and PPAT) that infect Pseudomonas aeruginosa PAO1 were isolated and characterized. The results of the phage plaque assay showed that PPAT plaques were transparent dots, while the PPAY plaques were translucent dots with a halo. Transmission electron microscopy results showed that PPAT (65 nm) and PPAY (60 nm) strains are similar in size and have an icosahedral head and a short tail. Therefore, these belong to the short-tailed phage family Podoviridae. One-step growth curves revealed the latent period of 20 min and burst time of 30 min for PPAT and PPAY. The burst size of PPAT (953 PFUs/infected cell) was higher than that of PPAY (457 PFUs/infected cell). Also, the adsorption rate constant of PPAT (5.97 × 10−7 ml/min) was higher than that of PPAY (1.32 × 10−7 ml/min) at 5 min. Whole-genome sequencing of phages was carried out using the Illumina HiSeq platform. The genomes of PPAT and PPAY have 54,888 and 50,154 bp, respectively. Only 17 of the 352 predicted ORFs of PPAT could be matched to homologous genes of known function. Likewise, among the 351 predicted ORFs of PPAY, only 18 ORFs could be matched to genes of established functions. Homology and evolutionary analysis indicated that PPAT and PPAY are closely related to PA11. The presence of tail fiber proteins in PPAY but not in PPAT may have contributed to the halo effect of its plaque spots. In all, PPAT and PPAY, newly discovered P. aeruginosa phages, showed growth inhibitory effects on bacteria and can be used for research and clinical purposes.
Collapse
Affiliation(s)
- Niu Yuanyuan
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Yang Xiaobo
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Wang Shang
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Yang Yutong
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhou Hongrui
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Li Chenyu
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Xue Bin
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhang Xi
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhao Chen
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Shen Zhiqiang
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Wang Jingfeng
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Ling Yun
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
- *Correspondence: Ling Yun,
| | - Yu Pingfeng
- College of Environment and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Qiu Zhigang
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
- Qiu Zhigang,
| |
Collapse
|
7
|
Kabwe M, Dashper S, Tucci J. The Microbiome in Pancreatic Cancer-Implications for Diagnosis and Precision Bacteriophage Therapy for This Low Survival Disease. Front Cell Infect Microbiol 2022; 12:871293. [PMID: 35663462 PMCID: PMC9160434 DOI: 10.3389/fcimb.2022.871293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
While the mortality rates for many cancers have decreased due to improved detection and treatments, that of pancreatic cancer remains stubbornly high. The microbiome is an important factor in the progression of many cancers. Greater understanding of the microbiome in pancreatic cancer patients, as well as its manipulation, may assist in diagnosis and treatment of this disease. In this report we reviewed studies that compared microbiome changes in pancreatic cancer patients and non-cancer patients. We then identified which bacterial genera were most increased in relative abundance across the oral, pancreatic, duodenal, and faecal tissue microbiomes. In light of these findings, we discuss the potential for utilising these bacteria as diagnostic biomarkers, as well as their potential control using precision targeting with bacteriophages, in instances where a causal oncogenic link is made.
Collapse
Affiliation(s)
- Mwila Kabwe
- Department of Rural Clinical Sciences, La Trobe Rural Health School, La Trobe University, Bendigo, VIC, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC, Australia
| | - Stuart Dashper
- Melbourne Dental School, University of Melbourne, Melbourne, VIC, Australia
| | - Joseph Tucci
- Department of Rural Clinical Sciences, La Trobe Rural Health School, La Trobe University, Bendigo, VIC, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC, Australia
| |
Collapse
|
8
|
Bujak K, Decewicz P, Kitowicz M, Radlinska M. Characterization of Three Novel Virulent Aeromonas Phages Provides Insights into the Diversity of the Autographiviridae Family. Viruses 2022; 14:1016. [PMID: 35632757 PMCID: PMC9145550 DOI: 10.3390/v14051016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022] Open
Abstract
In this study, we isolated and characterized three novel virulent Autographiviridae bacteriophages, vB_AspA_Bolek, vB_AspA_Lolek, and vB_AspA_Tola, which infect different Aeromonas strains. These three host-pathogen pairs were derived from the same sampling location-the arsenic-containing microbial mats of the Zloty Stok gold mine. Functional analysis showed they are psychrotolerant (4-25 °C), albeit with a much wider temperature range of propagation for the hosts (≤37 °C). Comparative genomic analyses revealed a high nucleotide and amino acid sequence similarity of vB_AspA_Bolek and vB_AspA_Lolek, with significant differences exclusively in the C-terminal region of their tail fibers, which might explain their host range discrimination. The protein-based phage network, together with a phylogenetic analysis of the marker proteins, allowed us to assign vB_AspA_Bolek and vB_AspA_Lolek to the Beijerinckvirinae and vB_AspA_Tola to the Colwellvirinae subfamilies, but as three novel species, due to their low nucleotide sequence coverage and identity with other known phage genomes. Global comparative analysis showed that the studied phages are also markedly different from most of the 24 Aeromonas autographiviruses known so far. Finally, this study provides in-depth insight into the diversity of the Autographiviridae phages and reveals genomic similarities between selected groups of this family as well as between autographiviruses and their relatives of other Caudoviricetes families.
