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Lum J, Koval C. The changing landscape of infections in the lung transplant recipient. Curr Opin Pulm Med 2024; 30:382-390. [PMID: 38411211 DOI: 10.1097/mcp.0000000000001060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
PURPOSE OF REVIEW Infections in lung transplant recipients remain a major challenge and can affect lung allograft function and cause significant morbidity and mortality. New strategies for the prevention and treatment of infection in lung transplantation have emerged and are reviewed. RECENT FINDINGS For important vaccine preventable infections (VPIs), guidance has been updated for at risk solid organ transplant (SOT) recipients. However, data on the efficacy of newer vaccines in lung transplant, including the respiratory syncytial virus (RSV) vaccine, are limited. Studies demonstrate improved vaccination rate with Infectious Diseases consultation during pretransplant evaluation. Two new antiviral agents for the treatment and prevention of cytomegalovirus (CMV) in SOT, letermovir and maribavir, are being incorporated into clinical care. CMV-specific cell-mediated immune function assays are more widely available. Antibiotics for the management of multidrug resistant pathogens and Burkholderia cepacia complex have been described in case series and case reports in lung transplant. SUMMARY Although new vaccines and novel therapies for preventing and treating infections are available, larger studies evaluating efficacy in lung transplant recipients are needed.
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Affiliation(s)
- Jessica Lum
- Division of Infectious Diseases, Cleveland Clinic Foundation, Cleveland, Ohio, USA
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2
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González-Gómez JP, Rodríguez-Arellano SN, Gomez-Gil B, Vergara-Jiménez MDJ, Chaidez C. Genomic and biological characterization of bacteriophages against Enterobacter cloacae, a high-priority pathogen. Virology 2024; 595:110100. [PMID: 38714025 DOI: 10.1016/j.virol.2024.110100] [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: 11/08/2023] [Revised: 04/20/2024] [Accepted: 05/02/2024] [Indexed: 05/09/2024]
Abstract
Enterobacter cloacae is a clinically significant pathogen due to its multi-resistance to antibiotics, presenting a challenge in the treatment of infections. As concerns over antibiotic resistance escalate, novel therapeutic approaches have been explored. Bacteriophages, characterized by their remarkable specificity and ability to self-replicate within target bacteria, are emerging as a promising alternative therapy. In this study, we isolated and partially characterized nine lytic bacteriophages targeting E. cloacae, with two selected for comprehensive genomic analysis based on their host range and bacteriolytic activity. All identified phages exhibited a narrow host range, demonstrated stability within a temperature range of 30-60 °C, displayed pH tolerance from 3 to 10, and showed an excellent bacteriolytic capacity for up to 18 h. Notably, the fully characterized phage genomes revealed an absence of lysogenic, virulence, or antibiotic-resistance genes, positioning them as promising candidates for therapeutic intervention against E. cloacae-related diseases. Nonetheless, translating this knowledge into practical therapeutic applications mandates a deeper understanding of bacteriophage interactions within complex biological environments.
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Affiliation(s)
- Jean Pierre González-Gómez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacan, Sinaloa, Mexico
| | | | - Bruno Gomez-Gil
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Unidad Mazatlán en Acuicultura y Manejo Ambiental, AP 711, Mazatlan, Sinaloa, Mexico
| | | | - Cristobal Chaidez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacan, Sinaloa, Mexico.
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3
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Markusková B, Elnwrani S, Andrezál M, Sedláčková T, Szemes T, Slobodníková L, Kajsik M, Drahovská H. Characterization of bacteriophages infecting multidrug-resistant uropathogenic Escherichia coli strains. Arch Virol 2024; 169:142. [PMID: 38851653 PMCID: PMC11162368 DOI: 10.1007/s00705-024-06063-x] [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: 01/08/2024] [Accepted: 04/29/2024] [Indexed: 06/10/2024]
Abstract
Uropathogenic Escherichia coli (UPEC) is the most common causative agent of urinary tract infections, and strains that are resistant to antibiotics are a major problem in treating these infections. Phage therapy is a promising alternative approach that can be used to treat infections caused by polyresistant bacterial strains. In the present study, 16 bacteriophages isolated from sewage and surface water were investigated. Phage host specificity was tested on a collection of 77 UPEC strains. The phages infected 2-44 strains, and 80% of the strains were infected by at least one phage. The susceptible E. coli strains belonged predominantly to the B2 phylogenetic group, including strains of two clones, CC131 and CC73, that have a worldwide distribution. All of the phages belonged to class Caudoviricetes and were identified as members of the families Straboviridae, Autographiviridae, and Drexlerviridae and the genera Kagunavirus, Justusliebigvirus, and Murrayvirus. A phage cocktail composed of six phages - four members of the family Straboviridae and two members of the family Autographiviridae - was prepared, and its antibacterial activity was tested in liquid medium. Complete suppression of bacterial growth was observed after 5-22 hours of cultivation, followed by partial regrowth. At 24 hours postinfection, the cocktail suppressed bacterial growth to 43-92% of control values. Similar results were obtained when testing the activity of the phage cocktail in LB and in artificial urine medium. The results indicate that our phage cocktail has potential to inhibit bacterial growth during infection, and they will therefore be preserved in the national phage bank, serving as valuable resources for therapeutic applications.
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Affiliation(s)
- Barbora Markusková
- University Science Park, Comenius University in Bratislava, Bratislava, Slovakia
| | - Sulafa Elnwrani
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Michal Andrezál
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Tatiana Sedláčková
- University Science Park, Comenius University in Bratislava, Bratislava, Slovakia
| | - Tomáš Szemes
- University Science Park, Comenius University in Bratislava, Bratislava, Slovakia
| | - Lívia Slobodníková
- Institute of Microbiology, Faculty of Medicine, Comenius University in Bratislava and University Hospital Bratislava, Bratislava, Slovakia
| | - Michal Kajsik
- University Science Park, Comenius University in Bratislava, Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Hana Drahovská
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.
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4
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Santamaría-Corral G, Pagán I, Aguilera-Correa JJ, Esteban J, García-Quintanilla M. A Novel Bacteriophage Infecting Multi-Drug- and Extended-Drug-Resistant Pseudomonas aeruginosa Strains. Antibiotics (Basel) 2024; 13:523. [PMID: 38927189 PMCID: PMC11200629 DOI: 10.3390/antibiotics13060523] [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: 04/11/2024] [Revised: 05/13/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
The prevalence of carbapenem-resistant P. aeruginosa has dramatically increased over the last decade, and antibiotics alone are not enough to eradicate infections caused by this opportunistic pathogen. Phage therapy is a fresh treatment that can be administered under compassionate use, particularly against chronic cases. However, it is necessary to thoroughly characterize the virus before therapeutic application. Our work describes the discovery of the novel sequenced bacteriophage, vB_PaeP-F1Pa, containing an integrase, performs a phylogenetical analysis, describes its stability at a physiological pH and temperature, latent period (40 min), and burst size (394 ± 166 particles per bacterial cell), and demonstrates its ability to infect MDR and XDR P. aeruginosa strains. Moreover, this novel bacteriophage was able to inhibit the growth of bacteria inside preformed biofilms. The present study offers a road map to analyze essential areas for successful phage therapy against MDR and XDR P. aeruginosa infections, and shows that a phage containing an integrase is also able to show good in vitro results, indicating that it is very important to perform a genomic analysis before any clinical use, in order to prevent adverse effects in patients.
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Affiliation(s)
- Guillermo Santamaría-Corral
- Clinical Microbiology Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain; (G.S.-C.); (J.J.A.-C.); (M.G.-Q.)
| | - Israel Pagán
- Centro de Biotecnología y Genómica de Plantas UPM-INIA/CSIC and E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28223 Madrid, Spain;
| | - John Jairo Aguilera-Correa
- Clinical Microbiology Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain; (G.S.-C.); (J.J.A.-C.); (M.G.-Q.)
- CIBERINFEC-Consorcio Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas, 28029 Madrid, Spain
| | - Jaime Esteban
- Clinical Microbiology Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain; (G.S.-C.); (J.J.A.-C.); (M.G.-Q.)
- CIBERINFEC-Consorcio Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas, 28029 Madrid, Spain
| | - Meritxell García-Quintanilla
- Clinical Microbiology Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain; (G.S.-C.); (J.J.A.-C.); (M.G.-Q.)
- CIBERINFEC-Consorcio Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas, 28029 Madrid, Spain
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Shymialevich D, Błażejak S, Średnicka P, Cieślak H, Ostrowska A, Sokołowska B, Wójcicki M. Biological Characterization and Genomic Analysis of Three Novel Serratia- and Enterobacter-Specific Virulent Phages. Int J Mol Sci 2024; 25:5944. [PMID: 38892136 PMCID: PMC11172527 DOI: 10.3390/ijms25115944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/22/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Due to the high microbiological contamination of raw food materials and the increase in the incidence of multidrug-resistant bacteria, new methods of ensuring microbiological food safety are being sought. One solution may be to use bacteriophages (so-called phages) as natural bacterial enemies. Therefore, the aim of this study was the biological and genomic characterization of three newly isolated Serratia- and Enterobacter-specific virulent bacteriophages as potential candidates for food biocontrol. Serratia phage KKP_3708 (vB_Sli-IAFB_3708), Serratia phage KKP_3709 (vB_Sma-IAFB_3709), and Enterobacter phage KKP_3711 (vB_Ecl-IAFB_3711) were isolated from municipal sewage against Serratia liquefaciens strain KKP 3654, Serratia marcescens strain KKP 3687, and Enterobacter cloacae strain KKP 3684, respectively. The effect of phage addition at different multiplicity of infection (MOI) rates on the growth kinetics of the bacterial hosts was determined using a Bioscreen C Pro growth analyzer. The phages retained high activity in a wide temperature range (from -20 °C to 60 °C) and active acidity values (pH from 3 to 12). Based on transmission electron microscopy (TEM) imaging and whole-genome sequencing (WGS), the isolated bacteriophages belong to the tailed bacteriophages from the Caudoviricetes class. Genomic analysis revealed that the phages have linear double-stranded DNA of size 40,461 bp (Serratia phage KKP_3708), 67,890 bp (Serratia phage KKP_3709), and 113,711 bp (Enterobacter phage KKP_3711). No virulence, toxins, or antibiotic resistance genes were detected in the phage genomes. The lack of lysogenic markers indicates that all three bacteriophages may be potential candidates for food biocontrol.
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Affiliation(s)
- Dziyana Shymialevich
- Culture Collection of Industrial Microorganisms—Microbiological Resources Center, Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland; (D.S.); (H.C.)
| | - Stanisław Błażejak
- Department of Biotechnology and Food Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences (WULS–SGGW), Nowoursynowska 166 Str., 02-776 Warsaw, Poland;
| | - Paulina Średnicka
- Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland;
| | - Hanna Cieślak
- Culture Collection of Industrial Microorganisms—Microbiological Resources Center, Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland; (D.S.); (H.C.)
| | - Agnieszka Ostrowska
- Department of Nanobiotechnology, Institute of Biology, Warsaw University of Life Sciences (WULS–SGGW), Ciszewskiego 8 Str., 02-786 Warsaw, Poland;
| | - Barbara Sokołowska
- Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland;
| | - Michał Wójcicki
- Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland;
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Sevilla-Navarro S, Torres-Boncompte J, Garcia-Llorens J, Bernabéu-Gimeno M, Domingo-Calap P, Catalá-Gregori P. Fighting Salmonella Infantis: bacteriophage-driven cleaning and disinfection strategies for broiler farms. Front Microbiol 2024; 15:1401479. [PMID: 38812676 PMCID: PMC11134195 DOI: 10.3389/fmicb.2024.1401479] [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] [Received: 03/15/2024] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
Introduction Salmonella is a bacterium that can cause food-borne infections and is responsible for the most common gastrointestinal illnesses. The emergence of multi-drug resistant (MDR) strains worldwide is a major threat, representing a major challenge in public health. To reduce its incidence, the One Health approach is required, and the development of new biocontrol protocols will help prevent or eliminate the spread of Salmonella. Prevention measures, such as on-farm cleaning and disinfection protocols, are a crucial step in reducing infection to new flocks and eliminating bacteria that remain in the facilities. However, MDR Salmonella species, such as S. Infantis, are highly resistant to conventional cleaning and disinfection protocols, with an increased ability to persist in the broiler farm environment. The need for alternative biocontrol methods has led to the use of bacteriophages or phages, viruses that target bacteria, as promising tools. Thus, the aim of this study was to evaluate the efficacy of phages as a biocide against S. Infantis isolates in combination with cleaning and disinfection protocols in 10 commercial poultry farms. Methods All commercial farms selected in this study had persistent Salmonella, even after the routinely used cleaning and disinfection procedures. In addition, Salmonella isolated before treatment were phenotypically characterized by antimicrobial resistance patterns. Results The results showed that 100% of S. Infantis were resistant to at least one antibiotic, and > 70% were MDR. Phages were then isolated against the in-farm bacteria, purified, and multiplied for each poultry farm. The cleaning and disinfection protocols included the application of the lytic phages (vB_Si_CECAV_FGS009; vB_Si_CECAV_FGS017; vB_Si_CECAV_FGS029 and vB_Si_CECAV _FGS030) twice at 24-h intervals between cleaning and disinfection. Following the cleaning and disinfection procedures, Salmonella detection was reduced from 100% after cleaning to 36% after applying the phages and dropped to 0% after the final step of disinfection, thus eliminating Salmonella from the farm facilities. Discussion This study demonstrates that bacteriophage application after cleaning and before disinfection enhances the removal of MDR Salmonella Infantis in commercial broiler farms, suggesting their use as biocontrol agents to reduce Salmonella, a major public health concern.
