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Chun SW, Somers ME, Burgener EB. Highly effective cystic fibrosis transmembrane conductance (regulator) modulator therapy: shifting the curve for most while leaving some further behind. Curr Opin Pediatr 2024; 36:290-295. [PMID: 38411576 DOI: 10.1097/mop.0000000000001338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
PURPOSE OF REVIEW Traditional cystic fibrosis (CF) care had been focused on early intervention and symptom mitigation. With the advent of highly effective cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy (HEMT), in particular, the approval of elexacaftor/tezacaftor/ivacaftor in 2019, there has been a dramatic improvement in outcomes in CF. The purpose of this article is to review the benefits, limitations, and impact of HEMT as well as discuss the new implications, challenges, and hope that modulators bring to people with CF (pwCF). RECENT FINDINGS HEMT has demonstrated sustained improvement in lung function, nutrition, quality of life, and survival for over 90% of pwCF. As HEMT has delivered such promise, there is a small but significant portion of pwCF who do not benefit from HEMT due to ineligible mutations, intolerance, or lack of accessibility to modulators. SUMMARY HEMT has significantly improved outcomes, but continued research is needed to understand the new challenges and implications the era of HEMT will bring, as well as how to provide equitable care to those who are unable to benefit from HEMT.
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Affiliation(s)
- Stanford W Chun
- Division of Pediatric Pulmonology & Sleep Medicine, Department of Pediatrics, Children's Hospital of Los Angeles, Keck School of Medicine at University of Southern California, Los Angeles
| | - Maya E Somers
- Division of Infectious Disease & Geographic Medicine, Department of Medicine, Stanford University, Stanford, California, USA
| | - Elizabeth B Burgener
- Division of Pediatric Pulmonology & Sleep Medicine, Department of Pediatrics, Children's Hospital of Los Angeles, Keck School of Medicine at University of Southern California, Los Angeles
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Schmidt AK, Schwartzkopf CM, Pourtois JD, Burgener EB, Faith DR, Joyce A, Lamma T, Kumar G, Bollyky PL, Secor PR. Targeted deletion of Pf prophages from diverse Pseudomonas aeruginosa isolates has differential impacts on quorum sensing and virulence traits. J Bacteriol 2024:e0040223. [PMID: 38687034 DOI: 10.1128/jb.00402-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 04/02/2024] [Indexed: 05/02/2024] Open
Abstract
Pseudomonas aeruginosa is an opportunistic bacterial pathogen that commonly causes medical hardware, wound, and respiratory infections. Temperate filamentous Pf phages that infect P. aeruginosa impact numerous virulence phenotypes. Most work on Pf phages has focused on Pf4 and its host P. aeruginosa PAO1. Expanding from Pf4 and PAO1, this study explores diverse Pf phages infecting P. aeruginosa clinical isolates. We describe a simple technique targeting the Pf lysogeny maintenance gene, pflM (PA0718), that enables the effective elimination of Pf prophages from diverse P. aeruginosa hosts. The pflM gene shows diversity among different Pf phage isolates; however, all examined pflM alleles encode the DUF5447 domain. We demonstrate that pflM deletion results in prophage excision but not replication, leading to total prophage loss, indicating a role for lysis/lysogeny decisions for the DUF5447 domain. This study also assesses the effects different Pf phages have on host quorum sensing, biofilm formation, pigment production, and virulence against the bacterivorous nematode Caenorhabditis elegans. We find that Pf phages have strain-specific impacts on quorum sensing and biofilm formation, but nearly all suppress pigment production and increase C. elegans avoidance behavior. Collectively, this research not only introduces a valuable tool for Pf prophage elimination from diverse P. aeruginosa isolates but also advances our understanding of the complex relationship between P. aeruginosa and filamentous Pf phages.IMPORTANCEPseudomonas aeruginosa is an opportunistic bacterial pathogen that is frequently infected by filamentous Pf phages (viruses) that integrate into its chromosome, affecting behavior. Although prior work has focused on Pf4 and PAO1, this study investigates diverse Pf in clinical isolates. A simple method targeting the deletion of the Pf lysogeny maintenance gene pflM (PA0718) effectively eliminates Pf prophages from clinical isolates. The research evaluates the impact Pf prophages have on bacterial quorum sensing, biofilm formation, and virulence phenotypes. This work introduces a valuable tool to eliminate Pf prophages from clinical isolates and advances our understanding of P. aeruginosa and filamentous Pf phage interactions.