Collapse
Affiliation(s)
| | | | | | - Monika Radlinska
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (K.B.); (P.D.); (M.K.)
| |
Collapse
|
9
|
Ford S, Moeskjær S, Young P, Santamaría RI, Harrison E. Introducing a Novel, Broad Host Range Temperate Phage Family Infecting Rhizobium leguminosarum and Beyond. Front Microbiol 2021; 12:765271. [PMID: 34858375 PMCID: PMC8631192 DOI: 10.3389/fmicb.2021.765271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/13/2021] [Indexed: 02/01/2023] Open
Abstract
Temperate phages play important roles in bacterial communities but have been largely overlooked, particularly in non-pathogenic bacteria. In rhizobia the presence of temperate phages has the potential to have significant ecological impacts but few examples have been described. Here we characterize a novel group of 5 Rhizobium leguminosarum prophages, capable of sustaining infections across a broad host range within their host genus. Genome comparisons identified further putative prophages infecting multiple Rhizobium species isolated globally, revealing a wider family of 10 temperate phages including one previously described lytic phage, RHEph01, which appears to have lost the ability to form lysogens. Phylogenetic discordance between prophage and host phylogenies suggests a history of active mobilization between Rhizobium lineages. Genome comparisons revealed conservation of gene content and order, with the notable exception of an approximately 5 kb region of hypervariability, containing almost exclusively hypothetical genes. Additionally, several horizontally acquired genes are present across the group, including a putative antirepressor present only in the RHEph01 genome, which may explain its apparent inability to form lysogens. In summary, both phenotypic and genomic comparisons between members of this group of phages reveals a clade of viruses with a long history of mobilization within and between Rhizobium species.
Collapse
Affiliation(s)
- Sam Ford
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Sara Moeskjær
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Peter Young
- Department of Biology, University of York, York, United Kingdom
| | - Rosa I Santamaría
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, México City, Mexico
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| |
Collapse
|
10
|
Dkhili S, Ribeiro M, Ghariani S, Yahia HB, Hillion M, Poeta P, Slama KB, Hébraud M, Igrejas G. Bacteriophages as Antimicrobial Agents? Proteomic Insights on Three Novel Lytic Bacteriophages Infecting ESBL-Producing Escherichia coli. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:626-640. [PMID: 34559008 DOI: 10.1089/omi.2021.0122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
With the emergence of multiresistant bacteria, the use of bacteriophages is gaining renewed interest as potential antimicrobial agents. The aim of this study was to analyze the structure of three lytic bacteriophages infecting Escherichia coli (SD1, SD2, and SD3) using a gel-based proteomics approach and the cellular response of this bacterium to phage SD1 infection at the proteome level. The combination of the results of 1-DE and 2-DE followed by mass spectrometry led to the identification of 3, 14, and 9 structure proteins for SD1, SD2, and SD3 phages, respectively. Different protein profiles with common proteins were noticed. We also analyzed phage-induced effects by comparing samples from infected cells to those of noninfected cells. We verified important changes in E. coli proteins expression during phage SD1 infection, where there was an overexpression of proteins involved in stress response. Our results indicated that viral infection caused bacterial oxidative stress and bacterial cells response to stress was orchestrated by antioxidant defense mechanisms. This article makes an empirical scientific contribution toward the concept of bacteriophages as potential antimicrobial agents. With converging ecological threats in the 21st century, novel approaches to address the innovation gaps in antimicrobial development are more essential than ever. Further research on bacteriophages is called for in this broader context of planetary health and integrative biology.
Collapse
Affiliation(s)
- Sadika Dkhili
- Laboratoire des Microorganismes et Biomolécules actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie.,Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Miguel Ribeiro
- Department of Genetics and Biotechnology and University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Functional Genomics and Proteomics Unity, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,LAQV-REQUIMTE, Faculty of Science and Technology, University Nova of Lisbon, Lisbon, Portugal
| | - Salma Ghariani
- Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Houssem Ben Yahia
- Laboratoire des Microorganismes et Biomolécules actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie.,Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Mélanie Hillion
- University Clermont Auvergne, INRAE, UMR0454 Microbiology Digestive Environment Health (MEDiS), Saint-Genès Champanelle, France.,INRAE, Metabolism Exploration Platform, Proteomic Component (PFEMcp), Saint-Genès Champanelle, France
| | - Patricia Poeta
- Department of Genetics and Biotechnology and University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Karim Ben Slama
- Laboratoire des Microorganismes et Biomolécules actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie.,Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Michel Hébraud
- University Clermont Auvergne, INRAE, UMR0454 Microbiology Digestive Environment Health (MEDiS), Saint-Genès Champanelle, France.,INRAE, Metabolism Exploration Platform, Proteomic Component (PFEMcp), Saint-Genès Champanelle, France
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology and University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Functional Genomics and Proteomics Unity, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,LAQV-REQUIMTE, Faculty of Science and Technology, University Nova of Lisbon, Lisbon, Portugal
| |
Collapse
|
11
|
Abdelrhim AS, Ahmad AA, Omar MOA, Hammad AMM, Huang Q. A new Streptomyces scabies-infecting bacteriophage from Egypt with promising biocontrol traits. Arch Microbiol 2021; 203:4233-4242. [PMID: 34091692 DOI: 10.1007/s00203-021-02415-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/19/2021] [Accepted: 05/28/2021] [Indexed: 11/26/2022]
Abstract
Potato common scab caused by Streptomyces scabies is one of the most economically important diseases infecting potato. It reduces the quality of potato tubers, which subsequently decreases the tuber prices and causes significant economic losses for potato growers. Biological control using bacteriophages is a promising strategy for controlling this disease. In this study, a novel bacteriophage with high lytic efficacy against S. scabies was isolated from a potato field at El-Minya, Egypt, and was designated SscP1EGY. The phage has an icosahedral head of 55 nm and a short tail of 7.5 nm, typical of a podovirus. Its infection cycle was 90 min, including 50 min of latent time and 40 min of rise period with a burst size of approximately 200 PFU per infected cell. The genome of SscP1EGY consists 51,751 nucleotides with 76 predicted genes. SscP1EGY infected and completely lysed seven tested S. scabies strains but showed no lytic activity against three beneficial Streptomyces species, other beneficial bacterial species, and non-target plant pathogenic bacteria. In greenhouse experiments, treatment of S. scabies-inoculated potato tubers with phage SscP1EGY resulted in reductions of (1) the severity of scab, (2) the number of lesions, and (3) the percentage of lesion surface, as compared to the inoculated tubers without phage treatment. Also, scab lesions appeared superficial in phage-treated tubers but pitted in non-phage-treated tubers. Our results suggest that SscP1EGY has a potential as a biological control agent for S. scabies. Based on our knowledge, SscP1EGY is the first sequenced S. scabies-infecting phage in Egypt.