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Affiliation(s)
- Sandra Sevilla-Navarro
- Centro de Calidad Avícola y Alimentación Animal de la Comunidad Valenciana (CECAV), Castellón, Spain
| | - Jan Torres-Boncompte
- Centro de Calidad Avícola y Alimentación Animal de la Comunidad Valenciana (CECAV), Castellón, Spain
| | - Josep Garcia-Llorens
- Centro de Calidad Avícola y Alimentación Animal de la Comunidad Valenciana (CECAV), Castellón, Spain
| | - Mireia Bernabéu-Gimeno
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Paterna, Spain
| | - Pilar Domingo-Calap
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Paterna, Spain
| | - Pablo Catalá-Gregori
- Centro de Calidad Avícola y Alimentación Animal de la Comunidad Valenciana (CECAV), Castellón, Spain
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7
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Dufour N, Delattre R, Debarbieux L. High-Throughput Bacteriophage Testing with Potency Determination: Validation of an Automated Pipetting and Phage Drop-Off Method. Biomedicines 2024; 12:466. [PMID: 38398068 PMCID: PMC10886619 DOI: 10.3390/biomedicines12020466] [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: 01/25/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
The development of bacteriophages (phages) as active pharmaceutical ingredients for the treatment of patients is on its way and regulatory agencies are calling for reliable methods to assess phage potency. As the number of phage banks is increasing, so is the number of phages that need to be tested to identify therapeutic candidates. Currently, assessment of phage potency on a semi-solid medium to observe plaque-forming units is unavoidable and proves to be labor intensive when considering dozens of phage candidates. Here, we present a method based on automated pipetting and phage drop-off performed by a liquid-handling robot, allowing high-throughput testing and phage potency determination (based on phage titer and efficiency of plaquing). Ten phages were tested, individually and assembled into one cocktail, against 126 Escherichia coli strains. This automated method was compared to the reference one (manual assay) and validated in terms of reproducibility and concordance (ratio of results according to the Bland and Altman method: 0.99; Lin's concordance correlation coefficient: 0.86). We found that coefficients of variation were lower with automated pipetting (mean CV: 13.3% vs. 24.5%). Beyond speeding up the process of phage screening, this method could be used to standardize phage potency evaluation.
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Affiliation(s)
- Nicolas Dufour
- Réanimation Médico-Chirurgicale, Hôpital NOVO—Site de Pontoise, 95300 Pontoise, France
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 75015 Paris, France (L.D.)
- IAME, Université de Paris, INSERM U1137, Université Sorbonne Paris Nord, 75018 Paris, France
| | - Raphaëlle Delattre
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 75015 Paris, France (L.D.)
- IAME, Université de Paris, INSERM U1137, Université Sorbonne Paris Nord, 75018 Paris, France
- Réanimation, Centre Hospitalier de Digne-les-Bains, 04000 Digne-les-Bains, France
| | - Laurent Debarbieux
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 75015 Paris, France (L.D.)
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8
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Gencay YE, Jasinskytė D, Robert C, Semsey S, Martínez V, Petersen AØ, Brunner K, de Santiago Torio A, Salazar A, Turcu IC, Eriksen MK, Koval L, Takos A, Pascal R, Schou TS, Bayer L, Bryde T, Johansen KC, Bak EG, Smrekar F, Doyle TB, Satlin MJ, Gram A, Carvalho J, Jessen L, Hallström B, Hink J, Damholt B, Troy A, Grove M, Clube J, Grøndahl C, Haaber JK, van der Helm E, Zdravkovic M, Sommer MOA. Engineered phage with antibacterial CRISPR-Cas selectively reduce E. coli burden in mice. Nat Biotechnol 2024; 42:265-274. [PMID: 37142704 PMCID: PMC10869271 DOI: 10.1038/s41587-023-01759-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 03/22/2023] [Indexed: 05/06/2023]
Abstract
Antibiotic treatments have detrimental effects on the microbiome and lead to antibiotic resistance. To develop a phage therapy against a diverse range of clinically relevant Escherichia coli, we screened a library of 162 wild-type (WT) phages, identifying eight phages with broad coverage of E. coli, complementary binding to bacterial surface receptors, and the capability to stably carry inserted cargo. Selected phages were engineered with tail fibers and CRISPR-Cas machinery to specifically target E. coli. We show that engineered phages target bacteria in biofilms, reduce the emergence of phage-tolerant E. coli and out-compete their ancestral WT phages in coculture experiments. A combination of the four most complementary bacteriophages, called SNIPR001, is well tolerated in both mouse models and minipigs and reduces E. coli load in the mouse gut better than its constituent components separately. SNIPR001 is in clinical development to selectively kill E. coli, which may cause fatal infections in hematological cancer patients.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Lev Koval
- SNIPR BIOME ApS, Copenhagen, Denmark
| | | | | | | | | | | | | | | | | | | | - Michael J Satlin
- Division of Infectious Diseases, Weill Cornell Medicine, New York City, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Morten Otto Alexander Sommer
- SNIPR BIOME ApS, Copenhagen, Denmark.
- Novo Nordisk Foundation Center for Biosustainability, DTU Biosustain, Kongens Lyngby, Denmark.
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9
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Nikolic N, Anagnostidis V, Tiwari A, Chait R, Gielen F. Droplet-based methodology for investigating bacterial population dynamics in response to phage exposure. Front Microbiol 2023; 14:1260196. [PMID: 38075890 PMCID: PMC10703435 DOI: 10.3389/fmicb.2023.1260196] [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: 07/17/2023] [Accepted: 10/23/2023] [Indexed: 02/12/2024] Open
Abstract
An alarming rise in antimicrobial resistance worldwide has spurred efforts into the search for alternatives to antibiotic treatments. The use of bacteriophages, bacterial viruses harmless to humans, represents a promising approach with potential to treat bacterial infections (phage therapy). Recent advances in microscopy-based single-cell techniques have allowed researchers to develop new quantitative methodologies for assessing the interactions between bacteria and phages, especially the ability of phages to eradicate bacterial pathogen populations and to modulate growth of both commensal and pathogen populations. Here we combine droplet microfluidics with fluorescence time-lapse microscopy to characterize the growth and lysis dynamics of the bacterium Escherichia coli confined in droplets when challenged with phage. We investigated phages that promote lysis of infected E. coli cells, specifically, a phage species with DNA genome, T7 (Escherichia virus T7) and two phage species with RNA genomes, MS2 (Emesvirus zinderi) and Qβ (Qubevirus durum). Our microfluidic trapping device generated and immobilized picoliter-sized droplets, enabling stable imaging of bacterial growth and lysis in a temperature-controlled setup. Temporal information on bacterial population size was recorded for up to 25 h, allowing us to determine growth rates of bacterial populations and helping us uncover the extent and speed of phage infection. In the long-term, the development of novel microfluidic single-cell and population-level approaches will expedite research towards fundamental understanding of the genetic and molecular basis of rapid phage-induced lysis and eco-evolutionary aspects of bacteria-phage dynamics, and ultimately help identify key factors influencing the success of phage therapy.
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Affiliation(s)
- Nela Nikolic
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- Department of Physics and Astronomy, Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
- Translational Research Exchange @ Exeter, University of Exeter, Exeter, United Kingdom
| | - Vasileios Anagnostidis
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- Department of Physics and Astronomy, Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
| | - Anuj Tiwari
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Remy Chait
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Fabrice Gielen
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- Department of Physics and Astronomy, Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
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10
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Zhao J, Lin Y, Wang C, Zayda M, Maung AT, Mohammadi TN, Duc HM, Yu P, Ma M, Gong D, Sato J, Masuda Y, Honjoh KI, Miyamoto T, Zeng Z. Biocontrol of Salmonella Typhimurium in milk, lettuce, raw pork meat and ready-to-eat steamed-chicken breast by using a novel bacteriophage with broad host range. Int J Food Microbiol 2023; 402:110295. [PMID: 37352774 DOI: 10.1016/j.ijfoodmicro.2023.110295] [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: 03/16/2023] [Revised: 06/07/2023] [Accepted: 06/10/2023] [Indexed: 06/25/2023]
Abstract
Salmonella spp., one of the most frequently reported bacteria, causes foodborne illness and economic losses. Due to the threat of increasing antibiotic resistant foodborne pathogens, application of bacteriophages as novel antibacterial agents in food matrices has become an emerging strategy. In this study, a novel Salmonella phage PS3-1 with high lytic activity against Salmonella Typhimurium was identified from previously isolated phages. PS3-1 belonged to the class Caudoviricetes with a broad host range, and had relatively short latent period (15 min), large burst size (92 PFU/cell), high pH stability (pH 3.0-11.0) and thermal tolerance (4-60 °C). Genome sequencing analysis showed that PS3-1 genome consisted of 107,110 bp DNA, without antibiotic resistance and virulence related genes. The results of growth curve and time-kill assay showed that PS3-1 not only inhibited the growth of S. Typhimurium, but also effectively decreased the viable cell counts (0.30-4.72 log) after 24-h incubation at 7, 25 and 37 °C (P < 0.05). Moreover, >1.28 log of established biofilm cells were effectively removed after 24-h treatment with PS3-1. Besides, PS3-1 significantly reduced the viability of S. Typhimurium in milk, lettuce, raw pork meat and ready-to-eat steamed-chicken breast at different temperatures (P < 0.05). These results demonstrated that PS3-1 may be an excellent antibacterial agent for controlling S. Typhimurium in food industry.
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Affiliation(s)
- Junxin Zhao
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China; Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yunzhi Lin
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Chen Wang
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Mahmoud Zayda
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, University of Sadat City, 32897 Sadat City, Egypt
| | - Aye Thida Maung
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Tahir Noor Mohammadi
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Hoang Minh Duc
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Ping Yu
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Maomao Ma
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Deming Gong
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Jun Sato
- Safety Science Research, R&D, Kao Corporation, 2606 Akabane, Ichikai-Machi, Haga-Gun, Tochigi 321-3497, Japan
| | - Yoshimitsu Masuda
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Ken-Ichi Honjoh
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takahisa Miyamoto
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Zheling Zeng
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China.
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11
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Esposito C, Kamper M, Trentacoste J, Galvin S, Pfister H, Wang J. Advances in the Cystic Fibrosis Drug Development Pipeline. Life (Basel) 2023; 13:1835. [PMID: 37763239 PMCID: PMC10532558 DOI: 10.3390/life13091835] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Cystic fibrosis is a genetic disease that results in progressive multi-organ manifestations with predominance in the respiratory and gastrointestinal systems. The significant morbidity and mortality seen in the CF population has been the driving force urging the CF research community to further advance treatments to slow disease progression and, in turn, prolong life expectancy. Enormous strides in medical advancements have translated to improvement in quality of life, symptom burden, and survival; however, there is still no cure. This review discusses the most current mainstay treatments and anticipated therapeutics in the CF drug development pipeline within the mechanisms of mucociliary clearance, anti-inflammatory and anti-infective therapies, restoration of the cystic fibrosis transmembrane conductance regulator (CFTR) protein (also known as highly effective modulator therapy (HEMT)), and genetic therapies. Ribonucleic acid (RNA) therapy, gene transfer, and gene editing are being explored in the hopes of developing a treatment and potential cure for people with CF, particularly for those not responsive to HEMT.