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Affiliation(s)
- Amelia K Schmidt
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | | | - Julie D Pourtois
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Elizabeth B Burgener
- Division of Pediatric Pulmonology and Sleep Medicine, Children's Hospital of Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- Center for Excellence in Pulmonary Biology, Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Dominick R Faith
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Alex Joyce
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Tyrza Lamma
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Geetha Kumar
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | - Paul L Bollyky
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Patrick R Secor
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
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Popescu MC, Haddock NL, Burgener EB, Rojas-Hernandez LS, Kaber G, Hargil A, Bollyky PL, Milla CE. The Inovirus Pf4 Triggers Antiviral Responses and Disrupts the Proliferation of Airway Basal Epithelial Cells. Viruses 2024; 16:165. [PMID: 38275975 PMCID: PMC10818373 DOI: 10.3390/v16010165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND The inovirus Pf4 is a lysogenic bacteriophage of Pseudomonas aeruginosa (Pa). People with Cystic Fibrosis (pwCF) experience chronic airway infection with Pa and a significant proportion have high numbers of Pf4 in their airway secretions. Given the known severe damage in the airways of Pa-infected pwCF, we hypothesized a high Pf4 burden can affect airway healing and inflammatory responses. In the airway, basal epithelial cells (BCs) are a multipotent stem cell population critical to epithelium homeostasis and repair. We sought to investigate the transcriptional responses of BCs under conditions that emulate infection with Pa and exposure to high Pf4 burden. METHODS Primary BCs isolated from pwCF and wild-type (WT) donors were cultured in vitro and exposed to Pf4 or bacterial Lipopolysaccharide (LPS) followed by transcriptomic and functional assays. RESULTS We found that BCs internalized Pf4 and this elicits a strong antiviral response as well as neutrophil chemokine production. Further, we found that BCs that take up Pf4 demonstrate defective migration and proliferation. CONCLUSIONS Our findings are highly suggestive of Pf4 playing a role in the pathogenicity of Pa in the airways. These findings provide additional evidence for the ability of inoviruses to interact with mammalian cells and disrupt cell function.
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Affiliation(s)
- Medeea C. Popescu
- Department of Infectious Diseases, Stanford University, Stanford, CA 94305, USA (P.L.B.)
- Immunology Program, Stanford University, Stanford, CA 94305, USA
| | - Naomi L. Haddock
- Department of Infectious Diseases, Stanford University, Stanford, CA 94305, USA (P.L.B.)
- Immunology Program, Stanford University, Stanford, CA 94305, USA
| | - Elizabeth B. Burgener
- Center for Excellence in Pulmonary Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laura S. Rojas-Hernandez
- Center for Excellence in Pulmonary Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gernot Kaber
- Department of Infectious Diseases, Stanford University, Stanford, CA 94305, USA (P.L.B.)
| | - Aviv Hargil
- Department of Infectious Diseases, Stanford University, Stanford, CA 94305, USA (P.L.B.)
| | - Paul L. Bollyky
- Department of Infectious Diseases, Stanford University, Stanford, CA 94305, USA (P.L.B.)
