1
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Backman T, Latorre SM, Symeonidi E, Muszyński A, Bleak E, Eads L, Martinez-Koury PI, Som S, Hawks A, Gloss AD, Belnap DM, Manuel AM, Deutschbauer AM, Bergelson J, Azadi P, Burbano HA, Karasov TL. A phage tail-like bacteriocin suppresses competitors in metapopulations of pathogenic bacteria. Science 2024; 384:eado0713. [PMID: 38870284 DOI: 10.1126/science.ado0713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/24/2024] [Indexed: 06/15/2024]
Abstract
Bacteria can repurpose their own bacteriophage viruses (phage) to kill competing bacteria. Phage-derived elements are frequently strain specific in their killing activity, although there is limited evidence that this specificity drives bacterial population dynamics. Here, we identified intact phage and their derived elements in a metapopulation of wild plant-associated Pseudomonas genomes. We discovered that the most abundant viral cluster encodes a phage remnant resembling a phage tail called a tailocin, which bacteria have co-opted to kill bacterial competitors. Each pathogenic Pseudomonas strain carries one of a few distinct tailocin variants that target the variable polysaccharides in the outer membrane of co-occurring pathogenic Pseudomonas strains. Analysis of herbarium samples from the past 170 years revealed that the same tailocin and bacterial receptor variants have persisted in Pseudomonas populations. These results suggest that tailocin genetic diversity can be mined to develop targeted "tailocin cocktails" for microbial control.
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Affiliation(s)
- Talia Backman
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Sergio M Latorre
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Efthymia Symeonidi
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Artur Muszyński
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Ella Bleak
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Lauren Eads
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Sarita Som
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Aubrey Hawks
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Andrew D Gloss
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - David M Belnap
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Allison M Manuel
- Mass Spectrometry and Proteomics Core, The University of Utah, Salt Lake City, UT 84112, USA
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Joy Bergelson
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Hernán A Burbano
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Talia L Karasov
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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2
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de Melo AG, Morency C, Moineau S. Virulence-associated factors as targets for phage infection. Curr Opin Microbiol 2024; 79:102471. [PMID: 38569419 DOI: 10.1016/j.mib.2024.102471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/18/2024] [Accepted: 03/20/2024] [Indexed: 04/05/2024]
Abstract
Bacterial pathogens can infect a wide range of hosts and pose a threat to public and animal health as well as to agriculture. The emergence of antibiotic-resistant strains has increased this risk by making the treatment of bacterial infections even more challenging. Pathogenic bacteria thrive in various ecological niches, but they can also be specifically targeted and killed by bacteriophages (phages). Lytic phages are now investigated and even used, in some cases, as alternatives or complements to antibiotics for preventing or treating bacterial infections (phage therapy). As such, it is key to identify factors responsible for phage specificity and efficiency. Here, we review recent advances in virulence-associated factors that are targeted by phages. We highlight components of the bacterial cell surface, effector systems, and motility structures exploited by phages and the effects of phages on cell aggregation and communication. We also look at the fitness trade-off of phage resistance.
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Affiliation(s)
- Alessandra G de Melo
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Québec City, QC G1V 0A6, Canada
| | - Carlee Morency
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Québec City, QC G1V 0A6, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Québec City, QC G1V 0A6, Canada; Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, QC G1V 0A6, Canada.