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Affiliation(s)
- Christine Esposito
- Division of Pulmonary, Critical Care and Sleep Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New Hyde Park, New York, NY 11042, USA; (M.K.); (J.W.)
| | - Martin Kamper
- Division of Pulmonary, Critical Care and Sleep Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New Hyde Park, New York, NY 11042, USA; (M.K.); (J.W.)
| | - Jessica Trentacoste
- Division of Pulmonary, Critical Care and Sleep Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New Hyde Park, New York, NY 11042, USA; (M.K.); (J.W.)
| | - Susan Galvin
- Division of Pediatric Pulmonology, The Steven and Alexandra Cohen Children’s Medical Center, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Lake Success, New York, NY 11042, USA;
| | - Halie Pfister
- Manhasset Office of Clinical Research, The Feinstein Institutes for Medical Research, Lake Success, New York, NY 11042, USA;
| | - Janice Wang
- Division of Pulmonary, Critical Care and Sleep Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New Hyde Park, New York, NY 11042, USA; (M.K.); (J.W.)
- Manhasset Office of Clinical Research, The Feinstein Institutes for Medical Research, Lake Success, New York, NY 11042, USA;
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12
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Kalpana S, Lin WY, Wang YC, Fu Y, Wang HY. Alternate Antimicrobial Therapies and Their Companion Tests. Diagnostics (Basel) 2023; 13:2490. [PMID: 37568853 PMCID: PMC10417861 DOI: 10.3390/diagnostics13152490] [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: 06/30/2023] [Accepted: 07/14/2023] [Indexed: 08/13/2023] Open
Abstract
New antimicrobial approaches are essential to counter antimicrobial resistance. The drug development pipeline is exhausted with the emergence of resistance, resulting in unsuccessful trials. The lack of an effective drug developed from the conventional drug portfolio has mandated the introspection into the list of potentially effective unconventional alternate antimicrobial molecules. Alternate therapies with clinically explicable forms include monoclonal antibodies, antimicrobial peptides, aptamers, and phages. Clinical diagnostics optimize the drug delivery. In the era of diagnostic-based applications, it is logical to draw diagnostic-based treatment for infectious diseases. Selection criteria of alternate therapeutics in infectious diseases include detection, monitoring of response, and resistance mechanism identification. Integrating these diagnostic applications is disruptive to the traditional therapeutic development. The challenges and mitigation methods need to be noted. Applying the goals of clinical pharmacokinetics that include enhancing efficacy and decreasing toxicity of drug therapy, this review analyses the strong correlation of alternate antimicrobial therapeutics in infectious diseases. The relationship between drug concentration and the resulting effect defined by the pharmacodynamic parameters are also analyzed. This review analyzes the perspectives of aligning diagnostic initiatives with the use of alternate therapeutics, with a particular focus on companion diagnostic applications in infectious diseases.
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Affiliation(s)
- Sriram Kalpana
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan;
| | - Wan-Ying Lin
- Department of Medicine, University of California San Diego, San Diego, CA 92093, USA;
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA;
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Yu-Chiang Wang
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA;
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Yiwen Fu
- Department of Medicine, Kaiser Permanente Santa Clara Medical Center, Santa Clara, CA 95051, USA;
| | - Hsin-Yao Wang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan;
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA;
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
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13
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Nicolas M, Trotereau A, Culot A, Moodley A, Atterbury R, Wagemans J, Lavigne R, Velge P, Schouler C. Isolation and Characterization of a Novel Phage Collection against Avian-Pathogenic Escherichia coli. Microbiol Spectr 2023; 11:e0429622. [PMID: 37140373 PMCID: PMC10269720 DOI: 10.1128/spectrum.04296-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 04/12/2023] [Indexed: 05/05/2023] Open
Abstract
The increase in antibiotic-resistant avian-pathogenic Escherichia coli (APEC), the causative agent of colibacillosis in poultry, warrants urgent research and the development of alternative therapies. This study describes the isolation and characterization of 19 genetically diverse, lytic coliphages, 8 of which were tested in combination for their efficacy in controlling in ovo APEC infections. Genome homology analysis revealed that the phages belong to nine different genera, one of them being a novel genus (Nouzillyvirus). One phage, REC, was derived from a recombination event between two Phapecoctavirus phages (ESCO5 and ESCO37) isolated in this study. Twenty-six of the 30 APEC strains tested were lysed by at least one phage. Phages exhibited varying infectious capacities, with narrow to broad host ranges. The broad host range of some phages could be partially explained by the presence of receptor-binding protein carrying a polysaccharidase domain. To demonstrate their therapeutic potential, a phage cocktail consisting of eight phages belonging to eight different genera was tested against BEN4358, an APEC O2 strain. In vitro, this phage cocktail fully inhibited the growth of BEN4358. In a chicken lethality embryo assay, the phage cocktail enabled 90% of phage-treated embryos to survive infection with BEN4358, compared with 0% of nontreated embryos, indicating that these novel phages are good candidates to successfully treat colibacillosis in poultry. IMPORTANCE Colibacillosis, the most common bacterial disease affecting poultry, is mainly treated by antibiotics. Due to the increased prevalence of multidrug-resistant avian-pathogenic Escherichia coli, there is an urgent need to assess the efficacy of alternatives to antibiotherapy, such as phage therapy. Here, we have isolated and characterized 19 coliphages that belong to nine phage genera. We showed that a combination of 8 of these phages was efficacious in vitro to control the growth of a clinical isolate of E. coli. Used in ovo, this phage combination allowed embryos to survive APEC infection. Thus, this phage combination represents a promising treatment for avian colibacillosis.
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Affiliation(s)
| | | | | | - Arshnee Moodley
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Robert Atterbury
- School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, United Kingdom
| | - Jeroen Wagemans
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
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14
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Uskudar-Guclu A, Yalcin S, Unlu S, Mirza HC, Basustaoglu A. Evaluation of the Lytic Activity of Various Phage Cocktails Against, ESBL-Producer, Non-Producer and Carbapenem-Resistant Escherichia coli Isolates. Indian J Microbiol 2023; 63:208-215. [PMID: 37325020 PMCID: PMC10267027 DOI: 10.1007/s12088-023-01074-9] [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: 11/29/2022] [Accepted: 03/01/2023] [Indexed: 06/17/2023] Open
Abstract
Bacteriophages have been proposed as an alternative therapy for the treatment of bacterial infections. This research aims to determine the lytic activity of bacteriophage-cocktails (BC) against carbapenem-resistant (CR-EC), ESBL-producer (EP-EC), and non-producer (NP-EC) E. coli isolates. Related resistance genes in 87 E. coli isolates were screened by PCR. The efficacies of BCs were determined by spot test and lytic zones were evaluated from fully-confluent to opaque. MOIs of the BCs were compared for fully-confluent and opaque lytic zones. BCs were also evaluated in terms of their biophysical characteristics including latency, burst size, pH and temperature stabilities. Among EP-EC, 96.9% of the isolates carry blaCTX-M, 25% of them blaSHV and 15.6% of them carry blaTEM. All CR-EC isolates carried blaOXA-48, but not blaKPC and blaNDM. CR-EC isolates were the least susceptible for the each of four BCs. MOIs for ENKO, SES and INTESTI-phage forming fully-confluent zone in E. coli isolates EC3 (NP-EC), EC8 (EP-EC) and EC27 (NP-EC), respectively were 10, 100 and 1, respectively. MOIs for ENKO, SES and INTESTI opaque zone in EC19 (EP-EC), EC10 (EP-EC), EC1(NP-EC), respectively were 0.01, 0.01, 0.1 PFU/CFU, respectively. The MOI for PYO-phage forming a semi-confluent zone in EC6 (NP-EC) isolate was 1 PFU/CFU. The phages were thermally stable and tolerant to a wide pH range. Comparison of MOIs according to lysis zone characteristics demonstrated that the activities of phages in phage cocktails vary depending on the characteristics of each bacterial host. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-023-01074-9.
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Affiliation(s)
- Aylin Uskudar-Guclu
- Department of Medical Microbiology, Faculty of Medicine, Baskent University, Ankara, Türkiye
| | - Suleyman Yalcin
- Microbiology References Laboratory, Ministry of Health General Directorate of Public Health, Ankara, Türkiye
| | - Sezin Unlu
- Department of Medical Microbiology, Faculty of Medicine, Baskent University, Ankara, Türkiye
| | - Hasan Cenk Mirza
- Department of Medical Microbiology, Faculty of Medicine, Baskent University, Ankara, Türkiye
| | - Ahmet Basustaoglu
- Department of Medical Microbiology, Faculty of Medicine, Baskent University, Ankara, Türkiye
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15
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What Lies Beneath? Taking the Plunge into the Murky Waters of Phage Biology. mSystems 2023; 8:e0080722. [PMID: 36651762 PMCID: PMC9948730 DOI: 10.1128/msystems.00807-22] [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: 01/19/2023] Open
Abstract
The sequence revolution revealed that bacteria-infecting viruses, known as phages, are Earth's most abundant biological entities. Phages have far-reaching impacts on the form and function of microbial communities and play a fundamental role in ecological processes. However, even well into the sequencing revolution, we have only just begun to explore the murky waters around the phage biology iceberg. Many viral reads cannot be assigned to a culturable isolate, and reference databases are biased toward more easily collectible samples, which likely distorts our conclusions. This minireview points out alternatives to mapping reads to reference databases and highlights innovative bioinformatic and experimental approaches that can help us overcome some of the challenges in phage research and better decipher the impact of phages on microbial communities. Moving beyond the identification of novel phages, we highlight phage metabolomics as an important influencer of bacterial host cell physiology and hope to inspire the reader to consider the effects of phages on host metabolism and ecosystems at large. We encourage researchers to report unassigned/unknown sequencing reads and contigs and to continue developing alternative methods to investigate phages within sequence data.
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16
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Expansion of Kuravirus-like Phage Sequences within the Past Decade, including Escherichia Phage YF01 from Japan, Prompt the Creation of Three New Genera. Viruses 2023; 15:v15020506. [PMID: 36851720 PMCID: PMC9965538 DOI: 10.3390/v15020506] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Bacteriophages, viruses that infect bacteria, are currently receiving significant attention amid an ever-growing global antibiotic resistance crisis. In tandem, a surge in the availability and affordability of next-generation and third-generation sequencing technologies has driven the deposition of a wealth of phage sequence data. Here, we have isolated a novel Escherichia phage, YF01, from a municipal wastewater treatment plant in Yokohama, Japan. We demonstrate that the YF01 phage shares a high similarity to a collection of thirty-five Escherichia and Shigella phages found in public databases, six of which have been previously classified into the Kuravirus genus by the International Committee on Taxonomy of Viruses (ICTV). Using modern phylogenetic approaches, we demonstrate that an expansion and reshaping of the current six-membered Kuravirus genus is required to accommodate all thirty-six member phages. Ultimately, we propose the creation of three additional genera, Vellorevirus, Jinjuvirus, and Yesanvirus, which will allow a more organized approach to the addition of future Kuravirus-like phages.
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17
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Nang SC, Lin YW, Petrovic Fabijan A, Chang RYK, Rao GG, Iredell J, Chan HK, Li J. Pharmacokinetics/pharmacodynamics of phage therapy: a major hurdle to clinical translation. Clin Microbiol Infect 2023:S1198-743X(23)00046-0. [PMID: 36736661 DOI: 10.1016/j.cmi.2023.01.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/05/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023]
Abstract
BACKGROUND The increasing emergence of antimicrobial resistance worldwide has led to renewed interest in phage therapy. Unlike antibiotics, the lack of pharmacokinetics/pharmacodynamics (PK/PD) information represents a major challenge for phage therapy. As therapeutic phages are biological entities with the ability to self-replicate in the presence of susceptible bacteria, their PK/PD is far more complicated than that of antibiotics. OBJECTIVES This narrative review examines the current literature on phage pharmacology and highlights major pharmacological challenges for phage therapy. SOURCES Included articles were identified by searching PubMed and Google Scholar till June 2022. The search terms were 'bacteriophage', 'antimicrobial', 'pharmacokinetics' and 'pharmacodynamics'. Additional relevant references were obtained from articles retrieved from the primary search. CONTENT In this review, phage PK is first discussed, focusing on absorption, distribution, metabolism, and elimination. Key factors affecting phage antimicrobial activities are reviewed, including multiplicity of infection, passive and active phage therapy, and the involvement of the human immune system. Importantly, we emphasize the impact of phage self-replication on the PK/PD and the fundamental phage characteristics that are required for PK/PD modelling and clinical translation. IMPLICATIONS Recent progress in phage pharmacology has shown that we are in a far better position now to treat infections with phage therapy than a century ago. However, phage therapy is still in its infancy when compared to antibiotics due to the scarce pharmacological knowledge (e.g. PK/PD). Optimization of phage PK/PD is key for translation of phage therapy in patients.