| | - Carlos E. Milla
- Center for Excellence in Pulmonary Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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4
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Burgener EB, Cornfield DN. Delivering a New Future for People With Cystic Fibrosis. Pediatrics 2023; 152:e2023062985. [PMID: 37671451 PMCID: PMC10522926 DOI: 10.1542/peds.2023-062985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/14/2023] [Indexed: 09/07/2023] Open
Abstract
Treatment, prognosis, and quality of life for people with cystic fibrosis (CF) have improved steadily since the initial description of the disease, but most dramatically in the past decade. In 2021, the median predicted survival increased to 53 years, compared with 17 years in 1970. The recent improvement in outcomes is attributable to the advent of cystic fibrosis transmembrane regulator (CFTR) modulators, small molecules that enhance the function of defective CFTR protein. The first CFTR modulator, ivacaftor, received Food and Drug Administration approval in 2011 to treat a single CFTR variant, comprising only 4% of those affected by CF. With the demonstration of efficacy, drug approval has been expanded to other variants. Multiple CFTR modulators used in combination with ivacaftor augment efficacy and increase the number of CFTR variants amenable to therapy. Approval of elexecaftor/tezecaftor/ivacaftor in 2019 increased the number of individuals who could benefit from highly effective modulator therapy (HEMT) to ∼90% of the CF population in the United States. HEMT has been dramatically effective, with overall improvements in lung function, quality of life, nutritional status, and, in women, increased fertility. HEMT may delay the onset of other CF-related comorbidities. Although off-target effects, including hepatotoxicity, drug-drug interactions, and putative mental health issues can complicate use, modulator therapy has been generally well tolerated. Ten percent of people with CF have variants that are not amenable to modulator treatment. HEMT, despite its great cost and limited global access, has brought legitimate hope and changed the lives of a significant majority of individuals and families affected by CF in North America.
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Affiliation(s)
- Elizabeth B. Burgener
- Center for Excellence in Pulmonary Biology, Divisions of Pulmonary, Asthma, and Sleep Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - David N. Cornfield
- Center for Excellence in Pulmonary Biology, Divisions of Pulmonary, Asthma, and Sleep Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
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Chen Q, Dharmaraj T, Cai PC, Burgener EB, Haddock NL, Spakowitz AJ, Bollyky PL. Bacteriophage and Bacterial Susceptibility, Resistance, and Tolerance to Antibiotics. Pharmaceutics 2022; 14:1425. [PMID: 35890320 PMCID: PMC9318951 DOI: 10.3390/pharmaceutics14071425] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022] Open
Abstract
Bacteriophages, viruses that infect and replicate within bacteria, impact bacterial responses to antibiotics in complex ways. Recent studies using lytic bacteriophages to treat bacterial infections (phage therapy) demonstrate that phages can promote susceptibility to chemical antibiotics and that phage/antibiotic synergy is possible. However, both lytic and lysogenic bacteriophages can contribute to antimicrobial resistance. In particular, some phages mediate the horizontal transfer of antibiotic resistance genes between bacteria via transduction and other mechanisms. In addition, chronic infection filamentous phages can promote antimicrobial tolerance, the ability of bacteria to persist in the face of antibiotics. In particular, filamentous phages serve as structural elements in bacterial biofilms and prevent the penetration of antibiotics. Over time, these contributions to antibiotic tolerance favor the selection of resistance clones. Here, we review recent insights into bacteriophage contributions to antibiotic susceptibility, resistance, and tolerance. We discuss the mechanisms involved in these effects and address their impact on bacterial fitness.
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Affiliation(s)
- Qingquan Chen
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center, 279 Campus Drive, Stanford, CA 94305, USA; (T.D.); (N.L.H.); (P.L.B.)
| | - Tejas Dharmaraj
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center, 279 Campus Drive, Stanford, CA 94305, USA; (T.D.); (N.L.H.); (P.L.B.)
| | - Pamela C. Cai
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA;
| | - Elizabeth B. Burgener
- Center for Excellence in Pulmonary Biology, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; (E.B.B.); (A.J.S.)
| | - Naomi L. Haddock
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center, 279 Campus Drive, Stanford, CA 94305, USA; (T.D.); (N.L.H.); (P.L.B.)
| | - Andy J. Spakowitz
- Center for Excellence in Pulmonary Biology, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; (E.B.B.); (A.J.S.)
| | - Paul L. Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center, 279 Campus Drive, Stanford, CA 94305, USA; (T.D.); (N.L.H.); (P.L.B.)