Collapse
Affiliation(s)
- Abdelrazek S Abdelrhim
- Department of Plant Pathology, Faculty of Agriculture, Minia University, El-Minia, 61519, Egypt
| | - Abdelmonim Ali Ahmad
- Department of Plant Pathology, Faculty of Agriculture, Minia University, El-Minia, 61519, Egypt
| | - Maha O A Omar
- Department of Microbiology, Faculty of Agriculture, Minia University, El-Minia, 61519, Egypt
| | - Adel M M Hammad
- Department of Microbiology, Faculty of Agriculture, Minia University, El-Minia, 61519, Egypt
| | - Qi Huang
- Floral and Nursery Plants Research Unit, United States Department of Agriculture, Agricultural Research Service, United States National Arboretum, Beltsville, MD, USA.
| |
Collapse
|
12
|
Kumar P, Meghvansi MK, Kamboj DV. Phenotypic Characterization and Whole-Genome Analysis of a Novel Bacteriophage HCF1 Infecting Citrobacter amalonaticus and C. freundii. Front Microbiol 2021; 12:644013. [PMID: 33569047 PMCID: PMC7868345 DOI: 10.3389/fmicb.2021.644013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 01/04/2021] [Indexed: 12/26/2022] Open
Abstract
Citrobacter species often occur in sewage, food, soil, wastewater, and in the intestinal tract of animals and humans. Citrobacter spp. cause urinary tract infections (UTIs) and infantile meningitis in humans. Due to the presence of plasmid-encoded resistance genes, Citrobacter spp. are often resistant to many antibiotics. In this study, Citrobacter virus HCF1, a novel virulent bacteriophage capable of killing Citrobacter amalonaticus and Citrobacter freundii, was isolated from the sewage water. The isolated bacteriophage was characterized with respect to transmission electron microscopy, one-step growth curve, host range, in vitro efficacy, storage stability, and environmental stress tolerance. The one-step growth curve analysis revealed that the latent period of HCF1 was 30 min and the estimated burst size was 121 plaque-forming units (PFU) per bacterial cell. Host range testing indicated that the HCF1 was specific to the Citrobacter genus. In vitro efficacy assay in the effluent of an anaerobic biodigester showed that the HCF1 completely eliminated the host within 4 and 5 h at MOI:100 and MOI:10, respectively, thereby indicating its potential for combating C. amalonaticus infections. The isolated bacteriophage is considerably stable and tolerant to environmental stress. Furthermore, the complete genome of HCF1 was sequenced using Oxford Nanopore sequencing and the data were subjected to detailed bioinformatic analyses. NCBI-BLASTn analysis revealed that the HCF1 genome had a query coverage of 15-21% and a maximum similarity of 77.27-78.49% with 11 bacteriophages of the Drexlerviridae family. Detailed bioinformatic analysis of the genome profile suggests that HCF1 is a novel T1svirus belonging to the Tempevirinae subfamily of the Drexlerviridae family.
Collapse
Affiliation(s)
| | | | - Dev V. Kamboj
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, India
| |
Collapse
|
13
|
Liu J, Liu P, Feng F, Zhang J, Li F, Wang M, Sun Y. Evaluation of Potential ARG Packaging by Two Environmental T7-Like Phage during Phage-Host Interaction. Viruses 2020; 12:v12101060. [PMID: 32977432 PMCID: PMC7598189 DOI: 10.3390/v12101060] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/11/2020] [Accepted: 09/21/2020] [Indexed: 12/20/2022] Open
Abstract
The increase in antimicrobial resistance is a threat to both human and animal health. The transfer of antibiotic resistance genes (ARG) via plasmids has been studied in detail whereas the contribution of bacteriophage-mediated ARG transmission is relatively little explored. We isolated and characterized two T7-like lytic bacteriophages that infected multidrug-resistant Escherichia coli hosts. The morphology and genomic analysis indicated that both phage HZP2 and HZ2R8 were evolutionarily related and their genomes did not encode ARGs. However, ARG-like raw reads were detected in offspring sequencing data with a different abundance level implying that potential ARG packaging had occurred. PCR results demonstrated that six fragments of genes (qnrS, cmlA, tetM, blaTEM, sul3, mcr-1) were potentially packaged by phage HZP2 and four (qnrS, cmlA, blaTEM, mcr-1) by phage HZ2R8. Further quantitative results showed that ARG abundance hierarchies were similar. The gene blaTEM was the most abundant (up to 1.38 × 107 copies/mL) whereas cmlA and qnrS were the least. Moreover, the clinically important mcr-1 gene was the second most abundant ARG indicating a possibility for spread through generalized transduction. Together, our results indicated that these structurally similar phage possessed similar characteristics and potential packaging during phage-host interaction displayed an ARG preference rather than occurring randomly.