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Affiliation(s)
- Sue C Nang
- Biomedicine Discovery Institute, Infection Program, Department of Microbiology, Monash University, Victoria, Australia
| | - Yu-Wei Lin
- Biomedicine Discovery Institute, Infection Program, Department of Microbiology, Monash University, Victoria, Australia
| | - Aleksandra Petrovic Fabijan
- Westmead Hospital, Western Sydney Local Health District, Westmead, New South Wales, Australia; Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia; School of Medicine, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, New South Wales, Australia
| | - Rachel Y K Chang
- Advanced Drug Delivery Group, Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, New South Wales, Australia; AcuraBio Pty Ltd, Darra, Queensland, Australia
| | - Gauri G Rao
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, North Carolina, USA
| | - Jonathan Iredell
- Westmead Hospital, Western Sydney Local Health District, Westmead, New South Wales, Australia; Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia; School of Medicine, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, New South Wales, Australia
| | - Hak-Kim Chan
- Advanced Drug Delivery Group, Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, New South Wales, Australia
| | - Jian Li
- Biomedicine Discovery Institute, Infection Program, Department of Microbiology, Monash University, Victoria, Australia.
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18
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Andrezal M, Oravcova L, Kadličekova V, Ozaee E, Elnwrani S, Bugala J, Markuskova B, Kajsik M, Drahovska H. Characterization and the host specificity of Pet-CM3-4, a new phage infecting Cronobacter and Enterobacter strains. Virus Res 2023; 324:199025. [PMID: 36528171 DOI: 10.1016/j.virusres.2022.199025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Bacteria belonging to Cronobacter and Enterobacter genera are opportunistic pathogens responsible for infections in immunocompromised patients including neonates. Phage therapy offers a safe method for pathogen elimination, however, phages must be well characterized before application. In the present study we isolated four closely related bacteriophages from the subfamily Tevenvirinae infecting Cronobacter and Enterobacter strains. Bacteriophage Pet-CM3-4 which was isolated on C. malonaticus strain possessed broader host specificity than other three phages with primary Enterobacter hosts. Based on genome sequences all these phages have been assigned to the genus Karamvirus. We also studied factors influencing the host specificity of Pet-CM3-4 phage and its host range mutant Pet-CM3-1 and observed that a lysine to glutamine substitution in the long tail fiber adhesin was the reason of the Pet-CM3-1 reduced host specificity. By characterization of phage-resistant mutants from transposon library of C. malonaticus KMB-72 strain we identified that LPS is the receptor of both phages. C. malonaticus O:3 antigen is the receptor of Pet-CM3-1 phage and the Pet-CM3-4 phage binds to structures of the LPS core region. Obtained results will contribute to our understanding of biology and evolution of Tevenvirinae phages.
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Affiliation(s)
- Michal Andrezal
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84104 Bratislava, Slovakia
| | - Lucia Oravcova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84104 Bratislava, Slovakia
| | - Veronika Kadličekova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84104 Bratislava, Slovakia
| | - Elham Ozaee
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84104 Bratislava, Slovakia
| | - Sulafa Elnwrani
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84104 Bratislava, Slovakia
| | - Juraj Bugala
- Comenius University Science Park, Ilkovičova 8, 84104 Bratislava, Slovakia
| | - Barbora Markuskova
- Comenius University Science Park, Ilkovičova 8, 84104 Bratislava, Slovakia
| | - Michal Kajsik
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84104 Bratislava, Slovakia; Comenius University Science Park, Ilkovičova 8, 84104 Bratislava, Slovakia; Medirex group academy n.o., Novozámocká 1/67, 949 05 Nitra, Slovakia
| | - Hana Drahovska
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84104 Bratislava, Slovakia; Comenius University Science Park, Ilkovičova 8, 84104 Bratislava, Slovakia.
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19
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Proof-of-Concept Standardized Approach Using a Single-Disk Method Analogous to Antibiotic Disk Diffusion Assays for Routine Phage Susceptibility Testing in Diagnostic Laboratories. Appl Environ Microbiol 2022; 88:e0030922. [PMID: 36416554 PMCID: PMC9746313 DOI: 10.1128/aem.00309-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Application of bacteriophages is increasingly being implemented in clinical therapies. Prior susceptibility testing should be regarded as mandatory, but standards are lacking. The objective of this research was to develop a highly standardized methodology to facilitate phage susceptibility testing (PST) in clinical microbiology routine laboratories. Therefore, EUCAST methods established for single disk-based antibiotic susceptibility testing (AST) were adapted. In a first step, basic parameters were evaluated using well-studied Escherichia phage T4-Escherichia coli combinations. In addition, test results were compared to those from conventional spot test and efficiency of plating (EOP) approaches. In a second step, the applicability of the methodology and the most promising test parameters were demonstrated for five other frequently isolated clinical bacterial species and their corresponding phages. At present, the method predominantly leads to qualitative rather than quantitative results. This disk-based approach provides a standardized, easy-to-handle, reproducible and reliable PST protocol by relying on well-established routine procedures in diagnostic laboratories. IMPORTANCE Application of bacteriophages in clinical therapies is attractive due to increasing rates of isolation of multidrug-resistant bacteria worldwide. As the phage effect is highly specific, prior susceptibility testing of target bacteria is mandatory. Of note, established standards are lacking. In this research, we adapted the single-disk method for antibiotic susceptibility testing to phage susceptibility testing (PST) in order to provide a standardized, easy-to-handle, reproducible, and reliable PST protocol for application in diagnostic routine laboratories.
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20
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Santiago-Rodriguez TM, Hollister EB. Unraveling the viral dark matter through viral metagenomics. Front Immunol 2022; 13:1005107. [PMID: 36189246 PMCID: PMC9523745 DOI: 10.3389/fimmu.2022.1005107] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Viruses are part of the microbiome and have essential roles in immunology, evolution, biogeochemical cycles, health, and disease progression. Viruses influence a wide variety of systems and processes, and the continued discovery of novel viruses is anticipated to reveal new mechanisms influencing the biology of diverse environments. While the identity and roles of viruses continue to be discovered and understood through viral metagenomics, most of the sequences in virome datasets cannot be attributed to known viruses or may be only distantly related to species already described in public sequence databases, at best. Such viruses are known as the viral dark matter. Ongoing discoveries from the viral dark matter have provided insights into novel viruses from a variety of environments, as well as their potential in immunological processes, virus evolution, health, disease, therapeutics, and surveillance. Increased understanding of the viral dark matter will continue with a combination of cultivation, microscopy, sequencing, and bioinformatic efforts, which are discussed in the present review.
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Abstract
Urinary tract infection (UTI) is among the most common infections treated worldwide each year and is caused primarily by uropathogenic Escherichia coli (UPEC). Rising rates of antibiotic resistance among uropathogens have spurred a consideration of alternative treatment strategies, such as bacteriophage (phage) therapy; however, phage-bacterial interactions within the urinary environment are poorly defined. Here, we assess the activity of two phages, namely, HP3 and ES17, against clinical UPEC isolates using in vitro and in vivo models of UTI. In both bacteriologic medium and pooled human urine, we identified phage resistance arising within the first 6 to 8 h of coincubation. Whole-genome sequencing revealed that UPEC strains resistant to HP3 and ES17 harbored mutations in genes involved in lipopolysaccharide (LPS) biosynthesis. Phage-resistant strains displayed several in vitro phenotypes, including alterations to adherence to and invasion of human bladder epithelial HTB-9 cells and increased biofilm formation in some isolates. Interestingly, these phage-resistant UPEC isolates demonstrated reduced growth in pooled human urine, which could be partially rescued by nutrient supplementation and were more sensitive to several outer membrane-targeting antibiotics than parental strains. Additionally, phage-resistant UPEC isolates were attenuated in bladder colonization in a murine UTI model. In total, our findings suggest that while resistance to phages, such as HP3 and ES17, may arise readily in the urinary environment, phage resistance is accompanied by fitness costs which may render UPEC more susceptible to host immunity or antibiotics. IMPORTANCE UTI is one of the most common causes of outpatient antibiotic use, and rising antibiotic resistance threatens the ability to control UTI unless alternative treatments are developed. Bacteriophage (phage) therapy is gaining renewed interest; however, much like with antibiotics, bacteria can readily become resistant to phages. For successful UTI treatment, we must predict how bacteria will evade killing by phage and identify the downstream consequences of phage resistance during bacterial infection. In our current study, we found that while phage-resistant bacteria quickly emerged in vitro, these bacteria were less capable of growing in human urine and colonizing the murine bladder. These results suggest that phage therapy poses a viable UTI treatment if phage resistance confers fitness costs for the uropathogen. These results have implications for developing cocktails of phage with multiple different bacterial targets, of which each is evaded only at the cost of bacterial fitness.
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22
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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.
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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,
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23
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Two Newly Isolated Enterobacter-Specific Bacteriophages: Biological Properties and Stability Studies. Viruses 2022; 14:v14071518. [PMID: 35891499 PMCID: PMC9319786 DOI: 10.3390/v14071518] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/05/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022] Open
Abstract
In an era of antibiotic therapy crisis caused by spreading antimicrobial resistance, and when recurrent urinary tract infections constitute a serious social and medical problem, the isolation and complex characterization of phages with a potential therapeutic application represents a promising solution. It is an inevitable, and even a necessary direction in the development of current phage research. In this paper, we present two newly isolated myoviruses that show lytic activity against multidrug-resistant clinical isolates of Enterobacter spp. (E. cloacae, E. hormaechei, and E. kobei), the genomes of which belong to a poorly represented phage group. Both phages were classified as part of the Tevenvirinae subfamily (Entb_43 was recognized as Karamvirus and Entb_45 as Kanagawavirus). Phage lytic spectra ranging from 40 to 60% were obtained. The most effective phage-to-bacteria ratios (MOI = 0.01 and MOI = 0.001) for both the phage amplification and their lytic activity against planktonic bacteria were also estimated. Complete adsorption to host cells were obtained after about 20 min for Entb_43 and 10 min for Entb_45. The phage lysates retained their initial titers even during six months of storage at both −70 °C and 4 °C, whereas storage at 37 °C caused a complete loss in their activity. We showed that phages retained their activity after incubation with solutions of silver and copper nanoparticles, which may indicate possible synergistic antibacterial activity. Moreover, a significant reduction in phage titers was observed after incubation with a disinfectant containing octenidinum dihydrochloridum and phenoxyethanol, as well as with 70% ethanol. The observed maintenance of phage activity during incubation in a urine sample, along with other described properties, may suggest a therapeutic potential of phages at the infection site after intravesical administration.
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24
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Tabassum R, Basit A, Alvi IA, Asif M, Ur Rehman S. TSP, a virulent Podovirus, can control the growth of Staphylococcus aureus for 12 h. Sci Rep 2022; 12:10008. [PMID: 35705576 PMCID: PMC9200855 DOI: 10.1038/s41598-022-13584-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 05/03/2022] [Indexed: 11/23/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a prevailing nosocomial pathogen that is increasingly isolated in community settings. It shows resistance against all beta-lactam drugs and has acquired mechanisms to resist other groups of antibiotics. To tackle this emerging issue of MRSA, there is an urgent need for antibiotic alternatives, and utilizing lytic bacteriophages is one of the most promising therapeutic approaches. In the present study, a lytic bacteriophage TSP was isolated from hospital wastewater against MRSA. The phage efficiently inhibited bacterial growth for up to 12 h at MOI of 1 and 10. TSP phage showed activity against various isolates of MRSA and MSSA, isolated from different clinical samples, with variable antibiotic susceptibility patterns. The bacteriophage TSP showed stability at varying temperatures (25 °C, 37 °C) and pH values (5–9), while its maximum storage stability was observed at 4 °C. It had a short latent period (20 min) and burst size of 103 ± 5pfu/infected cells. TSP genome sequence and restriction analysis revealed that its genome has a linear confirmation and length of 17,987 bp with an average GC content of 29.7%. According to comparative genomic analysis and phylogenetic tree,TSP phage can be considered a member of genus “P68viruses”. The strong lytic activity and short latent period in addition to its lytic nature makes it a good candidate for phage therapy against MRSA infections, if it proves to be effective in in-vivo studies.
