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Chitboonthavisuk C, Martin C, Huss P, Peters JM, Anantharaman K, Raman S. Systematic genome-wide discovery of host factors governing bacteriophage infectivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.20.590424. [PMID: 38659955 PMCID: PMC11042327 DOI: 10.1101/2024.04.20.590424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Bacterial host factors regulate the infection cycle of bacteriophages. Except for some well-studied host factors (e.g., receptors or restriction-modification systems), the contribution of the rest of the host genome on phage infection remains poorly understood. We developed PHAGEPACK, a pooled assay that systematically and comprehensively measures each host-gene impact on phage fitness. PHAGEPACK combines CRISPR interference with phage packaging to link host perturbation to phage fitness during active infection. Using PHAGEPACK, we constructed a genome-wide map of genes impacting T7 phage fitness in permissive E. coli, revealing pathways previously unknown to affect phage packaging. When applied to the non-permissive E. coli O121, PHAGEPACK identified pathways leading to host resistance; their removal increased phage susceptibility up to a billion-fold. Bioinformatic analysis indicates phage genomes carry homologs or truncations of key host factors, potentially for fitness advantage. In summary, PHAGEPACK offers valuable insights into phage-host interactions, phage evolution, and bacterial resistance.
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Chung KM, Nang SC, Tang SS. The Safety of Bacteriophages in Treatment of Diseases Caused by Multidrug-Resistant Bacteria. Pharmaceuticals (Basel) 2023; 16:1347. [PMID: 37895818 PMCID: PMC10610463 DOI: 10.3390/ph16101347] [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: 06/20/2023] [Revised: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 10/29/2023] Open
Abstract
Given the urgency due to the rapid emergence of multidrug-resistant (MDR) bacteria, bacteriophages (phages), which are viruses that specifically target and kill bacteria, are rising as a potential alternative to antibiotics. In recent years, researchers have begun to elucidate the safety aspects of phage therapy with the aim of ensuring safe and effective clinical applications. While phage therapy has generally been demonstrated to be safe and tolerable among animals and humans, the current research on phage safety monitoring lacks sufficient and consistent data. This emphasizes the critical need for a standardized phage safety assessment to ensure a more reliable evaluation of its safety profile. Therefore, this review aims to bridge the knowledge gap concerning phage safety for treating MDR bacterial infections by covering various aspects involving phage applications, including phage preparation, administration, and the implications for human health and the environment.
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Affiliation(s)
- Ka Mun Chung
- Division of Microbiology and Molecular Genetics, Institute of Biological Sciences, Faculty of Sciences, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Sue C Nang
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Swee Seong Tang
- Division of Microbiology and Molecular Genetics, Institute of Biological Sciences, Faculty of Sciences, University of Malaya, Kuala Lumpur 50603, Malaysia
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur 50603, Malaysia
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Lu J, Han M, Yu HH, Bergen PJ, Liu Y, Zhao J, Wickremasinghe H, Jiang X, Hu Y, Du H, Zhu Y, Velkov T. Lipid A Modification and Metabolic Adaptation in Polymyxin-Resistant, New Delhi Metallo-β-Lactamase-Producing Klebsiella pneumoniae. Microbiol Spectr 2023; 11:e0085223. [PMID: 37432123 PMCID: PMC10433984 DOI: 10.1128/spectrum.00852-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/12/2023] [Indexed: 07/12/2023] Open
Abstract
Polymyxins are last-line antibiotics employed against multidrug-resistant (MDR) Klebsiella pneumoniae. Worryingly, polymyxin resistance is rapidly on the rise globally. Polymyxins initially target lipid A of lipopolysaccharides (LPSs) in the cell outer membrane (OM), causing disorganization and cell lysis. While most studies focus on how genetic variations confer polymyxin resistance, the mechanisms of membrane remodeling and metabolic changes in polymyxin-resistant strains remain unclear, thus hampering the development of effective therapies to treat severe K. pneumoniae infections. In the present study, lipid A profiling, OM lipidomics, genomics, and metabolomics were integrated to elucidate the global mechanisms of polymyxin resistance and metabolic adaptation in a polymyxin-resistant strain (strain S01R; MIC of >128 mg/L) obtained from K. pneumoniae strain S01, a polymyxin-susceptible (MIC