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6
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Kratochvil MJ, Kaber G, Demirdjian S, Cai PC, Burgener EB, Nagy N, Barlow GL, Popescu M, Nicolls MR, Ozawa MG, Regula DP, Pacheco-Navarro AE, Yang S, de Jesus Perez VA, Karmouty-Quintana H, Peters AM, Zhao B, Buja ML, Johnson PY, Vernon RB, Wight TN, Milla CE, Rogers AJ, Spakowitz AJ, Heilshorn SC, Bollyky PL. Biochemical, biophysical, and immunological characterization of respiratory secretions in severe SARS-CoV-2 infections. JCI Insight 2022; 7:152629. [PMID: 35730564 PMCID: PMC9309048 DOI: 10.1172/jci.insight.152629] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 05/10/2022] [Indexed: 01/27/2023] Open
Abstract
Thick, viscous respiratory secretions are a major pathogenic feature of COVID-19, but the composition and physical properties of these secretions are poorly understood. We characterized the composition and rheological properties (i.e., resistance to flow) of respiratory secretions collected from intubated COVID-19 patients. We found the percentages of solids and protein content were greatly elevated in COVID-19 compared with heathy control samples and closely resembled levels seen in cystic fibrosis, a genetic disease known for thick, tenacious respiratory secretions. DNA and hyaluronan (HA) were major components of respiratory secretions in COVID-19 and were likewise abundant in cadaveric lung tissues from these patients. COVID-19 secretions exhibited heterogeneous rheological behaviors, with thicker samples showing increased sensitivity to DNase and hyaluronidase treatment. In histologic sections from these same patients, we observed increased accumulation of HA and the hyaladherin versican but reduced tumor necrosis factor-stimulated gene-6 staining, consistent with the inflammatory nature of these secretions. Finally, we observed diminished type I interferon and enhanced inflammatory cytokines in these secretions. Overall, our studies indicated that increases in HA and DNA in COVID-19 respiratory secretion samples correlated with enhanced inflammatory burden and suggested that DNA and HA may be viable therapeutic targets in COVID-19 infection.
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Affiliation(s)
- Michael J. Kratochvil
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Department of Materials Science and Engineering and
| | - Gernot Kaber
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Sally Demirdjian
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Pamela C. Cai
- Department of Chemical Engineering, Stanford University, Stanford, California, USA
| | | | - Nadine Nagy
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Graham L. Barlow
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Medeea Popescu
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Mark R. Nicolls
- Department of Pulmonology, Allergy and Critical Care Medicine
| | | | | | | | - Samuel Yang
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, California, USA
| | | | - Harry Karmouty-Quintana
- Department of Biochemistry and Molecular Biology;,Divisions of Critical Care Medicine and Pulmonary and Sleep Medicine, Department of Internal Medicine
| | | | - Bihong Zhao
- Department of Pathology and Laboratory Medicine; and,Department of Internal Medicine, University of Texas Health Science Center — McGovern Medical School, Houston, Texas, USA
| | - Maximilian L. Buja
- Department of Pathology and Laboratory Medicine; and,Department of Internal Medicine, University of Texas Health Science Center — McGovern Medical School, Houston, Texas, USA
| | - Pamela Y. Johnson
- Matrix Biology Program, Benaroya Research Institute, Seattle, Washington, USA
| | - Robert B. Vernon
- Matrix Biology Program, Benaroya Research Institute, Seattle, Washington, USA
| | - Thomas N. Wight
- Matrix Biology Program, Benaroya Research Institute, Seattle, Washington, USA
| | | | - Carlos E. Milla
- Center for Excellence in Pulmonary Biology, Department of Pediatrics
| | | | - Andrew J. Spakowitz
- Department of Chemical Engineering, Stanford University, Stanford, California, USA
| | | | - Paul L. Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
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7
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Bach MS, de Vries CR, Khosravi A, Sweere JM, Popescu MC, Chen Q, Demirdjian S, Hargil A, Van Belleghem JD, Kaber G, Hajfathalian M, Burgener EB, Liu D, Tran QL, Dharmaraj T, Birukova M, Sunkari V, Balaji S, Ghosh N, Mathew-Steiner SS, El Masry MS, Keswani SG, Banaei N, Nedelec L, Sen CK, Chandra V, Secor PR, Suh GA, Bollyky PL. Filamentous bacteriophage delays healing of Pseudomonas-infected wounds. Cell Rep Med 2022; 3:100656. [PMID: 35732145 PMCID: PMC9244996 DOI: 10.1016/j.xcrm.2022.100656] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/29/2022] [Accepted: 05/17/2022] [Indexed: 01/09/2023]
Abstract
Chronic wounds infected by Pseudomonas aeruginosa (Pa) are characterized by disease progression and increased mortality. We reveal Pf, a bacteriophage produced by Pa that delays healing of chronically infected wounds in human subjects and animal models of disease. Interestingly, impairment of wound closure by Pf is independent of its effects on Pa pathogenesis. Rather, Pf impedes keratinocyte migration, which is essential for wound healing, through direct inhibition of CXCL1 signaling. In support of these findings, a prospective cohort study of 36 human patients with chronic Pa wound infections reveals that wounds infected with Pf-positive strains of Pa are more likely to progress in size compared with wounds infected with Pf-negative strains. Together, these data implicate Pf phage in the delayed wound healing associated with Pa infection through direct manipulation of mammalian cells. These findings suggest Pf may have potential as a biomarker and therapeutic target in chronic wounds.