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Affiliation(s)
- Rabia Tabassum
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Abdul Basit
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Iqbal Ahmed Alvi
- Department of Microbiology, Hazara University, Mansehra, KPK, Pakistan
| | - Muhammad Asif
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan.,Department of Pathology, King Edward Medical University, Lahore, Pakistan
| | - Shafiq Ur Rehman
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan.
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25
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Hernandez Santos H, Clark J, Terwilliger A, Maresso A. Discovery of the First Lytic Staphylococcus pseudintermedius/ Staphylococcus aureus Polyvalent Bacteriophages. PHAGE (NEW ROCHELLE, N.Y.) 2022; 3:116-124. [PMID: 36157281 PMCID: PMC9248872 DOI: 10.1089/phage.2022.0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Background There are no verified lytic Staphylococcus pseudintermedius phages in the literature and few temperate phage genomes in databases. S. pseudintermedius is an opportunistic zoonotic pathogen of great importance in veterinary and human medicine. Materials and Methods We discovered phages against canine-derived S. pseudintermedius isolates by screening dog feces, hair, and skin swabs. Fourteen new phages were isolated and characterized by genomic analysis, transmission electron microscopy, and host range determination. Results Three phages-DH2, DH5, and DS10, a phage K variant-were predicted lytic by sequencing, a designation supported by mitomycin C induction. All three are S. pseudintermedius and Staphylococcus aureus polyvalent phages, with DH2 and DS10 being strong killers of both species. Conclusions We report discovery of the first verified lytic S. pseudintermedius phages and suggest dog hair as a novel reservoir. DH2, DH5, and DS10 are promising candidates toward developing an anti-Staphylococcal phage cocktail.
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Affiliation(s)
- Haroldo Hernandez Santos
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, Texas, USA
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, Texas, USA
| | - Justin Clark
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, Texas, USA
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, Texas, USA
| | - Austen Terwilliger
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, Texas, USA
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, Texas, USA
| | - Anthony Maresso
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, Texas, USA
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, Texas, USA
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26
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Totten KM, Cunningham SA, Gades NM, Etzioni A, Patel R. Pharmacokinetic Assessment of Staphylococcal Phage K Following Parenteral and Intra-articular Administration in Rabbits. Front Pharmacol 2022; 13:840165. [PMID: 35668926 PMCID: PMC9163985 DOI: 10.3389/fphar.2022.840165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
The therapeutic value of phage as an alternative to antibiotics for the treatment of bacterial infections is being considered in the wake of mounting antibiotic resistance. In this study, the pharmacokinetic properties of Staphylococcus aureus phage K following intravenous and intra-articular administration were investigated in a rabbit model. Using a traditional plaque assay and a novel quantitative PCR assay to measure phage levels in specimens over time, it was found that intra-articularly administered phage enters the systemic circulation; that phage may be detected in synovial fluid up to 24 h following the intra-articular, but not intravenous, administration; and that qPCR-based enumeration is generally more sensitive than plaque enumeration, with fair to moderate correlation between the two methods. Findings presented should inform the design of phage therapy experiments and therapeutic drug monitoring in preclinical and human phage studies.
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Affiliation(s)
- Katherine M.C. Totten
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN, United States
| | - Scott A. Cunningham
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Naomi M. Gades
- Department of Comparative Medicine, Mayo Clinic, Scottsdale, AZ, United States
| | - Athema Etzioni
- Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, AL, United States
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States,Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN, United States,*Correspondence: Robin Patel,
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27
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Sanchez BC, Heckmann ER, Green SI, Clark JR, Kaplan HB, Ramig RF, Muldrew KL, Hines-Munson C, Skelton F, Trautner BW, Maresso AW. Development of Phage Cocktails to Treat E. coli Catheter-Associated Urinary Tract Infection and Associated Biofilms. Front Microbiol 2022; 13:796132. [PMID: 35620093 PMCID: PMC9127763 DOI: 10.3389/fmicb.2022.796132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 04/04/2022] [Indexed: 11/16/2022] Open
Abstract
High rates of antimicrobial resistance and formation of biofilms makes treatment of Escherichia coli catheter-associated urinary tract infections (CAUTI) particularly challenging. CAUTI affect 1 million patients per year in the United States and are associated with morbidity and mortality, particularly as an etiology for sepsis. Phage have been proposed as a potential therapeutic option. Here, we report the development of phage cocktails that lyse contemporary E. coli strains isolated from the urine of patients with spinal cord injury (SCI) and display strong biofilm-forming properties. We characterized E. coli phage against biofilms in two in vitro CAUTI models. Biofilm viability was measured by an MTT assay that determines cell metabolic activity and by quantification of colony forming units. Nine phage decreased cell viability by >80% when added individually to biofilms of two E. coli strains in human urine. A phage cocktail comprising six phage lyses 82% of the strains in our E. coli library and is highly effective against young and old biofilms and against biofilms on silicon catheter materials. Using antibiotics together with our phage cocktail prevented or decreased emergence of E. coli resistant to phage in human urine. We created an anti-biofilm phage cocktail with broad host range against E. coli strains isolated from urine. These phage cocktails may have therapeutic potential against CAUTI.
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Affiliation(s)
- Belkys C. Sanchez
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Emmaline R. Heckmann
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Sabrina I. Green
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Justin R. Clark
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Heidi B. Kaplan
- Department of Microbiology and Molecular Genetics, McGovern Medical School, UTHealth Houston, Houston, TX, United States
| | - Robert F. Ramig
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Kenneth L. Muldrew
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States,Pathology and Laboratory Medicine, Michael E. DeBakey VA Medical Center, Houston, TX, United States,Section of Infectious Diseases, Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Casey Hines-Munson
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX, United States
| | - Felicia Skelton
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX, United States,H. Ben Taub Department of Physical Medicine and Rehabilitation, Baylor College of Medicine, Houston, TX, United States
| | - Barbara W. Trautner
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX, United States,Department of Medicine and Surgery, Baylor College of Medicine, Houston, TX, United States,Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey VA Medical Center, Houston, TX, United States
| | - Anthony W. Maresso
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States,*Correspondence: Anthony W. Maresso,
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28
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A Phage Foundry Framework to Systematically Develop Viral Countermeasures to Combat Antibiotic-Resistant Bacterial Pathogens. iScience 2022; 25:104121. [PMID: 35402883 PMCID: PMC8983348 DOI: 10.1016/j.isci.2022.104121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
At its current rate, the rise of antimicrobial-resistant (AMR) infections is predicted to paralyze our industries and healthcare facilities while becoming the leading global cause of loss of human life. With limited new antibiotics on the horizon, we need to invest in alternative solutions. Bacteriophages (phages)—viruses targeting bacteria—offer a powerful alternative approach to tackle bacterial infections. Despite recent advances in using phages to treat recalcitrant AMR infections, the field lacks systematic development of phage therapies scalable to different applications. We propose a Phage Foundry framework to establish metrics for phage characterization and to fill the knowledge and technological gaps in phage therapeutics. Coordinated investment in AMR surveillance, sampling, characterization, and data sharing procedures will enable rational exploitation of phages for treatments. A fully realized Phage Foundry will enhance the sharing of knowledge, technology, and viral reagents in an equitable manner and will accelerate the biobased economy.
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Abstract
Increasing antimicrobial resistance and medical device-related infections have led to a renewed interest in phage therapy as an alternative or adjunct to conventional antimicrobials. Expanded access and compassionate use cases have risen exponentially but have varied widely in approach, methodology, and clinical situations in which phage therapy might be considered. Large gaps in knowledge contribute to heterogeneity in approach and lack of consensus in many important clinical areas. The Antibacterial Resistance Leadership Group (ARLG) has convened a panel of experts in phage therapy, clinical microbiology, infectious diseases, and pharmacology, who worked with regulatory experts and a funding agency to identify questions based on a clinical framework and divided them into three themes: potential clinical situations in which phage therapy might be considered, laboratory testing, and pharmacokinetic considerations. Suggestions are provided as answers to a series of questions intended to inform clinicians considering experimental phage therapy for patients in their clinical practices.
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30
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Loose M, Sáez Moreno D, Mutti M, Hitzenhammer E, Visram Z, Dippel D, Schertler S, Tišáková LP, Wittmann J, Corsini L, Wagenlehner F. Natural Bred ε 2-Phages Have an Improved Host Range and Virulence against Uropathogenic Escherichia coli over Their Ancestor Phages. Antibiotics (Basel) 2021; 10:1337. [PMID: 34827275 PMCID: PMC8614997 DOI: 10.3390/antibiotics10111337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 12/22/2022] Open
Abstract
Alternative treatments for Escherichia coli infections are urgently needed, and phage therapy is a promising option where antibiotics fail, especially for urinary tract infections (UTI). We used wastewater-isolated phages to test their lytic activity against a panel of 47 E. coli strains reflecting the diversity of strains found in UTI, including sequence type 131, 73 and 69. The plaquing host range (PHR) was between 13 and 63%. In contrast, the kinetic host range (KHR), describing the percentage of strains for which growth in suspension was suppressed for 24 h, was between 0% and 19%, substantially lower than the PHR. To improve the phage host range and their efficacy, we bred the phages by mixing and propagating cocktails on a subset of E. coli strains. The bred phages, which we termed evolution-squared ε2-phages, of a mixture of Myoviridae have KHRs up to 23% broader compared to their ancestors. Furthermore, using constant phage concentrations, Myoviridae ε2-phages suppressed the growth of higher bacterial inocula than their ancestors did. Thus, the ε2-phages were more virulent compared to their ancestors. Analysis of the genetic sequences of the ε2-phages with the broadest host range reveals that they are mosaic intercrossings of 2-3 ancestor phages. The recombination sites are distributed over the whole length of the genome. All ε2-phages are devoid of genes conferring lysogeny, antibiotic resistance, or virulence. Overall, this study shows that ε2-phages are remarkably more suitable than the wild-type phages for phage therapy.
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Affiliation(s)
- Maria Loose
- Clinic for Urology, Pediatric Urology and Andrology, Justus-Liebig University Giessen, 35392 Giessen, Germany; (M.L.); (D.D.)
| | - David Sáez Moreno
- PhagoMed Biopharma GmbH, A-1110 Vienna, Austria; (D.S.M.); (M.M.); (E.H.); (Z.V.); (L.P.T.)
| | - Michele Mutti
- PhagoMed Biopharma GmbH, A-1110 Vienna, Austria; (D.S.M.); (M.M.); (E.H.); (Z.V.); (L.P.T.)
| | - Eva Hitzenhammer
- PhagoMed Biopharma GmbH, A-1110 Vienna, Austria; (D.S.M.); (M.M.); (E.H.); (Z.V.); (L.P.T.)
| | - Zehra Visram
- PhagoMed Biopharma GmbH, A-1110 Vienna, Austria; (D.S.M.); (M.M.); (E.H.); (Z.V.); (L.P.T.)
| | - David Dippel
- Clinic for Urology, Pediatric Urology and Andrology, Justus-Liebig University Giessen, 35392 Giessen, Germany; (M.L.); (D.D.)
| | - Susanne Schertler
- DSMZ—German Collection of Microorganism and Cell Cultures GmbH, Leibniz Institute, 38124 Braunschweig, Germany; (S.S.); (J.W.)
| | - Lenka Podpera Tišáková
- PhagoMed Biopharma GmbH, A-1110 Vienna, Austria; (D.S.M.); (M.M.); (E.H.); (Z.V.); (L.P.T.)
- DSMZ—German Collection of Microorganism and Cell Cultures GmbH, Leibniz Institute, 38124 Braunschweig, Germany; (S.S.); (J.W.)
| | - Johannes Wittmann
- DSMZ—German Collection of Microorganism and Cell Cultures GmbH, Leibniz Institute, 38124 Braunschweig, Germany; (S.S.); (J.W.)
| | - Lorenzo Corsini
- PhagoMed Biopharma GmbH, A-1110 Vienna, Austria; (D.S.M.); (M.M.); (E.H.); (Z.V.); (L.P.T.)
| | - Florian Wagenlehner
- Clinic for Urology, Pediatric Urology and Andrology, Justus-Liebig University Giessen, 35392 Giessen, Germany; (M.L.); (D.D.)