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3
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Baaziz H, Makhlouf R, McClelland M, Hsu BB. Bacterial resistance to temperate phage is influenced by the frequency of lysogenic establishment. iScience 2024; 27:109595. [PMID: 38623331 PMCID: PMC11016777 DOI: 10.1016/j.isci.2024.109595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/23/2024] [Accepted: 03/25/2024] [Indexed: 04/17/2024] Open
Abstract
Temperate phages can shape bacterial community dynamics and evolution through lytic and lysogenic life cycles. In response, bacteria that resist phage infection can emerge. This study explores phage-based factors that influence bacterial resistance using a model system of temperate P22 phage and Salmonella both inside and outside the mammalian host. Phages that remained functional despite gene deletions had minimal impact on lysogeny and phage resistance except for deletions in the immI region that substantially reduced lysogeny and increased phage resistance to levels comparable to that observed with an obligately lytic P22. This immI deletion does not make the lysogen less competitive but instead increases the frequency of bacterial lysis. Thus, subtle changes in the balance between lysis and lysogeny during the initial stages of infection can significantly influence the extent of phage resistance in the bacterial population. Our work highlights the complex nature of the phage-bacteria-mammalian host triad.
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Affiliation(s)
- Hiba Baaziz
- Department of Biological Sciences, Fralin Life Sciences Institute, Center for Emerging, and Zoonotic, Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA 24061, USA
| | - Rita Makhlouf
- Department of Biological Sciences, Fralin Life Sciences Institute, Center for Emerging, and Zoonotic, Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA 24061, USA
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Bryan B. Hsu
- Department of Biological Sciences, Fralin Life Sciences Institute, Center for Emerging, and Zoonotic, Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA 24061, USA
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Zhang H, Su X, Zheng X, Liu M, Zhao C, Liu X, Ma Z, Zhang S, Zhang W. vB_EcoM-P896 coliphage isolated from duck sewage can lyse both intestinal pathogenic Escherichia coli and extraintestinal pathogenic E. coli. Int Microbiol 2024:10.1007/s10123-024-00519-5. [PMID: 38613721 DOI: 10.1007/s10123-024-00519-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/17/2024] [Accepted: 03/22/2024] [Indexed: 04/15/2024]
Abstract
Pathogenic Escherichia coli strains cause diseases in both humans and animals. The limiting factors to prevent as well as control infections from pathogenic E. coli strains are their pathotypes, serotypes, and drug resistance. Herein, a bacteriophage (vB_EcoM-P896) has been isolated from duck sewage. Furthermore, aside from targeting intestinal pathogenic E. coli strains like enteropathogenic E. coli, Shiga toxin-producing E. coli, entero-invasive E. coli, and enteroaggregative E. coli, vB_EcoM-P896 can cause lysis in extraintestinal pathogenic E. coli strains such as avian pathogenic E. coli. Stability analysis revealed that vB_EcoM-P896 was stable under the following conditions: temperature, 4℃-50℃; pH, 3-11. The sequencing of the vB_EcoM-P896 genome was conducted utilizing an HiSeq system (Illumina, San Diego, CA) and subjected to de novo assembling with the aid of Spades 3.11.1. The characteristics of the DNA genome were as follows: size, 170,656 bp; GC content, 40.4%; the number of putative coding regions, 294. Transmission electron microscopy analysis of morphology and genome analysis revealed that the phage vB_EcoM-P896 belonged to the order Caudovirales and the family Myoviridae. The pan-genome analysis of vB_EcoM-P896 was divided into two levels. The first level involved the analysis of 91 strains of muscle tail phages, which were mainly divided into 5 groups. The second level involved the analysis of 24 strains of myophage with high homology. Of the 1480 gene clusters, 23 were shared core genes. Neighbor-joining phylogenetic trees were constructed using the Poisson model with MEGA6.0 based on the conserved sequences of phage proteins, the amino acid sequence of the terminase large subunit, and tail fibrin. Further analysis revealed that vB_EcoM-P896 was a typical T4-like potent phage with potential clinical applications.