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Affiliation(s)
- Michelle S Bach
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Immunology, Stanford University, Stanford, CA 94305, USA
| | - Christiaan R de Vries
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Arya Khosravi
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Johanna M Sweere
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Immunology, Stanford University, Stanford, CA 94305, USA
| | - Medeea C Popescu
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Immunology, Stanford University, Stanford, CA 94305, USA
| | - Qingquan Chen
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Sally Demirdjian
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Aviv Hargil
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jonas D Van Belleghem
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Gernot Kaber
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Maryam Hajfathalian
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth B Burgener
- Center for Excellence in Pulmonary Biology, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Dan Liu
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Quynh-Lam Tran
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Tejas Dharmaraj
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Immunology, Stanford University, Stanford, CA 94305, USA
| | - Maria Birukova
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Immunology, Stanford University, Stanford, CA 94305, USA
| | - Vivekananda Sunkari
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Immunology, Stanford University, Stanford, CA 94305, USA
| | - Swathi Balaji
- Division of Pediatric Surgery, Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nandini Ghosh
- Department of Surgery, Indiana University, Indianapolis, IN 46202, USA
| | | | | | - Sundeep G Keswani
- Division of Pediatric Surgery, Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Niaz Banaei
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Division of Pathology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Laurence Nedelec
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Chandan K Sen
- Department of Surgery, Indiana University, Indianapolis, IN 46202, USA
| | - Venita Chandra
- Department of Surgery, Division of Vascular Surgery, Stanford University, Stanford, CA 94305, USA
| | - Patrick R Secor
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Gina A Suh
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN 55902, USA
| | - Paul L Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA.
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8
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Rosser JI, Nagy N, Goel R, Kaber G, Demirdjian S, Saxena J, Bollyky JB, Frymoyer AR, Pacheco-Navarro AE, Burgener EB, Rajadas J, Wang Z, Arbach O, Dunn CE, Kalinowski A, Milla CE, Bollyky PL. Oral hymecromone decreases hyaluronan in human study participants. J Clin Invest 2022; 132:e157983. [PMID: 35499083 PMCID: PMC9057598 DOI: 10.1172/jci157983] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/08/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUNDHyaluronan (HA), an extracellular matrix glycosaminoglycan, has been implicated in the pathophysiology of COVID-19 infection, pulmonary hypertension, pulmonary fibrosis, and other diseases, but is not targeted by any approved drugs. We asked whether hymecromone (4-methylumbelliferone [4-MU]), an oral drug approved in Europe for biliary spasm treatment that also inhibits HA in vitro and in animal models, could be repurposed as an inhibitor of HA synthesis in humans.METHODSWe conducted an open-label, single-center, dose-response study of hymecromone in healthy adults. Subjects received hymecromone at 1200 (n = 8), 2400 (n = 9), or 3600 (n = 9) mg/d divided into 3 doses daily, administered orally for 4 days. We assessed safety and tolerability of hymecromone and analyzed HA, 4-MU, and 4-methylumbelliferyl glucuronide (4-MUG; the main metabolite of 4-MU) concentrations in sputum and serum.RESULTSHymecromone was well tolerated up to doses of 3600 mg/d. Both sputum and serum drug concentrations increased in a dose-dependent manner, indicating that higher doses lead to greater exposures. Across all dose arms combined, we observed a significant decrease in sputum HA from baseline after 4 days of treatment. We also observed a decrease in serum HA. Additionally, higher baseline sputum HA levels were associated with a greater decrease in sputum HA.CONCLUSIONAfter 4 days of exposure to oral hymecromone, healthy human subjects experienced a significant reduction in sputum HA levels, indicating this oral therapy may have potential in pulmonary diseases where HA is implicated in pathogenesis.TRIAL REGISTRATIONClinicalTrials.gov NCT02780752.FUNDINGStanford Medicine Catalyst, Stanford SPARK, Stanford Innovative Medicines Accelerator program, NIH training grants 5T32AI052073-14 and T32HL129970.
