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Mu A, McDonald D, Jarmusch AK, Martino C, Brennan C, Bryant M, Humphrey GC, Toronczak J, Schwartz T, Nguyen D, Ackermann G, D'Onofrio A, Strathdee SA, Schooley RT, Dorrestein PC, Knight R, Aslam S. Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection. Microbiome 2021; 9:92. [PMID: 33853672 PMCID: PMC8048313 DOI: 10.1186/s40168-021-01026-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 02/05/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND Infectious bacterial diseases exhibiting increasing resistance to antibiotics are a serious global health issue. Bacteriophage therapy is an anti-microbial alternative to treat patients with serious bacterial infections. However, the impacts to the host microbiome in response to clinical use of phage therapy are not well understood. RESULTS Our paper demonstrates a largely unchanged microbiota profile during 4 weeks of phage therapy when added to systemic antibiotics in a single patient with Staphylococcus aureus device infection. Metabolomic analyses suggest potential indirect cascading ecological impacts to the host (skin) microbiome. We did not detect genomes of the three phages used to treat the patient in metagenomic samples taken from saliva, stool, and skin; however, phages were detected using endpoint-PCR in patient serum. CONCLUSION Results from our proof-of-principal study supports the use of bacteriophages as a microbiome-sparing approach to treat bacterial infections. Video abstract.
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Affiliation(s)
- Andre Mu
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Alan K Jarmusch
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
| | - Cameron Martino
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of San Diego, La Jolla, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Caitriona Brennan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Mackenzie Bryant
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Gregory C Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Julia Toronczak
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tara Schwartz
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Dominic Nguyen
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Anthony D'Onofrio
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, USA
| | - Steffanie A Strathdee
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, USA
| | - Robert T Schooley
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, USA
| | - Pieter C Dorrestein
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Sciences and Engineering, University of California San Diego, La Jolla, CA, USA.
| | - Saima Aslam
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, USA
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