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31
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Terwilliger A, Clark J, Karris M, Hernandez-Santos H, Green S, Aslam S, Maresso A. Phage Therapy Related Microbial Succession Associated with Successful Clinical Outcome for a Recurrent Urinary Tract Infection. Viruses 2021; 13:v13102049. [PMID: 34696479 PMCID: PMC8541385 DOI: 10.3390/v13102049] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/28/2021] [Accepted: 10/07/2021] [Indexed: 01/29/2023] Open
Abstract
We rationally designed a bacteriophage cocktail to treat a 56-year-old male liver transplant patient with complex, recurrent prostate and urinary tract infections caused by an extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (E. coli) (UCS1). We screened our library for phages that killed UCS1, with four promising candidates chosen for their virulence, mucolytic properties, and ability to reduce bacterial resistance. The patient received 2 weeks of intravenous phage cocktail with concomitant ertapenem for 6 weeks. Weekly serum and urine samples were collected to track the patient’s response. The patient tolerated the phage therapy without any adverse events with symptom resolution. The neutralization of the phage activity occurred with sera collected 1 to 4 weeks after the first phage treatment. This was consistent with immunoassays that detected the upregulation of immune stimulatory analytes. The patient developed asymptomatic recurrent bacteriuria 6 and 11 weeks following the end of phage therapy—a condition that did not require antibiotic treatment. The bacteriuria was caused by a sister strain of E. coli (UCS1.1) that remained susceptible to the original phage cocktail and possessed putative mutations in the proteins involved in adhesion and invasion compared to UCS1. This study highlights the utility of rationally designed phage cocktails with antibiotics at controlling E. coli infection and suggests that microbial succession, without complete eradication, may produce desirable clinical outcomes.
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Affiliation(s)
- Austen Terwilliger
- TAILΦR Labs, Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX 77030, USA; (A.T.); (J.C.); (H.H.-S.); (S.G.)
| | - Justin Clark
- TAILΦR Labs, Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX 77030, USA; (A.T.); (J.C.); (H.H.-S.); (S.G.)
| | - Maile Karris
- Center for Innovative Phage Applications and Therapeutics, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA;
| | - Haroldo Hernandez-Santos
- TAILΦR Labs, Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX 77030, USA; (A.T.); (J.C.); (H.H.-S.); (S.G.)
| | - Sabrina Green
- TAILΦR Labs, Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX 77030, USA; (A.T.); (J.C.); (H.H.-S.); (S.G.)
| | - Saima Aslam
- Center for Innovative Phage Applications and Therapeutics, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA;
- Correspondence: (S.A.); (A.M.); Tel.: +1-858-657-7643 (S.A.); +1-713-798-7369 (A.M.)
| | - Anthony Maresso
- TAILΦR Labs, Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX 77030, USA; (A.T.); (J.C.); (H.H.-S.); (S.G.)
- Correspondence: (S.A.); (A.M.); Tel.: +1-858-657-7643 (S.A.); +1-713-798-7369 (A.M.)
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32
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Abstract
Mediators of the initiation, development, and recurrence of periodontitis include the oral microbiome embedded in subgingival plaque and the host immune response to a dysbiosis within this dynamic and complex microbial community. Although mediators have been studied extensively, researchers in the field have been unable to fully ascribe certain clinical presentations of periodontitis to their nature. Emergence of high-throughput sequencing technologies has resulted in better characterization of the microbial oral dysbiosis that extends beyond the extensively studied putative bacterial periodontopathogens to a shift in the oral virome composition during disease conditions. Although the biological dark matter inserted by retroviruses was once believed to be nonfunctional, research has revealed that it encodes historical viral-eukaryotic interactions and influences host development. The objective of this review is to evaluate the proposed association of herpesviruses to the etiology and pathogenesis of periodontal disease and survey the highly abundant prokaryotic viruses to delineate their potential roles in biofilm dynamics, as well as their interactions with putative bacterial periodontopathogens and eukaryotic cells. The findings suggest that potential novel periodontal therapies targeting or utilizing the oral virome can alleviate certain clinical presentations of periodontitis. Perhaps it is time to embrace the viral dark matter within the periodontal environment to fully comprehend the pathogenesis and systemic implications of periodontitis.
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Affiliation(s)
- April Martínez
- Orofacial Sciences DepartmentSchool of DentistryUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Ryutaro Kuraji
- Orofacial Sciences DepartmentSchool of DentistryUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
- Department of Life Science DentistryThe Nippon Dental UniversityTokyoJapan
- Department of PeriodontologyThe Nippon Dental University School of Life Dentistry at TokyoTokyoJapan
| | - Yvonne L. Kapila
- Orofacial Sciences DepartmentSchool of DentistryUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
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Evaluating the potential efficacy and limitations of a phage for joint antibiotic and phage therapy of Staphylococcus aureus infections. Proc Natl Acad Sci U S A 2021; 118:2008007118. [PMID: 33649203 PMCID: PMC7958385 DOI: 10.1073/pnas.2008007118] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
This study explores the potential of a phage, PYOSa, for treating Staphylococcus aureus infections in combination with antibiotics. Population dynamic and genomic analysis identified a limitation and potential liability of using PYOSa for therapy. Due to the production of potentially pathogenic atypical small colony variants, PYOSa alone cannot eliminate S. aureus populations. However, we demonstrate that by following the administration of PYOSa with bactericidal antibiotics, this limitation and potential liability can be addressed. The methods used in this investigation to explore the efficacy of combinations of PYOSa and antibiotics for treating S. aureus infections can be employed to evaluate the clinical potential and facilitate the design of treatment protocols for any bacteria and phage that can be cultured in vitro. In response to increasing frequencies of antibiotic-resistant pathogens, there has been a resurrection of interest in the use of bacteriophage to treat bacterial infections: phage therapy. Here we explore the potential of a seemingly ideal phage, PYOSa, for combination phage and antibiotic treatment of Staphylococcus aureus infections. This K-like phage has a broad host range; all 83 tested clinical isolates of S.aureus tested were susceptible to PYOSa. Because of the mode of action of PYOSa, S. aureus is unlikely to generate classical receptor-site mutants resistant to PYOSa; none were observed in the 13 clinical isolates tested. PYOSa kills S. aureus at high rates. On the downside, the results of our experiments and tests of the joint action of PYOSa and antibiotics raise issues that must be addressed before PYOSa is employed clinically. Despite the maintenance of the phage, PYOSa does not clear populations of S. aureus. Due to the ascent of a phenotyically diverse array of small-colony variants following an initial demise, the bacterial populations return to densities similar to that of phage-free controls. Using a combination of mathematical modeling and in vitro experiments, we postulate and present evidence for a mechanism to account for the demise–resurrection dynamics of PYOSa and S. aureus. Critically for phage therapy, our experimental results suggest that treatment with PYOSa followed by bactericidal antibiotics can clear populations of S. aureus more effectively than the antibiotics alone.
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Binnie A, Fernandes E, Almeida-Lousada H, de Mello RA, Castelo-Branco P. CRISPR-based strategies in infectious disease diagnosis and therapy. Infection 2021; 49:377-385. [PMID: 33393066 PMCID: PMC7779109 DOI: 10.1007/s15010-020-01554-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/06/2020] [Indexed: 12/21/2022]
Abstract
PURPOSE CRISPR gene-editing technology has the potential to transform the diagnosis and treatment of infectious diseases, but most clinicians are unaware of its broad applicability. Derived from an ancient microbial defence system, these so-called "molecular scissors" enable precise gene editing with a low error rate. However, CRISPR systems can also be targeted against pathogenic DNA or RNA sequences. This potential is being combined with innovative delivery systems to develop new therapeutic approaches to infectious diseases. METHODS We searched Pubmed and Google Scholar for CRISPR-based strategies in the diagnosis and treatment of infectious diseases. Reference lists were reviewed and synthesized for narrative review. RESULTS CRISPR-based strategies represent a novel approach to many challenging infectious diseases. CRISPR technologies can be harnessed to create rapid, low-cost diagnostic systems, as well as to identify drug-resistance genes. Therapeutic strategies, such as CRISPR systems that cleave integrated viral genomes or that target resistant bacteria, are in development. CRISPR-based therapies for emerging viruses, such as SARS-CoV-2, have also been proposed. Finally, CRISPR systems can be used to reprogram human B cells to produce neutralizing antibodies. The risks of CRISPR-based therapies include off-target and on-target modifications. Strategies to control these risks are being developed and a phase 1 clinical trials of CRISPR-based therapies for cancer and monogenic diseases are already underway. CONCLUSIONS CRISPR systems have broad applicability in the field of infectious diseases and may offer solutions to many of the most challenging human infections.
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Affiliation(s)
- Alexandra Binnie
- Department of Critical Care, William Osler Health System, Etobicoke, ON, Canada.
- Faculty of Medicine and Biomedical Sciences, University of Algarve, Edificio 2, Ala Norte, Campus Gambelas, 8005-139, Faro, Portugal.
- Algarve Biomedical Center Research Institute, Faro, Portugal.
- Centre for Biomedical Research, University of Algarve, Faro, Portugal.
| | - Emanuel Fernandes
- Faculty of Medicine and Biomedical Sciences, University of Algarve, Edificio 2, Ala Norte, Campus Gambelas, 8005-139, Faro, Portugal
- Algarve Biomedical Center Research Institute, Faro, Portugal
| | - Helder Almeida-Lousada
- Faculty of Medicine and Biomedical Sciences, University of Algarve, Edificio 2, Ala Norte, Campus Gambelas, 8005-139, Faro, Portugal
- Algarve Biomedical Center Research Institute, Faro, Portugal
- Centre for Biomedical Research, University of Algarve, Faro, Portugal
| | - Ramon Andrade de Mello
- Faculty of Medicine and Biomedical Sciences, University of Algarve, Edificio 2, Ala Norte, Campus Gambelas, 8005-139, Faro, Portugal
- Algarve Biomedical Center Research Institute, Faro, Portugal
- ONCOLOGY PRECISION & HEALTH ECONOMICS RESEARCH GROUP (ONCOPRECHE), Departamento de Oncologia Clínica da Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brasil, & Pós-graduação em Medicina da Universidade Nove de Julho (UNINOVE), São Paulo, Brasil
| | - Pedro Castelo-Branco
- Faculty of Medicine and Biomedical Sciences, University of Algarve, Edificio 2, Ala Norte, Campus Gambelas, 8005-139, Faro, Portugal
- Algarve Biomedical Center Research Institute, Faro, Portugal
- Centre for Biomedical Research, University of Algarve, Faro, Portugal
- Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
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Salazar KC, Ma L, Green SI, Zulk JJ, Trautner BW, Ramig RF, Clark JR, Terwilliger AL, Maresso AW. Antiviral Resistance and Phage Counter Adaptation to Antibiotic-Resistant Extraintestinal Pathogenic Escherichia coli. mBio 2021; 12:e00211-21. [PMID: 33906920 PMCID: PMC8092219 DOI: 10.1128/mbio.00211-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/19/2021] [Indexed: 12/14/2022] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC), often multidrug resistant (MDR), is a leading cause of urinary tract and systemic infections. The crisis of emergent MDR pathogens has led some to propose bacteriophages as a therapeutic. However, bacterial resistance to phage is a concerning issue that threatens to undermine phage therapy. Here, we demonstrate that E. coli sequence type 131, a circulating pandemic strain of ExPEC, rapidly develops resistance to a well-studied and therapeutically active phage (ϕHP3). Whole-genome sequencing of the resisters revealed truncations in genes involved in lipopolysaccharide (LPS) biosynthesis, the outer membrane transporter ompA, or both, implicating them as phage receptors. We found ExPEC resistance to phage is associated with a loss of fitness in host microenvironments and attenuation in a murine model of systemic infection. Furthermore, we constructed a novel phage-bacterium bioreactor to generate an evolved phage isolate with restored infectivity to all LPS-truncated ExPEC resisters. This study suggests that although the resistance of pandemic E. coli to phage is frequent, it is associated with attenuation of virulence and susceptibility to new phage variants that arise by directed evolution.IMPORTANCE In response to the rising crisis of antimicrobial resistance, bacteriophage (phage) therapy has gained traction. In the United States, there have been over 10 cases of largely successful compassionate-use phage therapy to date. The resilience of pathogens allowing their broad antibiotic resistance means we must also consider resistance to therapeutic phages. This work fills gaps in knowledge regarding development of phage resisters in a model of infection and finds critical fitness losses in those resisters. We also found that the phage was able to rapidly readapt to these resisters.