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Affiliation(s)
- Joelle I. Rosser
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine
| | - Nadine Nagy
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine
| | - Riya Goel
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine
| | - Gernot Kaber
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine
| | - Sally Demirdjian
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine
| | - Jamie Saxena
- Division of Infectious Diseases, Department of Pediatrics
| | | | | | | | | | - Jayakumar Rajadas
- Advanced Drug Delivery and Regenerative Biomaterials Laboratory, Cardiovascular Institute & Pulmonary and Critical Care, Department of Medicine, Stanford University, Stanford, California, USA
- Bioengineering and Therapeutic Sciences, UCSF School of Pharmacy, San Francisco, California, USA
| | - Zhe Wang
- Advanced Drug Delivery and Regenerative Biomaterials Laboratory, Cardiovascular Institute & Pulmonary and Critical Care, Department of Medicine, Stanford University, Stanford, California, USA
| | - Olga Arbach
- Department of Anesthesiology and Operative Intensive Care Medicine (CCM, CVK), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin Institute of Health, Berlin, Germany
| | - Colleen E. Dunn
- Center for Excellence in Pulmonary Biology, Department of Pediatrics, and
| | - Anissa Kalinowski
- Department of Epidemiology, Stanford University, Stanford, California, USA
| | - Carlos E. Milla
- Center for Excellence in Pulmonary Biology, Department of Pediatrics, and
| | - Paul L. Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine
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9
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Kratochvil MJ, Kaber G, Demirdjian S, Cai PC, Burgener EB, Nagy N, Barlow GL, Popescu M, Nicolls MR, Ozawa MG, Regula DP, Pacheco-navarro AE, Yang S, de Jesus Perez VA, Karmouty-quintana H, Peters AM, Zhao B, Buja ML, Johnson PY, Vernon RB, Wight TN, Milla CE, Rogers AJ, Spakowitz AJ, Heilshorn SC, Bollyky PL, Stanford COVID-19 Biobank Study Group. Biochemical, Biophysical, and Immunological Characterization of Respiratory Secretions in Severe SARS-CoV-2 (COVID-19) Infections.. [PMID: 35411348 PMCID: PMC8996635 DOI: 10.1101/2022.03.28.22272848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Thick, viscous respiratory secretions are a major pathogenic feature of COVID-19 disease, but the composition and physical properties of these secretions are poorly understood. We characterized the composition and rheological properties (i.e. resistance to flow) of respiratory secretions collected from intubated COVID-19 patients. We find the percent solids and protein content are greatly elevated in COVID-19 compared to heathy control samples and closely resemble levels seen in cystic fibrosis, a genetic disease known for thick, tenacious respiratory secretions. DNA and hyaluronan (HA) are major components of respiratory secretions in COVID-19 and are likewise abundant in cadaveric lung tissues from these patients. COVID-19 secretions exhibit heterogeneous rheological behaviors with thicker samples showing increased sensitivity to DNase and hyaluronidase treatment. In histologic sections from these same patients, we observe increased accumulation of HA and the hyaladherin versican but reduced tumor necrosis factor–stimulated gene-6 (TSG6) staining, consistent with the inflammatory nature of these secretions. Finally, we observed diminished type I interferon and enhanced inflammatory cytokines in these secretions. Overall, our studies indicate that increases in HA and DNA in COVID-19 respiratory secretion samples correlate with enhanced inflammatory burden and suggest that DNA and HA may be viable therapeutic targets in COVID-19 infection.