Collapse
Affiliation(s)
- Junlin Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510640, China; (J.L.); (F.F.); (J.Z.); (F.L.); (M.W.)
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510640, China
| | - Peng Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China;
| | - Fenglin Feng
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510640, China; (J.L.); (F.F.); (J.Z.); (F.L.); (M.W.)
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510640, China
| | - Junxuan Zhang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510640, China; (J.L.); (F.F.); (J.Z.); (F.L.); (M.W.)
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510640, China
| | - Fulin Li
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510640, China; (J.L.); (F.F.); (J.Z.); (F.L.); (M.W.)
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510640, China
| | - Mianzhi Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510640, China; (J.L.); (F.F.); (J.Z.); (F.L.); (M.W.)
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510640, China
| | - Yongxue Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510640, China; (J.L.); (F.F.); (J.Z.); (F.L.); (M.W.)
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510640, China
- Correspondence: ; Tel.: +86-135-0304-8309
| |
Collapse
|
14
|
Isolation, characterization, and efficacy of bacteriophages isolated against Citrobacter spp. an in vivo approach in a zebrafish model (Danio rerio). Res Microbiol 2020; 171:341-350. [PMID: 32919052 DOI: 10.1016/j.resmic.2020.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022]
Abstract
Citrobacter infections are becoming an increasingly significant health problem in aquaculture in South-Eastern countries. The objective of this study was to isolate and evaluate the potential of lytic bacteriophages against Citrobacter infections. TEM analysis revealed that the isolated phages Citrophage MRM19 and Citrophage MRM57 were identified to be Siphovirus and Podovirus family of the order Caudovirales. The phage life-cycle studies showed that Citrophage MRM19 had an adsorption time of 18 ± 1 min and a latency period of 25 ± 3 min with burst size of 110 ± 20 phages/infected cell and Citrophage MRM57 had an adsorption time of 15 ± 1 min and a latency period of 25 ± 2 min with burst size of 50 ± 5 phages/infected cell. In vitro studies indicated that the bacterial load was reduced by 5 and 7 log units within 12 h by Citrophage MRM19 and Citrophage MRM57. The in vivo efficacy of the phages was studied using zebrafish (Danio rerio) as a model organism in low-scale tanks. The study unveiled that the use of phages increased the survival up to 17%, 23%, and 26% in the case of Citrophage MRM19, Citrophage MRM57, and phage cocktail treatment, respectively. Our study indicated that bacteriophages are suitable biocontrol agents against Citrobacter spp. especially in aquaculture industry.
Collapse
|
15
|
Mizuno CM, Luong T, Cederstrom R, Krupovic M, Debarbieux L, Roach DR. Isolation and Characterization of Bacteriophages That Infect Citrobacter rodentium, a Model Pathogen for Intestinal Diseases. Viruses 2020; 12:E737. [PMID: 32650458 PMCID: PMC7412075 DOI: 10.3390/v12070737] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/30/2020] [Accepted: 07/07/2020] [Indexed: 12/22/2022] Open
Abstract
Enteropathogenic Escherichia coli (EPEC) is a major pathogen for diarrheal diseases among children. Antibiotics, when used appropriately, are effective; however, their overuse and misuse have led to the rise of antibiotic resistance worldwide. Thus, there are renewed efforts into the development of phage therapy as an alternative antibacterial therapy. Because EPEC in vivo models have shortcomings, a surrogate is used to study the mouse pathogen Citrobacter rodentium in animal models. In this study, two new phages CrRp3 and CrRp10, which infect C. rodentium, were isolated and characterized. CrRp3 was found to be a new species within the genus Vectrevirus, and CrRp10 is a new strain within the species Escherichia virus Ime09, in the genus Tequatrovirus. Both phages appear to have independently evolved from E. coli phages, rather than other Citrobacter spp. phages. Neither phage strain carries known genes associated with bacterial virulence, antibiotic resistance, or lysogeny. CrRp3 is more potent, having a 24-fold faster adsorption rate and shorter lytic cycle when compared to the same properties of CrRp10. However, a lysis curve analysis revealed that CrRp10 prevented growth of C. rodentium for 18 h, whereas resistance developed against CrRp3 within 9 h. We also show that hypoxic (5% oxygen) conditions decreased CrRp3 ability to control bacterial densities in culture. In contrast, low oxygen conditions did not affect CrRp10 ability to replicate on C. rodentium. Together, CrRp10 is likely to be the better candidate for future phage therapy investigations.