of 2 mg/L), New Delhi metallo-β-lactamase (NDM)-producing MDR clinical isolate. Genomic analysis revealed a novel in-frame deletion at position V258 of PhoQ in S01R, potentially leading to lipid A modification with 4-amino-4-deoxy-l-arabinose (L-Ara4N) despite the absence of polymyxin B. Comparative metabolomic analysis revealed slightly elevated levels of energy production and amino acid metabolism in S01R compared to their levels in S01. Exposure to polymyxin B (4 mg/L for S01 and 512 mg/L for S01R) substantially altered energy, nucleotide, and amino acid metabolism and resulted in greater accumulation of lipids in both strains. Furthermore, the change induced by polymyxin B treatment was dramatic at both 1 and 4 h in S01 but only significant at 4 h in S01R. Overall, profound metabolic adaptation was observed in S01R following polymyxin B treatment. These findings contribute to our understanding of polymyxin resistance mechanisms in problematic NDM-producing K. pneumoniae strains and may facilitate the discovery of novel therapeutic targets. IMPORTANCE Antimicrobial resistance (AMR) is a major threat to global health. The emergence of resistance to the polymyxins that are the last line of defense in so-called Gram-negative "superbugs" has further increased the urgency to develop novel therapies. There are frequent outbreaks of K. pneumoniae infections in hospitals being reported, and polymyxin usage is increasing remarkably. Importantly, the polymyxin-resistant K. pneumoniae strains are imposing more severe consequences to health systems. Using metabolomics, lipid A profiling, and outer membrane lipidomics, our findings reveal (i) changes in the pentose phosphate pathway and amino acid and nucleotide metabolism in a susceptible strain following polymyxin treatment and (ii) how cellular metabolism, lipid A modification, and outer membrane remodeling were altered in K. pneumoniae following the acquisition of polymyxin resistance. Our study provides, for the first time, mechanistic insights into metabolic responses to polymyxin treatment in a multidrug-resistant, NDM-producing K. pneumoniae clinical isolate with acquired polymyxin resistance. Overall, these results will assist in identifying new therapeutic targets to combat and prevent polymyxin resistance.
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Affiliation(s)
- Jing Lu
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Meiling Han
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Heidi H. Yu
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Phillip J. Bergen
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Yiyun Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jinxin Zhao
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Hasini Wickremasinghe
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Xukai Jiang
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Yang Hu
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Haiyan Du
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Yan Zhu
- Infection Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Tony Velkov
- Department of Pharmacology, The Faculty of Medicine Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
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Tisalema-Guanopatín E, Cabezas-Mera F, Nolivos-Rodríguez K, Fierro I, Pazmiño L, Garzon-Chavez D, Debut A, Vizuete K, Reyes JA. New Bacteriophages Members of the Ackermannviridae Family Specific for Klebsiella pneumoniae ST258. PHAGE (NEW ROCHELLE, N.Y.) 2023; 4:99-107. [PMID: 37350993 PMCID: PMC10282792 DOI: 10.1089/phage.2022.0039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
Abstract
Background Carbapenem-resistant Klebsiella pneumoniae, particularly isolates classified as sequence-type 258 (ST258), are multidrug-resistant strains that are strongly associated with poor-prognosis nosocomial infections, as current therapeutic options are limited and ineffective. In recent years, phage therapy has emerged as a promising treatment option for these scenarios. Methodology and Results We report the isolation and characterization of three new phages against Klebsiella pneumoniae ST258 strains recovered from Machángara river wastewater. These new members of the Ackermannviridae family showed stability over a wide temperature and pH range and burst sizes ranging from 6 to 44 plaque-forming units per bacteria. Their genomes were about 157 kilobases, with an average guanine-cytosine content of 46.4% and showed presence of several transfer RNAs, which also allowed us to predict in silico a lytic replicative cycle due to the presence of endolysins and lysozymes. Conclusion Three lytic phages of Ackermannviridae family were recovered against Klebsiella pneumoniae ST258 strains from sewage; however, further characterization is needed for future consideration as therapeutic alternatives.