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Affiliation(s)
- Keiko C Salazar
- Department of Integrative Molecular and Biomedical Science, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Li Ma
- School of Biological and Physical Sciences, Northwestern State University, Natchitoches, Louisiana, USA
| | - Sabrina I Green
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Jacob J Zulk
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Barbara W Trautner
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Robert F Ramig
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Justin R Clark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Austen L Terwilliger
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Anthony W Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
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Łobocka M, Dąbrowska K, Górski A. Engineered Bacteriophage Therapeutics: Rationale, Challenges and Future. BioDrugs 2021; 35:255-280. [PMID: 33881767 PMCID: PMC8084836 DOI: 10.1007/s40259-021-00480-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2021] [Indexed: 12/20/2022]
Abstract
The current problems with increasing bacterial resistance to antibacterial therapies, resulting in a growing frequency of incurable bacterial infections, necessitates the acceleration of studies on antibacterials of a new generation that could offer an alternative to antibiotics or support their action. Bacteriophages (phages) can kill antibiotic-sensitive as well as antibiotic-resistant bacteria, and thus are a major subject of such studies. Their efficacy in curing bacterial infections has been demonstrated in in vivo experiments and in the clinic. Unlike antibiotics, phages have a narrow range of specificity, which makes them safe for commensal microbiota. However, targeting even only the most clinically relevant strains of pathogenic bacteria requires large collections of well characterized phages, whose specificity would cover all such strains. The environment is a rich source of diverse phages, but due to their complex relationships with bacteria and safety concerns, only some naturally occurring phages can be considered for therapeutic applications. Still, their number and diversity make a detailed characterization of all potentially promising phages virtually impossible. Moreover, no single phage combines all the features required of an ideal therapeutic agent. Additionally, the rapid acquisition of phage resistance by bacteria may make phages already approved for therapy ineffective and turn the search for environmental phages of better efficacy and new specificity into an endless race. An alternative strategy for acquiring phages with desired properties in a short time with minimal cost regarding their acquisition, characterization, and approval for therapy could be based on targeted genome modifications of phage isolates with known properties. The first example demonstrating the potential of this strategy in curing bacterial diseases resistant to traditional therapy is the recent successful treatment of a progressing disseminated Mycobacterium abscessus infection in a teenage patient with the use of an engineered phage. In this review, we briefly present current methods of phage genetic engineering, highlighting their advantages and disadvantages, and provide examples of genetically engineered phages with a modified host range, improved safety or antibacterial activity, and proven therapeutic efficacy. We also summarize novel uses of engineered phages not only for killing pathogenic bacteria, but also for in situ modification of human microbiota to attenuate symptoms of certain bacterial diseases and metabolic, immune, or mental disorders.
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Affiliation(s)
- Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Krystyna Dąbrowska
- Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences, Wrocław, Poland
| | - Andrzej Górski
- Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences, Wrocław, Poland
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Sáez Moreno D, Visram Z, Mutti M, Restrepo-Córdoba M, Hartmann S, Kremers AI, Tišáková L, Schertler S, Wittmann J, Kalali B, Monecke S, Ehricht R, Resch G, Corsini L. ε 2-Phages Are Naturally Bred and Have a Vastly Improved Host Range in Staphylococcus aureus over Wild Type Phages. Pharmaceuticals (Basel) 2021; 14:325. [PMID: 33918287 PMCID: PMC8065394 DOI: 10.3390/ph14040325] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 12/24/2022] Open
Abstract
Due to the rapid spread of antibiotic resistance, and the difficulties of treating biofilm-associated infections, alternative treatments for S. aureus infections are urgently needed. We tested the lytic activity of several wild type phages against a panel of 110 S. aureus strains (MRSA/MSSA) composed to reflect the prevalence of S. aureus clonal complexes in human infections. The plaquing host ranges (PHR) of the wild type phages were in the range of 51% to 60%. We also measured what we called the kinetic host range (KHR), i.e., the percentage of strains for which growth in suspension was suppressed for 24 h. The KHR of the wild type phages ranged from 2% to 49%, substantially lower than the PHRs. To improve the KHR and other key pharmaceutical properties, we bred the phages by mixing and propagating cocktails on a subset of S. aureus strains. These bred phages, which we termed evolution-squared (ε2) phages, have broader KHRs up to 64% and increased virulence compared to the ancestors. The ε2-phages with the broadest KHR have genomes intercrossed from up to three different ancestors. We composed a cocktail of three ε2-phages with an overall KHR of 92% and PHR of 96% on 110 S. aureus strains and called it PM-399. PM-399 has a lower propensity to resistance formation than the standard of care antibiotics vancomycin, rifampicin, or their combination, and no resistance was observed in laboratory settings (detection limit: 1 cell in 1011). In summary, ε2-phages and, in particular PM-399, are promising candidates for an alternative treatment of S. aureus infections.
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Affiliation(s)
- David Sáez Moreno
- PhagoMed Biopharma GmbH, Leberstrasse 20, A-1110 Vienna, Austria; (D.S.M.); (Z.V.); (M.M.); (M.R.-C.); (S.H.); (A.I.K.); (L.T.)
| | - Zehra Visram
- PhagoMed Biopharma GmbH, Leberstrasse 20, A-1110 Vienna, Austria; (D.S.M.); (Z.V.); (M.M.); (M.R.-C.); (S.H.); (A.I.K.); (L.T.)
| | - Michele Mutti
- PhagoMed Biopharma GmbH, Leberstrasse 20, A-1110 Vienna, Austria; (D.S.M.); (Z.V.); (M.M.); (M.R.-C.); (S.H.); (A.I.K.); (L.T.)
| | - Marcela Restrepo-Córdoba
- PhagoMed Biopharma GmbH, Leberstrasse 20, A-1110 Vienna, Austria; (D.S.M.); (Z.V.); (M.M.); (M.R.-C.); (S.H.); (A.I.K.); (L.T.)
| | - Susana Hartmann
- PhagoMed Biopharma GmbH, Leberstrasse 20, A-1110 Vienna, Austria; (D.S.M.); (Z.V.); (M.M.); (M.R.-C.); (S.H.); (A.I.K.); (L.T.)
| | - Ana Isabel Kremers
- PhagoMed Biopharma GmbH, Leberstrasse 20, A-1110 Vienna, Austria; (D.S.M.); (Z.V.); (M.M.); (M.R.-C.); (S.H.); (A.I.K.); (L.T.)
| | - Lenka Tišáková
- PhagoMed Biopharma GmbH, Leberstrasse 20, A-1110 Vienna, Austria; (D.S.M.); (Z.V.); (M.M.); (M.R.-C.); (S.H.); (A.I.K.); (L.T.)
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (S.S.); (J.W.)
| | - Susanne Schertler
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (S.S.); (J.W.)
| | - Johannes Wittmann
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (S.S.); (J.W.)
| | - Benham Kalali
- Bactrace Biotec AG, Neherstr. 1, 81675 Munich, Germany;
| | - Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (S.M.); (R.E.)
- Institute of Medical Microbiologye and Hygiene, Faculty of Medicine Carl Gustav Carus, Technical University Dresden, Fiedlerstr. 42, D-01307 Dresden, Germany
- InfectoGnostics Research Campus Jena, 07743 Jena, Germany
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (S.M.); (R.E.)
- InfectoGnostics Research Campus Jena, 07743 Jena, Germany
- Institute of Physical Chemistry, Friedrich-Schiller University, 07743 Jena, Germany
| | - Grégory Resch
- Department of Fundamental Microbiology, University Lausanne, CH-1015 Lausanne, Switzerland;
| | - Lorenzo Corsini
- PhagoMed Biopharma GmbH, Leberstrasse 20, A-1110 Vienna, Austria; (D.S.M.); (Z.V.); (M.M.); (M.R.-C.); (S.H.); (A.I.K.); (L.T.)
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Lin RC, Sacher JC, Ceyssens PJ, Zheng J, Khalid A, Iredell JR. Phage Biobank: Present Challenges and Future Perspectives. Curr Opin Biotechnol 2021; 68:221-230. [PMID: 33581425 DOI: 10.1016/j.copbio.2020.12.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/14/2020] [Accepted: 12/23/2020] [Indexed: 11/24/2022]
Abstract
After a century of use in human infection, the preparation and administration of therapeutic bacteriophages (phages) still relies on ad hoc partnerships of researchers, biotech companies, clinicians and regulators. There is a clear need to improve the reproducibility, safety and speed of the provision of suitable phages. Here we discuss the specific characteristics and challenges of a sustainable phage biobank and, as we build a national consortium aimed at delivering phage therapeutics, suggest a roadmap toward national biobanking and phage therapy initiatives using the Australian context as a model.
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Affiliation(s)
- Ruby Cy Lin
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Sydney, Australia; Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, Australia; School of Medical Sciences, University of New South Wales, Sydney, Australia.
| | | | - Pieter-Jan Ceyssens
- Antibiotics and Resistance Unit, The National Reference Centres for Salmonella, Shigella, Listeria, Neisseria and Mycobacteria, Sciensano, Belgium
| | - Jan Zheng
- Phage Directory, Atlanta, Georgia, USA.
| | - Ali Khalid
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Sydney, Australia; Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Jonathan R Iredell
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Sydney, Australia; Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, Australia; Westmead Hospital, Western Sydney Local Health District, Sydney, Australia.
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Green SI, Gu Liu C, Yu X, Gibson S, Salmen W, Rajan A, Carter HE, Clark JR, Song X, Ramig RF, Trautner BW, Kaplan HB, Maresso AW. Targeting of Mammalian Glycans Enhances Phage Predation in the Gastrointestinal Tract. mBio 2021; 12:e03474-20. [PMID: 33563833 PMCID: PMC7885116 DOI: 10.1128/mbio.03474-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/21/2022] Open
Abstract
The human gastrointestinal mucosal surface consists of a eukaryotic epithelium, a prokaryotic microbiota, and a carbohydrate-rich interface that separates them. In the gastrointestinal tract, the interaction of bacteriophages (phages) and their prokaryotic hosts influences the health of the mammalian host, especially colonization with invasive pathobionts. Antibiotics may be used, but they also kill protective commensals. Here, we report a novel phage whose lytic cycle is enhanced in intestinal environments. The tail fiber gene, whose protein product binds human heparan sulfated proteoglycans and localizes the phage to the epithelial cell surface, positions it near its bacterial host, a type of locational targeting mechanism. This finding offers the prospect of developing mucosal targeting phage to selectively remove invasive pathobiont species from mucosal surfaces.IMPORTANCE Invasive pathobionts or microbes capable of causing disease can reside deep within the mucosal epithelium of our gastrointestinal tract. Targeted effective antibacterial therapies are needed to combat these disease-causing organisms, many of which may be multidrug resistant. Here, we isolated a lytic bacteriophage (phage) that can localize to the epithelial surface by binding heparan sulfated glycans, positioning it near its host, Escherichia coli This targeted therapy can be used to selectively remove invasive pathobionts from the gastrointestinal tract, preventing the development of disease.
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Affiliation(s)
- Sabrina I Green
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Carmen Gu Liu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Xue Yu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Shelley Gibson
- Department of Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Wilhem Salmen
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Hannah E Carter
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Justin R Clark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Xuezheng Song
- Department of Biochemistry, Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Robert F Ramig
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Barbara W Trautner
- Michael E. Debakey Veterans Affairs Medical Center, Houston, Texas, USA
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Heidi B Kaplan
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Anthony W Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
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Samir S. Bacteriophages as Therapeutic Agents: Alternatives to Antibiotics. Recent Pat Biotechnol 2021; 15:25-33. [PMID: 33475081 DOI: 10.2174/1872208315666210121094311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/07/2020] [Accepted: 12/21/2020] [Indexed: 11/22/2022]
Abstract
Bacteriophages are bacterio-specific viruses that constitute the main portion of the environment. Bacteriophages inject their genome into the targeted bacterial cells and some of them can disrupt the metabolism of bacteria and cause bacterial cell disintegration. The application of bacteriophages to kill bacteria is known as bacteriophage therapy. Since bacteriophages target bacteria and are strain-specific, every bacteriophage/bacterial host pair is unique. They are believed to cause no harm to humans. An additional advantage of the strain-specific nature of bacteriophages is that they do not disrupt the beneficial natural flora in the body. Bacteriophage therapy in the West is not a recognized medicine at this time, and no products are registered. Some clinicians are turning to bacteriophage therapy for the treatment of antibiotic-resistant infections. Lack of adverse effects makes bacteriophage therapy ideal for use. Funding research, media attention, and the increased publication of articles helped in a widespread understanding of its therapeutic potential. The first prerequisite for the use of bacteriophage therapy is simply the availability of bacteriophages for treatment, which is often complicated at this stage of bacteriophage production. This includes providing access to all biologically active bacteriophages against the bacterial isolate of the patient and meeting regulatory criteria of purity, traceability, and characterization. A monophage preparation, which is a single bacteriophage, or a phage cocktail, which consists of a number of combined bacteriophages against one or more bacterial species may be used. Accordingly, the antibiotic resistance crisis brought back bacteriophage therapy as a potential complementary or alternative treatment. Bacteriophages are promising cheap antibacterials.