Collapse
Affiliation(s)
- Carolina M. Mizuno
- Department of Microbiology, Institut Pasteur, 75015 Paris, France; (C.M.M.); (M.K.); (L.D.)
| | - Tiffany Luong
- Department of Biology, San Diego State University, San Diego, CA 92182, USA; (T.L.); (R.C.)
| | - Robert Cederstrom
- Department of Biology, San Diego State University, San Diego, CA 92182, USA; (T.L.); (R.C.)
| | - Mart Krupovic
- Department of Microbiology, Institut Pasteur, 75015 Paris, France; (C.M.M.); (M.K.); (L.D.)
| | - Laurent Debarbieux
- Department of Microbiology, Institut Pasteur, 75015 Paris, France; (C.M.M.); (M.K.); (L.D.)
| | - Dwayne R. Roach
- Department of Biology, San Diego State University, San Diego, CA 92182, USA; (T.L.); (R.C.)
- Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| |
Collapse
|
16
|
Kim Y, Ko S, Yeon YE, Kim H, Oh CS, Ahn JK, Kim D. Genomic and Phenotypic Characterization of a Lytic Bacteriophage CF1 Infecting the Multi-drug Resistant Bacterium Citrobacter freundii. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0505-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
17
|
Álvarez B, López MM, Biosca EG. Biocontrol of the Major Plant Pathogen Ralstonia solanacearum in Irrigation Water and Host Plants by Novel Waterborne Lytic Bacteriophages. Front Microbiol 2019; 10:2813. [PMID: 31866979 PMCID: PMC6908813 DOI: 10.3389/fmicb.2019.02813] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/20/2019] [Indexed: 12/31/2022] Open
Abstract
Three new lytic bacteriophages were found to effectively control the pathogen Ralstonia solanacearum, a quarantine bacterium in many countries, and causative agent of bacterial wilt, one of the most important vascular plant diseases. Bacterial wilt management has been carried out with fluctuating effects, suggesting the need to find alternative treatments. In this work, three lytic phages were isolated from environmental water from geographically distant regions in Spain. They proved to specifically infect a collection of R. solanacearum strains, and some of the closely related pathogenic species Ralstonia pseudosolanacearum, without affecting non-target environmental bacteria, and were able to lyze the pathogen populations within a wide range of conditions comprising environmental values of water temperatures, pH, salinity, and lack of aeration found in storage tanks. The three bacteriophages displayed high efficiency in controlling R. solanacearum, with reductions of the bacterial populations of several orders of magnitude in just a few hours, and proved to be able to survive in freshwater for months at environmental temperatures keeping activity on R. solanacearum, pointing out their suitability for field application through irrigation. Concerning their biocontrol potential, they were effective in reducing high populations of the pathogen in environmental water, and bacterial wilt incidence in planta by watering with either one phage or their combinations in assays with more than 300 plants. This is the first report on effective R. solanacearum biocontrol by applying single or combined bacteriophages through irrigation water in conditions mimicking those of the natural settings. The three phages belong to the Podoviridae family and are members of the T7likevirus genus. They are the first isolated phages from river water with activity against R. solanacearum, showing the longest persistence in natural water reported until now for phages with biocontrol potential, and consistently being able to control the disease in the host plant under environmental conditions. Consequently, the use of these bacteriophages for the prevention and/or biocontrol of the bacterial wilt disease caused by R. solanacearum has been patented. Evidence provided reveals the suitability of these waterborne phages to be effectively considered as a valuable strategy within the frame of sustainable integrated management programs.
Collapse
Affiliation(s)
- Belén Álvarez
- Departamento de Bacteriología, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
- Departamento de Microbiología y Ecología, Universitat de València, Valencia, Spain
| | - María M. López
- Departamento de Bacteriología, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Elena G. Biosca
- Departamento de Microbiología y Ecología, Universitat de València, Valencia, Spain
| |
Collapse
|
18
|
Abstract
Citrobacter freundii is a nosocomial opportunistic pathogen that can cause urinary and bloodstream infections. Phage therapies against C. freundii may prove useful in treating infections caused by this ubiquitous bacterium. Here, we report the complete genome of a T4-like myophage, Maroon, that infects C. freundii.
Collapse
|
19
|
Complete Genome Sequence of Citrobacter freundii Myophage Maleficent. Microbiol Resour Announc 2019; 8:8/42/e01153-19. [PMID: 31624155 PMCID: PMC6797544 DOI: 10.1128/mra.01153-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Citrobacter freundii, a member of the Enterobacteriaceae family, has been linked to opportunistic infections in neonates and immunocompromised adults. Here, we report the complete genome sequence of a T4-like myophage, Maleficent, which infects C. freundii.