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Affiliation(s)
- Estefanía Tisalema-Guanopatín
- Facultad de Ciencias Químicas, Universidad Central del Ecuador (UCE), Ciudadela Universitaria Avenida América, Quito, Pichincha, Ecuador
- Faculty of Engineering and Applied Sciences, Universidad Internacional SEK, Quito, Ecuador
| | - Fausto Cabezas-Mera
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales (COCIBA), Universidad San Francisco de Quito (USFQ), Diego de Robles y Vía Interoceánica, Quito, Ecuador
| | - Karla Nolivos-Rodríguez
- Facultad de Ciencias Químicas, Universidad Central del Ecuador (UCE), Ciudadela Universitaria Avenida América, Quito, Pichincha, Ecuador
| | - Isabel Fierro
- Facultad de Ciencias Químicas, Universidad Central del Ecuador (UCE), Ciudadela Universitaria Avenida América, Quito, Pichincha, Ecuador
| | - Lourdes Pazmiño
- Facultad de Ciencias Químicas, Universidad Central del Ecuador (UCE), Ciudadela Universitaria Avenida América, Quito, Pichincha, Ecuador
| | - Daniel Garzon-Chavez
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias de la Salud (COCSA), Diego de Robles y Vía Interoceánica, Quito, Ecuador
| | - Alexis Debut
- Centro de Nanociencia y Nanotecnología (CENCINAT), Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador
| | - Karla Vizuete
- Centro de Nanociencia y Nanotecnología (CENCINAT), Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador
| | - Jorge Aníbal Reyes
- Facultad de Ciencias Químicas, Universidad Central del Ecuador (UCE), Ciudadela Universitaria Avenida América, Quito, Pichincha, Ecuador
- Departamento de Microbiología, Hospital del IESS Quito Sur, Avenida Moraspungo, Quito, Ecuador
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Zaki BM, Hussein AH, Hakim TA, Fayez MS, El-Shibiny A. Phages for treatment of Klebsiella pneumoniae infections. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:207-239. [PMID: 37739556 DOI: 10.1016/bs.pmbts.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Klebsiella pneumoniae is an opportunistic pathogen involved in both hospital- and community-acquired infections. K. pneumoniae is associated with various infections, including pneumonia, septicemia, meningitis, urinary tract infection, and surgical wound infection. K. pneumoniae possesses serious virulence, biofilm formation ability, and severe resistance to many antibiotics especially hospital-acquired strains, due to excessive use in healthcare systems. This limits the available effective antibiotics that can be used for patients suffering from K. pneumoniae infections; therefore, alternative treatments are urgently needed. Bacteriophages (for short, phages) are prokaryotic viruses capable of infecting, replicating, and then lysing (lytic phages) the bacterial host. Phage therapy exhibited great potential for treating multidrug-resistant bacterial infections comprising K. pneumoniae. Hence, this chapter emphasizes and summarizes the research articles in the PubMed database from 1948 until the 15th of December 2022, addressing phage therapy against K. pneumoniae. The chapter provides an overview of K. pneumoniae phages covering different aspects, including phage isolation, different morphotypes of isolated phages, in vitro characterization, anti-biofilm activity, various therapeutic forms, in vivo research and clinical studies.
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Affiliation(s)
- Bishoy Maher Zaki
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Microbiology and Immunology Department, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
| | - Assmaa H Hussein
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Toka A Hakim
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Mohamed S Fayez
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Faculty of Environmental Agricultural Sciences, Arish University, Arish, Egypt.