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Affiliation(s)
- Haiyan Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Food and Biology Engineering, Wuhu Institute of Technology, Wuhu, 241003, China
- Detection of Food-Borne Pathogenic Microorganisms Engineering Research Center of Wuhu, Wuhu, 241000, China
| | - Xiazhu Su
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210095, China
| | - Xiangkuan Zheng
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210095, China
| | - Meihan Liu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210095, China
| | - Chengxin Zhao
- Fushan Economic Development Zone, Yantai Jinhai Pharmaceutical Co. LTD 28 Jilin Road, Yantai City, China
| | - Xiao Liu
- Fushan Economic Development Zone, Yantai Jinhai Pharmaceutical Co. LTD 28 Jilin Road, Yantai City, China
| | - Zhenxing Ma
- Department of Food and Biology Engineering, Wuhu Institute of Technology, Wuhu, 241003, China
- Detection of Food-Borne Pathogenic Microorganisms Engineering Research Center of Wuhu, Wuhu, 241000, China
| | - Shuang Zhang
- Department of Food and Biology Engineering, Wuhu Institute of Technology, Wuhu, 241003, China.
- Detection of Food-Borne Pathogenic Microorganisms Engineering Research Center of Wuhu, Wuhu, 241000, China.
| | - Wei Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
- Detection of Food-Borne Pathogenic Microorganisms Engineering Research Center of Wuhu, Wuhu, 241000, China.
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210095, China.
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Bisen M, Kharga K, Mehta S, Jabi N, Kumar L. Bacteriophages in nature: recent advances in research tools and diverse environmental and biotechnological applications. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:22199-22242. [PMID: 38411907 DOI: 10.1007/s11356-024-32535-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/15/2024] [Indexed: 02/28/2024]
Abstract
Bacteriophages infect and replicate within bacteria and play a key role in the environment, particularly in microbial ecosystems and bacterial population dynamics. The increasing recognition of their significance stems from their wide array of environmental and biotechnological uses, which encompass the mounting issue of antimicrobial resistance (AMR). Beyond their therapeutic potential in combating antibiotic-resistant infections, bacteriophages also find vast applications such as water quality monitoring, bioremediation, and nutrient cycling within environmental sciences. Researchers are actively involved in isolating and characterizing bacteriophages from different natural sources to explore their applications. Gaining insights into key aspects such as the life cycle of bacteriophages, their host range, immune interactions, and physical stability is vital to enhance their application potential. The establishment of diverse phage libraries has become indispensable to facilitate their wide-ranging uses. Consequently, numerous protocols, ranging from traditional to cutting-edge techniques, have been developed for the isolation, detection, purification, and characterization of bacteriophages from diverse environmental sources. This review offers an exploration of tools, delves into the methods of isolation, characterization, and the extensive environmental applications of bacteriophages, particularly in areas like water quality assessment, the food sector, therapeutic interventions, and the phage therapy in various infections and diseases.
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Affiliation(s)
- Monish Bisen
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Kusum Kharga
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Sakshi Mehta
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Nashra Jabi
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Lokender Kumar
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India.
- Cancer Biology Laboratory, Raj Khosla Centre for Cancer Research, Shoolini University, Himachal Pradesh, Solan, 173229, India.
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6
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Backman T, Latorre SM, Symeonidi E, Muszyński A, Bleak E, Eads L, Martinez-Koury PI, Som S, Hawks A, Gloss AD, Belnap DM, Manuel AM, Deutschbauer AM, Bergelson J, Azadi P, Burbano HA, Karasov TL. A weaponized phage suppresses competitors in historical and modern metapopulations of pathogenic bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.17.536465. [PMID: 38352526 PMCID: PMC10862724 DOI: 10.1101/2023.04.17.536465] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Bacteriophages, the viruses of bacteria, are proposed to drive bacterial population dynamics, yet direct evidence of their impact on natural populations is limited. Here we identified viral sequences in a metapopulation of wild plant-associated Pseudomonas spp. genomes. We discovered that the most abundant viral cluster does not encode an intact phage but instead encodes a tailocin - a phage-derived element that bacteria use to kill competitors for interbacterial warfare. Each pathogenic Pseudomonas sp. strain carries one of a few distinct tailocin variants, which target variable polysaccharides in the outer membrane of co-occurring pathogenic strains. Analysis of historic herbarium samples from the last 170 years revealed that the same tailocin and receptor variants have persisted in the Pseudomonas populations for at least two centuries, suggesting the continued use of a defined set of tailocin haplotypes and receptors. These results indicate that tailocin genetic diversity can be mined to develop targeted "tailocin cocktails" for microbial control. One-Sentence Summary Bacterial pathogens in a host-associated metapopulation use a repurposed prophage to kill their competitors.