Collapse
|
20
|
Zhao C, Wang X, Zhang C, Liu B, Jing H, Ming L, Jiang H, Zheng Y, Liu P, Liu G, Jiang Y. Development of a TaqMan Array card to target 21 purulent meningitis-related pathogens. BMC Infect Dis 2019; 19:289. [PMID: 30922257 PMCID: PMC6438039 DOI: 10.1186/s12879-019-3856-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/27/2019] [Indexed: 02/08/2023] Open
Abstract
Background Purulent meningitis (PM) is a serious life-threatening infection of the central nervous system (CNS) by bacteria or fungi and associated with high mortality and high incidence of CNS sequelae in children. However, the conventional cerebrospinal fluid (CSF) culture method is time-consuming and has a low sensitivity. Methods Our study developed a real-time PCR-based purulent meningitis-TaqMan array card (PM-TAC) that targeted 21 PM-related pathogens and could produce results within 3 h. Primers and probes were adapted from published sources possibly. The performance of them were evaluated and optimized and then they were spotted on TAC. Results The PM-TAC showed a sensitivity and specificity of 95 and 96%, respectively. For all of the 21 targeted pathogens, the PM-TAC assay had a LOD ranging from 5 copies/reaction to 100 copies/reaction, an intra-assay variation of 0.07–4.45%, and an inter-assay variation of 0.11–6.81%. Of the 15 CSF samples collected from patients with PM after empiric antibiotic therapies, the positive rate was 53.3% (8/15) for our PM-TAC assay but was only 13.3% (2/15) for the CSF culture method. Of the 17 CSF samples showing negative CSF culture, the PM-TAC assay identified a case of Neisseria meningitidis infection. Furthermore, all of the 10 CSF samples from patients without CNS infection showed negative for the PM-TAC assay. Conclusions Our PM-TAC assay also demonstrated that the pathogen loads in the CSF samples correlated with the severity of PM. Thus, the PM-TAC may be helpful to improve the prognosis of PM and clinical outcomes from antibiotic therapies. Electronic supplementary material The online version of this article (10.1186/s12879-019-3856-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Chengna Zhao
- Anhui Medical University, Hefei, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xi Wang
- Department of Infectious Medicine, Beijing Children's Hospital, Capital Medical University, National Center for Chidren's Health, Beijing, China
| | - Chao Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bing Liu
- Department of Infectious Medicine, Beijing Children's Hospital, Capital Medical University, National Center for Chidren's Health, Beijing, China
| | - Hongbo Jing
- Shunyi District Center for Disease Control and Prevention, Beijing, China
| | - Lihua Ming
- Chest Hospital of Xinjiang, Urumqi, China
| | - Hua Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuling Zheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Peng Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
| | - Gang Liu
- Department of Infectious Medicine, Beijing Children's Hospital, Capital Medical University, National Center for Chidren's Health, Beijing, China.
| | - Yongqiang Jiang
- Anhui Medical University, Hefei, China. .,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
| |
Collapse
|
21
|
Kajsík M, Bugala J, Kadličeková V, Szemes T, Turňa J, Drahovská H. Characterization of Dev-CD-23823 and Dev-CT57, new Autographivirinae bacteriophages infecting Cronobacter spp. Arch Virol 2019; 164:1383-1391. [DOI: 10.1007/s00705-019-04202-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/09/2019] [Indexed: 02/04/2023]
|
22
|
Wang Q, Zeng X, Yang Q, Yang C. Identification of a bacteriophage from an environmental multidrug-resistant E. coli isolate and its function in horizontal transfer of ARGs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 639:617-623. [PMID: 29803035 DOI: 10.1016/j.scitotenv.2018.05.213] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/08/2018] [Accepted: 05/17/2018] [Indexed: 06/08/2023]
Abstract
Horizontal transfer of ARGs was generally considered to be mediated by three methods - transformation, conjugation and transduction through phages - during which the contribution of bacteriophages to gene transfer in the environment is unclear or even questioned. In this study, a multiple-antibiotic-resistant Escherichia coli strain and its phage (YZ1) were isolated from a municipal wastewater treatment system. The results of the morphological and genomic analyses of phage YZ1 showed that it is a member of the T7 viral genus in the subfamily Autographivirinae. Its genome is similar to that of the E. coli phage K1F in both organization and sequence and does not encode ARGs. However, 28 paired reads in the raw sequencing data aligned to ARGs, including those promoting β-lactam, aminoglycoside, and fluoroquinolone resistance, among others. Quantitative PCR showed that ARGs were present in bacteriophage DNA (approximately 103 copies/mL) and were also detected in the bacterial host DNA. The results suggested that while infrequent, some ARG-carrying transducing phages were presumably generated by erroneous packaging during infection of antibiotic-resistant bacteria, which may create the possibility of horizontal transfer of ARGs.
Collapse
Affiliation(s)
- Qiang Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Key Laboratory for Microorganisms and Functional Molecules (Henan Normal University), University of Henan Province, Xinxiang 453007, China
| | - Xiangpeng Zeng
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Qingxiang Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Key Laboratory for Microorganisms and Functional Molecules (Henan Normal University), University of Henan Province, Xinxiang 453007, China.