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Raza A, Zehra M, Ramzan M, Siddiqui AJ, Akbar A, Ahmed A, Musharraf SG. Untargeted Metabolomics Analysis of Gentamicin-Induced Tolerant Colonies of Klebsiella pneumoniae. Eur J Pharm Sci 2023; 185:106436. [PMID: 36965642 DOI: 10.1016/j.ejps.2023.106436] [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: 12/06/2022] [Revised: 03/13/2023] [Accepted: 03/21/2023] [Indexed: 03/27/2023]
Abstract
PURPOSE Antibiotic resistance development in pathogenic bacteria like Klebsiella pneumoniae seriously threatens humankind. Therefore, it is important to understand the interaction of bacteria with antibiotic agents and how it acquires resistance at the molecular level. The current study describes metabolomics analysis of K. pneumoniae sensitive strains and its gentamicin-tolerant (resistant) strains. METHODS K. pneumoniae strains were treated at five different concentrations of gentamicin, increasing from a low dose (16.2 µg/mL) to the highest dose (250 µg/mL) at three incubation time periods (24h, 48h, and 72h). Colonies obtained at various concentrations and time intervals were subjected to metabolomic analysis using GC-MS. RESULTS A drastic change was observed in the morphology of K. pneumoniae colonies with the increasing gentamicin concentration. Moreover, K. pneumoniae strains grown at the highest concentration (250 µg/mL) were found tolerant to 1 mg/mL gentamicin (4-folds) and considered resistant strains. A total of 459 metabolites were identified. A sequential down/up-regulation in 4, 3, and 4 metabolites were observed in association with the increasing gentamicin concentration at 24h, 48h, and 72h, respectively. While with the comparative analysis of resistant and sensitive strains, a total of seven down- and sixteen up-regulated metabolites were observed. The concentration of some fatty acids and sugars have been found to increase while, a few metabolites like inosine, tyrosine, 1-propionylproline, and 2-hydroxyacetic acid have been found down-regulated in resistant samples. CONCLUSION These regulator metabolites might be associated with resistance development in K. pneumoniae against gentamicin and might be helpful in the rapid detection of gentamicin-resistant clinical strains.
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Affiliation(s)
- Ali Raza
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Moatter Zehra
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Muhammad Ramzan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Amna Jabbar Siddiqui
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Azra Akbar
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Ayaz Ahmed
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
| | - Syed Ghulam Musharraf
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
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7
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Pertics BZ, Kovács T, Schneider G. Characterization of a Lytic Bacteriophage and Demonstration of Its Combined Lytic Effect with a K2 Depolymerase on the Hypervirulent Klebsiella pneumoniae Strain 52145. Microorganisms 2023; 11:microorganisms11030669. [PMID: 36985241 PMCID: PMC10051899 DOI: 10.3390/microorganisms11030669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Klebsiella pneumoniae is a nosocomial pathogen. Among its virulence factors is the capsule with a prominent role in defense and biofilm formation. Bacteriophages (phages) can evoke the lysis of bacterial cells. Due to the mode of action of their polysaccharide depolymerase enzymes, phages are typically specific for one bacterial strain and its capsule type. In this study, we characterized a bacteriophage against the capsule-defective mutant of the nosocomial K. pneumoniae 52145 strain, which lacks K2 capsule. The phage showed a relatively narrow host range but evoked lysis on a few strains with capsular serotypes K33, K21, and K24. Phylogenetic analysis showed that the newly isolated Klebsiella phage 731 belongs to the Webervirus genus in the Drexlerviridae family; it has a 31.084 MDa double-stranded, linear DNA with a length of 50,306 base pairs and a G + C content of 50.9%. Out of the 79 open reading frames (ORFs), we performed the identification of orf22, coding for a trimeric tail fiber protein with putative capsule depolymerase activity, along with the mapping of other putative depolymerases of phage 731 and homologous phages. Efficacy of a previously described recombinant K2 depolymerase (B1dep) was tested by co-spotting phage 731 on K. pneumoniae strains, and it was demonstrated that the B1dep-phage 731 combination allows the lysis of the wild type 52145 strain, originally resistant to the phage 731. With phage 731, we showed that B1dep is a promising candidate for use as a possible antimicrobial agent, as it renders the virulent strain defenseless against other phages. Phage 731 alone is also important due to its efficacy on K. pneumoniae strains possessing epidemiologically important serotypes.