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7
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Aguilera M, Tobar-Calfucoy E, Rojas-Martínez V, Norambuena R, Serrano MJ, Cifuentes O, Zamudio MS, San Martín D, Lara P, Sabag A, Zabner M, Tichy D, Camejo P, León L, Pino M, Ulloa S, Rojas F, Pieringer C, Muster C, Castillo D, Ferreira N, Avendaño C, Canaval M, Pieringer H, Cifuentes P, Cifuentes Muñoz N. Development and characterization of a bacteriophage cocktail with high lytic efficacy against field-isolated Salmonella enterica. Poult Sci 2023; 102:103125. [PMID: 37879168 PMCID: PMC10618821 DOI: 10.1016/j.psj.2023.103125] [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: 08/14/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 10/27/2023] Open
Abstract
Salmonella spp. is a prevalent pathogen that causes great public health concern worldwide. Bacteriophage-based cocktails have arisen as an alternative to antibiotics to inhibit the growth of Salmonella. However, the bactericidal effect of bacteriophage cocktails in vivo largely differs from their observed effect in vitro. This is partly because in vitro developments of cocktails do not always consider the bacterial diversity nor the environmental conditions where bacteriophages will have to replicate. Here, we isolated and sequenced 47 bacteriophages that showed variable degrees of lytic activity against 258 Salmonella isolates from a commercial broiler company in Brazil. Three of these bacteriophages were characterized and selected to assemble a cocktail. In vitro quantitative assays determined the cocktail to be highly effective against multiple serovars of Salmonella, including Minnesota and Heidelberg. Remarkably, the in vitro lytic activity of the cocktail was retained or improved in conditions that more closely resembled the chicken gut, such as anaerobiosis, 42°C, and Salmonella mono-strain biofilms. Analysis of bacterial cross-resistance between the 3 bacteriophages composing the cocktail revealed limited or no generation of cross-resistance. Our results highlight the relevance of an optimized flux of work to develop bacteriophage cocktails against Salmonella with high lytic efficacy and strong potential to be applied in vivo in commercial broiler farms.
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Affiliation(s)
- Matías Aguilera
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Eduardo Tobar-Calfucoy
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Victoria Rojas-Martínez
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Rodrigo Norambuena
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - María Jesús Serrano
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Onix Cifuentes
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - María Sofía Zamudio
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Daniel San Martín
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Pabla Lara
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Andrea Sabag
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Marcela Zabner
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Daniel Tichy
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Pamela Camejo
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Luis León
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Michael Pino
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Soledad Ulloa
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Felipe Rojas
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Christian Pieringer
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Cecilia Muster
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Daniel Castillo
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Nicolás Ferreira
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Camilo Avendaño
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Mauro Canaval
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Hans Pieringer
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Pablo Cifuentes
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Nicolás Cifuentes Muñoz
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile..