| | - Chuanzhen Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| |
Collapse
|
23
|
Elhalag K, Nasr-Eldin M, Hussien A, Ahmad A. Potential use of soilborne lytic Podoviridae phage as a biocontrol agent against Ralstonia solanacearum. J Basic Microbiol 2018; 58:658-669. [PMID: 29938804 DOI: 10.1002/jobm.201800039] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 05/03/2018] [Accepted: 05/31/2018] [Indexed: 11/11/2022]
Abstract
A new podovirus RsPod1EGY Ralstonia phage (GenBank accession no MG711516) with a specific action against R. solanacearum phylotype IIa, sequevar I (race 3, biovar 2) was isolated from Egyptian soil. The potential efficacy of the isolated phage to be used as biocontrol agent was evaluated in vitro and under greenhouse conditions. The podovirus phage produced a plaque size of 3.0-4.0 mm in diameter and completed its infection cycle in 180 min after infection with a burst size of ∼27 virions per infected cell. On the basis of restriction endonuclease analysis, the genome size of the phage was about 41 kb of double-stranded DNA. In vitro studies showed that RsPod1EGY is stable at higher temperatures (up to 60 °C), and at a wide pH range (5-9). SDS-PAGE analysis indicated the major structural protein to be approximately 32 kDa. Bacteriolytic activity of RsPod1EGY against R. solanacearum was detected at different multiplicity of infection (MOI). RsPod1EGY proved to be effective in reduction and prevention of formation of surface polysaccharides of R. solanacearum, during the exponential growth phase of the latter. Interestingly, RsPod1EGY was effective in suppression of R. solanacearum under greenhouse conditions. All Phage-treated tomato plants showed no wilt symptoms or any latent infection during the experimental period, whereas all untreated plants have wilted by 10 days post-infection. The lytic stability of RsPod1EGY phage at higher temperature as well as its effective suppression of wilting symptoms under greenhouse conditions would contribute to biocontrol the bacterial wilt disease in Egypt under field conditions.
Collapse
Affiliation(s)
- Kamel Elhalag
- Bacterial Diseases Research Department, Plant Pathology Research Institute, Agricultural Research Center (ARC), Giza, Egypt.,Potato Brown Rot Project, Ministry of Agriculture, Dokki, Giza, Egypt
| | - Mohamed Nasr-Eldin
- Faculty of Science, Department of Botany, Benha University, Benha, Egypt
| | - Ahmed Hussien
- Potato Brown Rot Project, Ministry of Agriculture, Dokki, Giza, Egypt.,Central Administration of Plant Quarantine, Dokki, Giza, Egypt
| | - Abdelmonim Ahmad
- Faculty of Agriculture, Department of Plant Pathology, Minia University, El-minia, Egypt
| |
Collapse
|
24
|
Tie K, Yuan Y, Yan S, Yu X, Zhang Q, Xu H, Zhang Y, Gu J, Sun C, Lei L, Han W, Feng X. Isolation and identification of Salmonella pullorum bacteriophage YSP2 and its use as a therapy for chicken diarrhea. Virus Genes 2018; 54:446-456. [PMID: 29564689 DOI: 10.1007/s11262-018-1549-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/05/2018] [Indexed: 11/28/2022]
Abstract
Salmonella pullorum is the major pathogen that is harmful to the poultry industry in developing countries, and the treatment of chicken diarrhea caused by S. pullorum has become increasingly difficult. In this study, a virulent bacteriophage YSP2, which was able to specifically infect Salmonella, was isolated and characterized. Phage YSP2 was classified in the Siphoviridae family and had a short latent period of 10 min. No bacterial virulence- or lysogenesis-related ORF is present in the YSP2 genome, making it eligible for use in phage therapy. Experiments in vivo investigated the potential use of phages as a therapy against diarrhea in chickens caused by S. pullorum in a chicken diarrhea model, demonstrating that a single oral administration of YSP2 (1 × 1010 PFU/mL, 80 μL/chicken) 2 h after S. pullorum oral administration at a double median lethal dose was sufficient to protect chickens against diarrhea. Gross inspection showed that YSP2 can effectively reduce organ damage and significantly relieve hemorrhage in the intestine and liver tissue. Moreover, YSP2 can maintain a high curative effect when diluted to 108 PFU/mL. In light of its therapeutic effect on chicken diarrhea, YSP2 may serve as an alternative treatment strategy for infections caused by S. pullorum.
Collapse
Affiliation(s)
- Kunyuan Tie
- College of Veterinary Medicine, Jilin University, No. 5333 Xi'an Road, Changchun, 130062, Jilin, People's Republic of China
| | - Yuyu Yuan
- College of Life Science and Technology, Dalian University of Technology, No. 2 Lingshui Road, Dalian, 116024, Liaoning, People's Republic of China
| | - Shiqing Yan
- College of Veterinary Medicine, Jilin University, No. 5333 Xi'an Road, Changchun, 130062, Jilin, People's Republic of China
| | - Xi Yu
- College of Animal Science, Jilin University, No. 5333 Xi'an Road, Changchun, 130062, Jilin, People's Republic of China
| | - Qiuyang Zhang
- College of Veterinary Medicine, Jilin University, No. 5333 Xi'an Road, Changchun, 130062, Jilin, People's Republic of China
| | - Huihui Xu
- College of Veterinary Medicine, Jilin University, No. 5333 Xi'an Road, Changchun, 130062, Jilin, People's Republic of China
| | - Yang Zhang
- College of Veterinary Medicine, Jilin University, No. 5333 Xi'an Road, Changchun, 130062, Jilin, People's Republic of China
| | - Jingmin Gu
- College of Veterinary Medicine, Jilin University, No. 5333 Xi'an Road, Changchun, 130062, Jilin, People's Republic of China
| | - Changjiang Sun
- College of Veterinary Medicine, Jilin University, No. 5333 Xi'an Road, Changchun, 130062, Jilin, People's Republic of China
| | - Liancheng Lei
- College of Veterinary Medicine, Jilin University, No. 5333 Xi'an Road, Changchun, 130062, Jilin, People's Republic of China
| | - Wenyu Han
- College of Veterinary Medicine, Jilin University, No. 5333 Xi'an Road, Changchun, 130062, Jilin, People's Republic of China
| | - Xin Feng
- College of Veterinary Medicine, Jilin University, No. 5333 Xi'an Road, Changchun, 130062, Jilin, People's Republic of China.