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Affiliation(s)
- Botond Zsombor Pertics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti St. 12., H-7624 Pécs, Hungary
| | - Tamás Kovács
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Kertváros St. 2., H-7632 Pécs, Hungary
| | - György Schneider
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti St. 12., H-7624 Pécs, Hungary
- Correspondence: ; Tel.: +36-72-536-200 (ext. 1908)
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Dantas R, Brocchi M, Pacheco Fill T. Chemical-Biology and Metabolomics Studies in Phage-Host Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:71-100. [PMID: 37843806 DOI: 10.1007/978-3-031-41741-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
For many years, several studies have explored the molecular mechanisms involved in the infection of bacteria by their specific phages to understand the main infection strategies and the host defense strategies. The modulation of the mechanisms involved in the infection, as well as the expression of key substances in the development of the different life cycles of phages, function as a natural source of strategies capable of promoting the control of different pathogens that are harmful to human and animal health. Therefore, this chapter aims to provide an overview of the mechanisms involved in virus-bacteria interaction to explore the main compounds produced or altered as a chemical survival strategy and the metabolism modulation when occurring a host-phage interaction. In this context, emphasis will be given to the chemistry of peptides/proteins and enzymes encoded by bacteriophages in the control of pathogenic bacteria and the use of secondary metabolites recently reported as active participants in the mechanisms of phage-bacteria interaction. Finally, metabolomics strategies developed to gain new insights into the metabolism involved in the phage-host interaction and the metabolomics workflow in host-phage interaction will be presented.
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Affiliation(s)
- Rodolfo Dantas
- Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil
| | - Marcelo Brocchi
- Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Taícia Pacheco Fill
- Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil.
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Lorenzo-Rebenaque L, Casto-Rebollo C, Diretto G, Frusciante S, Rodríguez JC, Ventero MP, Molina-Pardines C, Vega S, Marin C, Marco-Jiménez F. Examining the effects of Salmonella phage on the caecal microbiota and metabolome features in Salmonella-free broilers. Front Genet 2022; 13:1060713. [PMID: 36437955 PMCID: PMC9691336 DOI: 10.3389/fgene.2022.1060713] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/26/2022] [Indexed: 10/29/2023] Open
Abstract
Bacteriophages selectively infect and kill their target bacterial host, being a promising approach to controlling zoonotic bacteria in poultry production. To ensure confidence in its use, fundamental questions of safety and toxicity monitoring of phage therapy should be raised. Due to its high specificity, a minimal impact on the gut ecology is expected; however, more in-depth research into key parameters that influence the success of phage interventions has been needed to reach a consensus on the impact of bacteriophage therapy in the gut. In this context, this study aimed to investigate the interaction of phages with animals; more specifically, we compared the caecum microbiome and metabolome after a Salmonella phage challenge in Salmonella-free broilers, evaluating the role of the phage administration route. To this end, we employed 45 caecum content samples from a previous study where Salmonella phages were administered via drinking water or feed for 24 h from 4, 5 to 6-weeks-old broilers. High-throughput 16S rRNA gene sequencing showed a high level of similarity (beta diversity) but revealed a significant change in alpha diversity between broilers with Salmonella-phage administered in the drinking water and control. Our results showed that the phages affected only a few genera of the microbiota's structure, regardless of the administration route. Among these, we found a significant increase in Streptococcus and Sellimonas in the drinking water and Lactobacillus, Anaeroplasma and Clostridia_vadinBB60_group in the feed. Nevertheless, the LC-HRMS-based metabolomics analyses revealed that despite few genera were significantly affected, a substantial number of metabolites, especially in the phage administered in the drinking water were significantly altered (64 and 14 in the drinking water and feed groups, respectively). Overall, our study shows that preventive therapy with bacteriophages minimally alters the caecal microbiota but significantly impacts their metabolites, regardless of the route of administration.