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Affiliation(s)
- Safia Samir
- Department of Biochemistry and Molecular Biology, Theodor Bilharz Research Institute, Giza, Egypt
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Royer S, Morais AP, da Fonseca Batistão DW. Phage therapy as strategy to face post-antibiotic era: a guide to beginners and experts. Arch Microbiol 2021; 203:1271-1279. [PMID: 33474609 DOI: 10.1007/s00203-020-02167-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 11/20/2020] [Accepted: 12/27/2020] [Indexed: 01/05/2023]
Abstract
Interest in the therapeutic use of bacteriophages (phages) has emerged in recent years, driven mainly by the antimicrobial resistance crisis. This review aimed to summarize some important studies addressing the use of phages as a therapeutic alternative for multiresistant bacterial infections. To this end, a literature search was conducted to address the efficacy and versatility of phage therapy, the advantages and disadvantages of its use, and potential limitations for the application of phage therapy that need to be overcome, especially in Western countries. Thus, this review highlights that phage therapy may be a promising route in the treatment of infections caused by multidrug-resistant pathogens and that a combined approach has the potential to prolong the life of the current available antimicrobials. In addition, standardized clinical trials using monoclonal or polyclonal phages, alone or in combination with antimicrobials, are crucial to determine the real potential of these treatments in clinical practice.
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Affiliation(s)
- Sabrina Royer
- Laboratory of Molecular Microbiology, Biomedical Science Institute, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil. .,Laboratory of Molecular Microbiology, Biomedical Science Institute, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil.
| | - Aléxia Pinheiro Morais
- Laboratory of Molecular Microbiology, Biomedical Science Institute, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil.,Laboratory of Molecular Microbiology, Biomedical Science Institute, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
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42
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The Safety and Efficacy of Phage Therapy for Bone and Joint Infections: A Systematic Review. Antibiotics (Basel) 2020; 9:antibiotics9110795. [PMID: 33182795 PMCID: PMC7697170 DOI: 10.3390/antibiotics9110795] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/30/2020] [Accepted: 11/05/2020] [Indexed: 12/29/2022] Open
Abstract
Bacterial resistance to antibiotics has catalysed interest in alternative antimicrobial strategies. Bacteriophages (phages) are viruses of bacteria with a long history of successful therapeutic use. Phage therapy is a promising antibacterial strategy for infections with a biofilm component, including recalcitrant bone and joint infections, which have significant social, financial and human impacts. Here, we report a systematic review of the safety and efficacy of phage therapy for the treatment of bone and joint infections. Three electronic databases were systematically searched for articles that reported primary data about human phage therapy for bone and joint infections. Two authors independently assessed study eligibility and performed data extraction. Seventeen reports were eligible for inclusion in this review, representing the treatment of 277 patients. A cautionary, crude, efficacy estimate revealed that 93.1% (n = 258/277) achieved clinical resolution, 3.3% (n = 9/277) had improvement and 3.6% (n = 10/277) showed no improvement. Seven of the nine reports that directly commented on the safety of phage therapy did not express safety concerns. The adverse effects reported in the remaining two were not severe and were linked to the presence of contaminating endotoxins and pre-existing liver pathology in a patient treated with high-titre intravenous phage therapy. Three other reports, from 1940-1987, offered general comments on the safety of phage therapy and documented adverse effects consistent with endotoxin co-administration concomitant with the use of raw phage lysates. Together, the reports identified by this review suggest that appropriately purified phages represent a safe and highly efficacious treatment option for complex and intractable bone and joint infections.
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Li C, Yuan X, Li N, Wang J, Yu S, Zeng H, Zhang J, Wu Q, Ding Y. Isolation and Characterization of Bacillus cereus Phage vB_BceP-DLc1 Reveals the Largest Member of the Φ29-Like Phages. Microorganisms 2020; 8:E1750. [PMID: 33171789 PMCID: PMC7695010 DOI: 10.3390/microorganisms8111750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 10/31/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
Bacillus phage φ29 and its relatives have been considered as one of the most important model organisms for DNA replication, transcription, morphogenesis, DNA packaging studies, and nanotechnology applications. Here, we isolated and characterized a new member of the φ29-like phage, named Bacillus cereus phage vB_BceP-DLc1. This phage, with a unique inserted gene cluster, has the largest genome among known φ29-like phages. DLc1 can use the surface carbohydrate structures of the host cell as receptors and only infects the most related B. cereus strains, showing high host-specificity. The adsorption rate constant and life cycle of DLc1 under experimental conditions were also determined. Not only stable under temperatures below 55 °C and pH range from 5 to 11, the new phage also showed tolerance to high concentrations of NaCl, 75% ethanol, chloroform, and mechanical vortex, which is preferable for practical use in the food and pharmaceutical industries.
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Affiliation(s)
- Chun Li
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, College of Science & Engineering, Jinan University, Guangzhou 510632, China; (C.L.); (X.Y.); (N.L.)
| | - Xiaoming Yuan
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, College of Science & Engineering, Jinan University, Guangzhou 510632, China; (C.L.); (X.Y.); (N.L.)
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (S.Y.); (H.Z.); (J.Z.); (Q.W.)
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Na Li
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, College of Science & Engineering, Jinan University, Guangzhou 510632, China; (C.L.); (X.Y.); (N.L.)
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (S.Y.); (H.Z.); (J.Z.); (Q.W.)
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou 510642, China;
| | - Shubo Yu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (S.Y.); (H.Z.); (J.Z.); (Q.W.)
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Haiyan Zeng
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (S.Y.); (H.Z.); (J.Z.); (Q.W.)
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Jumei Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (S.Y.); (H.Z.); (J.Z.); (Q.W.)
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Qingping Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (S.Y.); (H.Z.); (J.Z.); (Q.W.)
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Yu Ding
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, College of Science & Engineering, Jinan University, Guangzhou 510632, China; (C.L.); (X.Y.); (N.L.)
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (S.Y.); (H.Z.); (J.Z.); (Q.W.)
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
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Steele A, Stacey HJ, de Soir S, Jones JD. The Safety and Efficacy of Phage Therapy for Superficial Bacterial Infections: A Systematic Review. Antibiotics (Basel) 2020; 9:E754. [PMID: 33138253 PMCID: PMC7692203 DOI: 10.3390/antibiotics9110754] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/21/2022] Open
Abstract
Superficial bacterial infections, such as dermatological, burn wound and chronic wound/ulcer infections, place great human and financial burdens on health systems globally and are often complicated by antibiotic resistance. Bacteriophage (phage) therapy is a promising alternative antimicrobial strategy with a 100-year history of successful application. Here, we report a systematic review of the safety and efficacy of phage therapy for the treatment of superficial bacterial infections. Three electronic databases were systematically searched for articles that reported primary data about human phage therapy for dermatological, burn wound or chronic wound/ulcer infections secondary to commonly causative bacteria. Two authors independently assessed study eligibility and performed data extraction. Of the 27 eligible reports, eight contained data on burn wound infection (n = 156), 12 on chronic wound/ulcer infection (n = 327) and 10 on dermatological infections (n = 1096). Cautionary pooled efficacy estimates from the studies that clearly reported efficacy data showed clinical resolution or improvement in 77.5% (n = 111) of burn wound infections, 86.1% (n = 310) of chronic wound/ulcer infections and 94.14% (n = 734) of dermatological infections. Over half of the reports that commented on safety (n = 8/15), all published in or after 2002, did not express safety concerns. Seven early reports (1929-1987), described adverse effects consistent with the administration of raw phage lysate and co-administered bacterial debris or broth. This review strongly suggests that the use of purified phage to treat superficial bacterial infections can be highly effective and, by various routes of administration, is safe and without adverse effects.
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Affiliation(s)
- Angharad Steele
- Infection Medicine, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK;
| | - Helen J. Stacey
- Edinburgh Medical School, University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK;
| | - Steven de Soir
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Rue Bruyn, 1120 Brussels, Belgium;
- Cellular & Molecular Pharmacology, Louvain Drug Research Institute, Université Catholique de Louvain (UCLouvain), avenue E. Mounier 73, 1200 Brussels, Belgium
| | - Joshua D. Jones
- Infection Medicine, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK;
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Luong T, Salabarria AC, Roach DR. Phage Therapy in the Resistance Era: Where Do We Stand and Where Are We Going? Clin Ther 2020; 42:1659-1680. [DOI: 10.1016/j.clinthera.2020.07.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022]
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Phage-Antibiotic Synergy Is Driven by a Unique Combination of Antibacterial Mechanism of Action and Stoichiometry. mBio 2020; 11:mBio.01462-20. [PMID: 32753497 PMCID: PMC7407087 DOI: 10.1128/mbio.01462-20] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The continued rise in antibiotic resistance is precipitating a medical crisis. Bacteriophage (phage) has been hailed as one possible therapeutic option to augment the efficacy of antibiotics. However, only a few studies have addressed the synergistic relationship between phage and antibiotics. Here, we report a comprehensive analysis of phage-antibiotic interaction that evaluates synergism, additivism, and antagonism for all classes of antibiotics across clinically achievable stoichiometries. We combined an optically based real-time microtiter plate readout with a matrix-like heat map of treatment potencies to measure phage and antibiotic synergy (PAS), a process we term synography. Phage-antibiotic synography was performed against a pandemic drug-resistant clonal group of extraintestinal pathogenic Escherichia coli (ExPEC) with antibiotic levels blanketing the MIC across seven orders of viral titers. Our results suggest that, under certain conditions, phages provide an adjuvating effect by lowering the MIC for drug-resistant strains. Furthermore, synergistic and antagonistic interactions are highly dependent on the mechanism of bacterial inhibition by the class of antibiotic paired to the phage, and when synergism is observed, it suppresses the emergence of resistant cells. Host conditions that simulate the infection environment, including serum and urine, suppress PAS in a bacterial growth-dependent manner. Lastly, two different related phages that differed in their burst sizes produced drastically different synograms. Collectively, these data suggest lytic phages can resuscitate an ineffective antibiotic for previously resistant bacteria while also synergizing with antibiotics in a class-dependent manner, processes that may be dampened by lower bacterial growth rates found in host environments.IMPORTANCE Bacteriophage (phage) therapy is a promising approach to combat the rise of multidrug-resistant bacteria. Currently, the preferred clinical modality is to pair phage with an antibiotic, a practice thought to improve efficacy. However, antagonism between phage and antibiotics has been reported, the choice of phage and antibiotic is not often empirically determined, and the effect of the host factors on the effectiveness is unknown. Here, we interrogate phage-antibiotic interactions across antibiotics with different mechanisms of action. Our results suggest that phage can lower the working MIC for bacterial strains already resistant to the antibiotic, is dependent on the antibiotic class and stoichiometry of the pairing, and is dramatically influenced by the host microenvironment.
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Terwilliger AL, Gu Liu C, Green SI, Clark JR, Salazar KC, Hernandez Santos H, Heckmann ER, Trautner BW, Ramig RF, Maresso AW. Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research: Personalized Infectious Disease Medicine for the Most Vulnerable At-Risk Patients. PHAGE (NEW ROCHELLE, N.Y.) 2020; 1:66-74. [PMID: 32626851 PMCID: PMC7327541 DOI: 10.1089/phage.2020.0007] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mutation is the most powerful driver of change for life on Earth. Pathogenic bacteria utilize mutation as a means to survive strong live-die selective pressures generated by chemical antibiotics. As such, the traditional drug-making pipeline, characterized by significant financial and time investment, is insufficient to keep pace with the rapid evolution of bacterial resistance to structurally fixed and chemically unmalleable antibacterial compounds. In contrast, the genetic diversity and adaptive mutability of the bacteriophage can be leveraged to not only overcome resistance but also used for the development of enhanced traits that increase lytic potential and therapeutic efficacy in relevant host microenvironments. This is the fundamental premise behind Baylor College of Medicine's Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR) initiative. In this perspective, we outline the concept, structure, and process behind TAILΦR's attempt to generate a personalized therapeutic phage that addresses the most clinically challenging of bacterial infections.
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Affiliation(s)
- Austen L. Terwilliger
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Carmen Gu Liu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Sabrina I. Green
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Justin R. Clark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Keiko C. Salazar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Haroldo Hernandez Santos
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Emmaline R. Heckmann
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Barbara W. Trautner
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Center for Innovations in Quality, Effectiveness and Safety (IQuESt), Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
- Section of Health Services Research, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Robert F. Ramig
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Anthony W. Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
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