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Marques A, Carabineiro SAC, Aureliano M, Faleiro L. Evaluation of Gold Complexes to Address Bacterial Resistance, Quorum Sensing, Biofilm Formation, and Their Antiviral Properties against Bacteriophages. TOXICS 2023; 11:879. [PMID: 37999531 PMCID: PMC10674251 DOI: 10.3390/toxics11110879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/25/2023]
Abstract
The worldwide increase in antibiotic resistance poses a significant challenge, and researchers are diligently seeking new drugs to combat infections and prevent bacterial pathogens from developing resistance. Gold (I and III) complexes are suitable for this purpose. In this study, we tested four gold (I and III) complexes, (1) chlorotrimethylphosphine gold(I); (2) chlorotriphenylphosphine gold(I); (3) dichloro(2-pyridinecarboxylate) gold (III); and (4) 1,3-bis(2,6-diisopropylphenyl)imidazole-2-ylidene gold(I) chloride, for their antibacterial, antibiofilm, antiviral, and anti-quorum sensing activities. Results reveal that 1 significantly inhibits Escherichia coli DSM 1077 and Staphylococcus aureus ATCC 6538, while 2, 3, and 4 only inhibit S. aureus ATCC 6538. The minimum inhibitory concentration (MIC) of 1 for S. aureus ATCC 6538 is 0.59 μg/mL (1.91 μM), and for methicillin-resistant S. aureus strains MRSA 12 and MRSA 15, it is 1.16 μg/mL (3.75 μM). For E. coli DSM 1077 (Gram-negative), the MIC is 4.63 μg/mL (15 μM), and for multi-resistant E. coli I731940778-1, it is 9.25 μg/mL (30 μM). Complex 1 also disrupts biofilm formation in E. coli and S. aureus after 6 h or 24 h exposure. Moreover, 1 and 2 inhibit the replication of two enterobacteria phages. Anti-quorum sensing potential still requires further clarification. These findings highlight the potential of gold complexes as effective agents to combat bacterial and viral infections.
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Affiliation(s)
- Ana Marques
- Faculdade de Ciências e Tecnologia, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal;
- Algarve Biomedical Center—Research Institute, 8005-139 Faro, Portugal
| | - Sónia A. C. Carabineiro
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal;
| | - Manuel Aureliano
- Faculdade de Ciências e Tecnologia, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal;
- Centro de Ciências do Mar (CCMar), Universidade do Algarve, 8005-139 Faro, Portugal
| | - Leonor Faleiro
- Faculdade de Ciências e Tecnologia, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal;
- Algarve Biomedical Center—Research Institute, 8005-139 Faro, Portugal
- Champalimaud Research Program, Champalimaud Centre for the Unknown, 1400-038 Lisbon, Portugal
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9
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López-Pérez J, Otero J, Sánchez-Osuna M, Erill I, Cortés P, Llagostera M. Impact of mutagenesis and lateral gene transfer processes in bacterial susceptibility to phage in food biocontrol and phage therapy. Front Cell Infect Microbiol 2023; 13:1266685. [PMID: 37842006 PMCID: PMC10569123 DOI: 10.3389/fcimb.2023.1266685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction The emergence of resistance and interference mechanisms to phage infection can hinder the success of bacteriophage-based applications, but the significance of these mechanisms in phage therapy has not been determined. This work studies the emergence of Salmonella isolates with reduced susceptibility to a cocktail of three phages under three scenarios: i) Salmonella cultures (LAB), ii) biocontrol of cooked ham slices as a model of food safety (FOOD), and iii) oral phage therapy in broilers (PT). Methods S. Typhimurium ATCC 14028 RifR variants with reduced phage susceptibility were isolated from the three scenarios and conventional and molecular microbiology techniques were applied to study them. Results and discussion In LAB, 92% of Salmonella isolates lost susceptibility to all three phages 24 h after phage infection. This percentage was lower in FOOD, with 4.3% of isolates not susceptible to at least two of the three phages after seven days at 4°C following phage treatment. In PT, 9.7% and 3.3 % of isolates from untreated and treated broilers, respectively, displayed some mechanism of interference with the life cycle of some of the phages. In LAB and FOOD scenarios, resistant variants carrying mutations in rfc and rfaJ genes involved in lipopolysaccharide synthesis (phage receptor) were identified. However, in PT, the significant decrease of EOP, ECOI, and burst size observed in isolates was prompted by lateral gene transfer of large IncI1 plasmids, which may encode phage defense mechanisms. These data indicate that the acquisition of specific conjugative plasmids has a stronger impact than mutagenesis on the emergence of reduced phage-susceptibility bacteria in certain environments. In spite of this, neither mechanism seems to significantly impair the success of Salmonella biocontrol and oral phage therapy.