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Affiliation(s)
- Laura Lorenzo-Rebenaque
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Valencia, Spain
| | - Cristina Casto-Rebollo
- Institute of Science and Animal Technology, Universitat Politècnica de València, Valencia, Spain
| | - Gianfranco Diretto
- Italian Agency for New Technologies, Energy and Sustainable Development (ENEA), Biotechnology Laboratory, Centro Ricerche Casaccia, Santa Maria di Galeria, Rome, Italy
| | - Sarah Frusciante
- Italian Agency for New Technologies, Energy and Sustainable Development (ENEA), Biotechnology Laboratory, Centro Ricerche Casaccia, Santa Maria di Galeria, Rome, Italy
| | - Juan Carlos Rodríguez
- Microbiology Department, Balmis General University Hospital, Microbiology Division, Miguel Hernández University, ISABIAL, Alicante, Spain
| | - María-Paz Ventero
- Microbiology Department, Balmis General University Hospital, ISABIAL, Alicante, Spain
| | | | - Santiago Vega
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Valencia, Spain
| | - Clara Marin
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Valencia, Spain
| | - Francisco Marco-Jiménez
- Institute of Science and Animal Technology, Universitat Politècnica de València, Valencia, Spain
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Identification of metabolite extraction method for targeted exploration of antimicrobial resistance associated metabolites of Klebsiella pneumoniae. Sci Rep 2022; 12:8939. [PMID: 35624184 PMCID: PMC9142494 DOI: 10.1038/s41598-022-12153-0] [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: 01/06/2022] [Accepted: 04/22/2022] [Indexed: 11/08/2022] Open
Abstract
Antimicrobial resistant Klebsiella pneumoniae (K. pneumoniae), as being a pathogen of critical clinical concern, urgently demands effective therapeutic options. However, the discovery of novel antibiotics over the last three decades has declined drastically and necessitates exploring novel strategies. Metabolomic modulation has been the promising approach for the development of effective therapeutics to deal with AMR; however, only limited efforts have been made to-date, possibly due to the unavailability of suitable metabolites extraction protocols. Therefore, in order to establish a detailed metabolome of K. pneumoniae and identify a method for targeted exploration of metabolites that are involved in the regulation of AMR associated processes, metabolites were extracted using multiple methods of metabolites extraction (freeze-thaw cycle (FTC) and sonication cycle (SC) method alone or in combination (FTC followed by SC; FTC + SC)) from K. pneumoniae cells and then identified using an orbitrap mass analyzer (ESI-LC-MS/MS). A total of 151 metabolites were identified by using FTC, 132 metabolites by using FTC+SC, 103 metabolites by using SC and 69 metabolites common among all the methods used which altogether enabled the identification of 199 unique metabolites. Of these 199, 70 metabolites were known to have an association with AMR phenotype and among these, the FTC + SC method yielded better (identified 55 metabolites), quantitatively and qualitatively compared to FTC and SC alone (identified 51 and 41 metabolites respectively). Each method of metabolite extraction showed a definite degree of biasness and specificity towards chemical classes of metabolites and jointly contributed to the development of a detailed metabolome of the pathogen. FTC method was observed to give higher metabolomic coverage as compared to SC alone and FTC + SC. However, FTC + SC resulted in the identification of a higher number of AMR associated metabolites of K. pneumoniae compared to FTC and SC alone.
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