| |
Collapse
|
25
|
A Genome Comparison of T7-like Podoviruses That Infect Caulobacter crescentus. Curr Microbiol 2018; 75:760-765. [PMID: 29423729 DOI: 10.1007/s00284-018-1445-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/27/2018] [Indexed: 10/18/2022]
Abstract
Bacteriophages remain an understudied component of bacterial communities. Therefore, our laboratory has initiated an effort to isolate large numbers of bacteriophages that infect Caulobacter crescentus to provide an estimate of the diversity of bacteriophages that infect this common environmental bacterium. The majority of the new isolates are phicbkviruses, a genus of giant viruses that appear to be Caulobacter specific. However, we have also isolated several Podoviruses with icosahedral heads and small tails. One of these Podoviruses, designated Lullwater, is similar to two previously isolated Caulobacter phages, Cd1 and Percy. All three have genomes that are approximately 45 kb and contain approximately 30 genes. The gene order is conserved among the three genomes with one of the genes coding for a DNA polymerase that has homology to the family of T7 DNA polymerases. Phylogenetic trees based on either the DNA polymerase or the RNA polymerase amino acid sequences suggests that the three phages represent a new branch of the T7virus tree. Based on these similarities, we concluded that Cd1, Lullwater, and Percy comprise a new group in the T7virus genus.
Collapse
|
26
|
Geagea H, Gomaa A, Remondetto G, Moineau S, Subirade M. Molecular Structure of Lactoferrin Influences the Thermal Resistance of Lactococcal Phages. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:2214-2221. [PMID: 28241118 DOI: 10.1021/acs.jafc.6b05166] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The protective effect of whey proteins on phages of lactic acid bacteria during heat treatment limits the recycling of whey proteins into cheese. To investigate this protective effect, we used lactoferrin (LF) as a whey protein model as a result of its unique physicochemical properties and its antiviral activity. First, the thermal inactivation of lactococcal thermoresistant virulent phage P1532 was measured in LF at 95 °C and under different pH values. Phage inactivation results revealed a strong protective effect of LF on P1532 phage at pH 5 but none at pH 7. The structural conformational changes of LF were then monitored by Fourier transform infrared and circular dichroism spectroscopies. Spectroscopic analysis showed that LF was unfolded after heating at pH 7, while it preserved its tertiary and secondary structures when heated at pH 5. There is a direct correlation between the thermal stability of LF and its ability to protect P1532 phage from heat treatment.
Collapse
Affiliation(s)
| | - Ahmed Gomaa
- Department of Food Science and Nutrition, National Research Centre , Cairo, Egypt
| | | | | | | |
Collapse
|
27
|
Hamdi S, Rousseau GM, Labrie SJ, Tremblay DM, Kourda RS, Ben Slama K, Moineau S. Characterization of two polyvalent phages infecting Enterobacteriaceae. Sci Rep 2017; 7:40349. [PMID: 28091598 PMCID: PMC5238451 DOI: 10.1038/srep40349] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/05/2016] [Indexed: 01/30/2023] Open
Abstract
Bacteriophages display remarkable genetic diversity and host specificity. In this study, we explore phages infecting bacterial strains of the Enterobacteriaceae family because of their ability to infect related but distinct hosts. We isolated and characterized two novel virulent phages, SH6 and SH7, using a strain of Shigella flexneri as host bacterium. Morphological and genomic analyses revealed that phage SH6 belongs to the T1virus genus of the Siphoviridae family. Conversely, phage SH7 was classified in the T4virus genus of the Myoviridae family. Phage SH6 had a short latent period of 16 min and a burst size of 103 ± 16 PFU/infected cell while the phage SH7 latent period was 23 min with a much lower burst size of 26 ± 5 PFU/infected cell. Moreover, phage SH6 was sensitive to acidic conditions (pH < 5) while phage SH7 was stable from pH 3 to 11 for 1 hour. Of the 35 bacterial strains tested, SH6 infected its S. flexneri host strain and 8 strains of E. coli. Phage SH7 lysed additionally strains of E. coli O157:H7, Salmonella Paratyphi, and Shigella dysenteriae. The broader host ranges of these two phages as well as their microbiological properties suggest that they may be useful for controlling bacterial populations.
Collapse
Affiliation(s)
- Sana Hamdi
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisie
- Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisie
| | - Geneviève M. Rousseau
- Département de Biochimie, de Microbiologie, et de Bio-informatique and PROTEO, Faculté des Sciences et de Génie, Félix d’Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada
| | - Simon J. Labrie
- Département de Biochimie, de Microbiologie, et de Bio-informatique and PROTEO, Faculté des Sciences et de Génie, Félix d’Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada
| | - Denise M. Tremblay
- Département de Biochimie, de Microbiologie, et de Bio-informatique and PROTEO, Faculté des Sciences et de Génie, Félix d’Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada
| | - Rim Saïed Kourda
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisie
- Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisie
| | - Karim Ben Slama
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisie
- Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisie
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie, et de Bio-informatique and PROTEO, Faculté des Sciences et de Génie, Félix d’Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada
| |
Collapse
|