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Affiliation(s)
- Júlia López-Pérez
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Jennifer Otero
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- SK8 Biotech, Parc Científic de Barcelona, Barcelona, Spain
| | - Miquel Sánchez-Osuna
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ivan Erill
- Department of Biological Sciences, University of Maryland, Baltimore, MD, United States
- Departament Enginyeria de la Informació i de les Comunicacions, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Montserrat Llagostera
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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10
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Hussain W, Yang X, Ullah M, Wang H, Aziz A, Xu F, Asif M, Ullah MW, Wang S. Genetic engineering of bacteriophages: Key concepts, strategies, and applications. Biotechnol Adv 2023; 64:108116. [PMID: 36773707 DOI: 10.1016/j.biotechadv.2023.108116] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/12/2023]
Abstract
Bacteriophages are the most abundant biological entity in the world and hold a tremendous amount of unexplored genetic information. Since their discovery, phages have drawn a great deal of attention from researchers despite their small size. The development of advanced strategies to modify their genomes and produce engineered phages with desired traits has opened new avenues for their applications. This review presents advanced strategies for developing engineered phages and their potential antibacterial applications in phage therapy, disruption of biofilm, delivery of antimicrobials, use of endolysin as an antibacterial agent, and altering the phage host range. Similarly, engineered phages find applications in eukaryotes as a shuttle for delivering genes and drugs to the targeted cells, and are used in the development of vaccines and facilitating tissue engineering. The use of phage display-based specific peptides for vaccine development, diagnostic tools, and targeted drug delivery is also discussed in this review. The engineered phage-mediated industrial food processing and biocontrol, advanced wastewater treatment, phage-based nano-medicines, and their use as a bio-recognition element for the detection of bacterial pathogens are also part of this review. The genetic engineering approaches hold great potential to accelerate translational phages and research. Overall, this review provides a deep understanding of the ingenious knowledge of phage engineering to move them beyond their innate ability for potential applications.
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Affiliation(s)
- Wajid Hussain
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaohan Yang
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Mati Ullah
- Department of Biotechnology, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Huan Wang
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Ayesha Aziz
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Fang Xu
- Huazhong University of Science and Technology Hospital, Wuhan 430074, China
| | - Muhammad Asif
- Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, School of Materials Science and Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Muhammad Wajid Ullah
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Shenqi Wang
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
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11
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Schroer WF, Kepner HE, Uchimiya M, Mejia C, Rodriguez LT, Reisch CR, Moran MA. Functional annotation and importance of marine bacterial transporters of plankton exometabolites. ISME COMMUNICATIONS 2023; 3:37. [PMID: 37185952 PMCID: PMC10130141 DOI: 10.1038/s43705-023-00244-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/01/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023]
Abstract
Metabolite exchange within marine microbial communities transfers carbon and other major elements through global cycles and forms the basis of microbial interactions. Yet lack of gene annotations and concern about the quality of existing ones remain major impediments to revealing currencies of carbon flux. We employed an arrayed mutant library of the marine bacterium Ruegeria pomeroyi DSS-3 to experimentally annotate substrates of organic compound transporter systems, using mutant growth and compound drawdown analyses to link transporters to their cognate substrates. Mutant experiments verified substrates for thirteen R. pomeroyi transporters. Four were previously hypothesized based on gene expression data (taurine, glucose/xylose, isethionate, and cadaverine/putrescine/spermidine); five were previously hypothesized based on homology to experimentally annotated transporters in other bacteria (citrate, glycerol, N-acetylglucosamine, fumarate/malate/succinate, and dimethylsulfoniopropionate); and four had no previous annotations (thymidine, carnitine, cysteate, and 3-hydroxybutyrate). These bring the total number of experimentally-verified organic carbon influx transporters to 18 of 126 in the R. pomeroyi genome. In a longitudinal study of a coastal phytoplankton bloom, expression patterns of the experimentally annotated transporters linked them to different stages of the bloom, and also led to the hypothesis that citrate and 3-hydroxybutyrate were among the most highly available bacterial substrates. Improved functional annotation of the gatekeepers of organic carbon uptake is critical for deciphering carbon flux and fate in microbial ecosystems.
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Affiliation(s)
- William F Schroer
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Hannah E Kepner
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Mario Uchimiya
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Catalina Mejia
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | | | - Christopher R Reisch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA.
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Strathdee SA, Hatfull GF, Mutalik VK, Schooley RT. Phage therapy: From biological mechanisms to future directions. Cell 2023; 186:17-31. [PMID: 36608652 PMCID: PMC9827498 DOI: 10.1016/j.cell.2022.11.017] [Citation(s) in RCA: 124] [Impact Index Per Article: 124.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/01/2022] [Accepted: 11/16/2022] [Indexed: 01/07/2023]
Abstract
Increasing antimicrobial resistance rates have revitalized bacteriophage (phage) research, the natural predators of bacteria discovered over 100 years ago. In order to use phages therapeutically, they should (1) preferably be lytic, (2) kill the bacterial host efficiently, and (3) be fully characterized to exclude side effects. Developing therapeutic phages takes a coordinated effort of multiple stakeholders. Herein, we review the state of the art in phage therapy, covering biological mechanisms, clinical applications, remaining challenges, and future directions involving naturally occurring and genetically modified or synthetic phages.
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Affiliation(s)
- Steffanie A Strathdee
- Center for Innovative Phage Applications and Therapeutics, Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA 92093-0507, USA.
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Vivek K Mutalik
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert T Schooley
- Center for Innovative Phage Applications and Therapeutics, Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA 92093-0507, USA
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13
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Greig DR, Bird MT, Chattaway MA, Langridge GC, Waters EV, Ribeca P, Jenkins C, Nair S. Characterization of a P1-bacteriophage-like plasmid (phage-plasmid) harbouring bla CTX-M-15 in Salmonella enterica serovar Typhi. Microb Genom 2022; 8:mgen000913. [PMID: 36748517 PMCID: PMC9837566 DOI: 10.1099/mgen.0.000913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial-resistance (AMR) genes can be transferred between microbial cells via horizontal gene transfer (HGT), which involves mobile and integrative elements such as plasmids, bacteriophages, transposons, integrons and pathogenicity islands. Bacteriophages are found in abundance in the microbial world, but their role in virulence and AMR has not fully been elucidated in the Enterobacterales. With short-read sequencing paving the way to systematic high-throughput AMR gene detection, long-read sequencing technologies now enable us to establish how such genes are structurally connected into meaningful genomic units, raising questions about how they might cooperate to achieve their biological function. Here, we describe a novel ~98 kbp circular P1-bacteriophage-like plasmid termed ph681355 isolated from a clinical Salmonella enterica serovar Typhi isolate. It carries bla CTX-M-15, an IncY plasmid replicon (repY gene) and the ISEcP1 mobile element and is, to our knowledge, the first reported P1-bacteriophage-like plasmid (phage-plasmid) in S. enterica Typhi. We compared ph681355 to two previously described phage-plasmids, pSJ46 from S. enterica serovar Indiana and pMCR-1-P3 from Escherichia coli, and found high nucleotide similarity across the backbone. However, we saw low ph681355 backbone similarity to plasmid p60006 associated with the extensively drug-resistant S. enterica Typhi outbreak isolate in Pakistan, providing evidence of an alternative route for bla CTX-M-15 transmission. Our discovery highlights the importance of utilizing long-read sequencing in interrogating bacterial genomic architecture to fully understand AMR mechanisms and their clinical relevance. It also raises questions regarding how widespread bacteriophage-mediated HGT might be, suggesting that the resulting genomic plasticity might be higher than previously thought.
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Affiliation(s)
- David R. Greig
- National Infection Service, UK Health Security Agency, London NW9 5EQ, UK,NIHR Health Protection Research Unit in Gastrointestinal Pathogens, Liverpool, UK,Division of Infection and Immunity, Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK
| | - Matthew T. Bird
- National Infection Service, UK Health Security Agency, London NW9 5EQ, UK,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Oxford, UK
| | | | | | - Emma V. Waters
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Paolo Ribeca
- National Infection Service, UK Health Security Agency, London NW9 5EQ, UK,NIHR Health Protection Research Unit in Genomics and Enabling Data, Warwick, UK
| | - Claire Jenkins
- National Infection Service, UK Health Security Agency, London NW9 5EQ, UK,NIHR Health Protection Research Unit in Gastrointestinal Pathogens, Liverpool, UK
| | - Satheesh Nair
- National Infection Service, UK Health Security Agency, London NW9 5EQ, UK,*Correspondence: Satheesh Nair,
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Shaidullina A, Harms A. Toothpicks, logic, and next-generation sequencing: systematic investigation of bacteriophage-host interactions. Curr Opin Microbiol 2022; 70:102225. [PMID: 36327691 DOI: 10.1016/j.mib.2022.102225] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/27/2022] [Accepted: 10/01/2022] [Indexed: 01/25/2023]
Abstract
Bacteriophages are abundant and diverse predators that drive community dynamics in many ecosystems and hold great potential for biotechnology and as therapeutics for bacterial infections. Previous research has largely explored phage-host interactions one-by-one, which limited our ability to observe phenotypic patterns, to uncover their genetic basis, and to unravel the underlying molecular mechanisms. However, the famous 'toothpicks and logic' were recently joined by large-scale sequencing of phage genomes and bacterial genome-wide screens that enable us to systematically investigate phage-host interactions. In this article, we highlight recent breakthroughs from the molecular basis of phage host range and receptor recognition over new insights into bacterial immunity to the serendipitous discovery of a new bacterial surface glycan. Future work will enable the understanding, prediction, and engineering of more complicated phage traits for new applications and extend the scope of these studies from simple test tube experiments to natural communities of phages and hosts.
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Genetic Mining of Newly Isolated Salmophages for Phage Therapy. Int J Mol Sci 2022; 23:ijms23168917. [PMID: 36012174 PMCID: PMC9409062 DOI: 10.3390/ijms23168917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/29/2022] [Accepted: 08/07/2022] [Indexed: 11/16/2022] Open
Abstract
Salmonella enterica, a Gram-negative zoonotic bacterium, is mainly a food-borne pathogen and the main cause of diarrhea in humans worldwide. The main reservoirs are found in poultry farms, but they are also found in wild birds. The development of antibiotic resistance in S. enterica species raises concerns about the future of efficient therapies against this pathogen and revives the interest in bacteriophages as a useful therapy against bacterial infections. Here, we aimed to decipher and functionally annotate 10 new Salmonella phage genomes isolated in Spain in the light of phage therapy. We designed a bioinformatic pipeline using available building blocks to de novo assemble genomes and perform syntaxic annotation. We then used genome-wide analyses for taxonomic annotation enabled by vContact2 and VICTOR. We were also particularly interested in improving functional annotation using remote homologies detection and comparisons with the recently published phage-specific PHROG protein database. Finally, we searched for useful functions for phage therapy, such as systems encoded by the phage to circumvent cellular defenses with a particular focus on anti-CRISPR proteins. We, thus, were able to genetically characterize nine virulent phages and one temperate phage and identify putative functions relevant to the formulation of phage cocktails for Salmonella biocontrol.
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Thomas GH. Microbial Musings – December 2021. Microbiology (Reading) 2021; 167. [PMID: 35099370 PMCID: PMC8914246 DOI: 10.1099/mic.0.001141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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