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10
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Pourtois JD, Kratochvil MJ, Chen Q, Haddock NL, Burgener EB, De Leo GA, Bollyky PL. Filamentous Bacteriophages and the Competitive Interaction between Pseudomonas aeruginosa Strains under Antibiotic Treatment: a Modeling Study. mSystems 2021; 6:e0019321. [PMID: 34156288 PMCID: PMC8269214 DOI: 10.1128/msystems.00193-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/24/2021] [Indexed: 01/22/2023] Open
Abstract
Pseudomonas aeruginosa (Pa) is a major bacterial pathogen responsible for chronic lung infections in cystic fibrosis patients. Recent work has implicated Pf bacteriophages, nonlytic filamentous viruses produced by Pa, in the chronicity and severity of Pa infections. Pf phages act as structural elements in Pa biofilms and sequester aerosolized antibiotics, thereby contributing to antibiotic tolerance. Consistent with a selective advantage in this setting, the prevalence of Pf-positive (Pf+) bacteria increases over time in these patients. However, the production of Pf phages comes at a metabolic cost to bacteria, such that Pf+ strains grow more slowly than Pf-negative (Pf-) strains in vitro. Here, we use a mathematical model to investigate how these competing pressures might influence the relative abundance of Pf+ versus Pf- strains in different settings. Our model suggests that Pf+ strains of Pa cannot outcompete Pf- strains if the benefits of phage production falls onto both Pf+ and Pf- strains for a majority of parameter combinations. Further, phage production leads to a net positive gain in fitness only at antibiotic concentrations slightly above the MIC (i.e., concentrations for which the benefits of antibiotic sequestration outweigh the metabolic cost of phage production) but which are not lethal for Pf+ strains. As a result, our model suggests that frequent administration of intermediate doses of antibiotics with low decay rates and high killing rates favors Pf+ over Pf- strains. These models inform our understanding of the ecology of Pf phages and suggest potential treatment strategies for Pf+ Pa infections. IMPORTANCE Filamentous phages are a frontier in bacterial pathogenesis, but the impact of these phages on bacterial fitness is unclear. In particular, Pf phages produced by Pa promote antibiotic tolerance but are metabolically expensive to produce, suggesting that competing pressures may influence the prevalence of Pf+ versus Pf- strains of Pa in different settings. Our results identify conditions likely to favor Pf+ strains and thus antibiotic tolerance. This study contributes to a better understanding of the unique ecology of filamentous phages in both environmental and clinical settings and may facilitate improved treatment strategies for combating antibiotic tolerance.
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Affiliation(s)
- Julie D. Pourtois
- Department of Biology, Stanford University, Stanford, California, USA
- Hopkins Marine Station, Stanford University, Pacific Grove, California, USA
| | - Michael J. Kratochvil
- Department of Materials Science and Engineering, Stanford University, Stanford, California, USA
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Qingquan Chen
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Naomi L. Haddock
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Elizabeth B. Burgener
- Center for Excellence in Pulmonary Biology, Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Giulio A. De Leo
- Department of Biology, Stanford University, Stanford, California, USA
- Hopkins Marine Station, Stanford University, Pacific Grove, California, USA
| | - Paul L. Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
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11
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Cai PC, Krajina BA, Kratochvil MJ, Zou L, Zhu A, Burgener EB, Bollyky PL, Milla CE, Webber MJ, Spakowitz AJ, Heilshorn SC. Dynamic light scattering microrheology for soft and living materials. Soft Matter 2021; 17:1929-1939. [PMID: 33427280 PMCID: PMC7938343 DOI: 10.1039/d0sm01597k] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We present a method for using dynamic light scattering in the single-scattering limit to measure the viscoelastic moduli of soft materials. This microrheology technique only requires a small sample volume of 12 μL to measure up to six decades in time of rheological behavior. We demonstrate the use of dynamic light scattering microrheology (DLSμR) on a variety of soft materials, including dilute polymer solutions, covalently-crosslinked polymer gels, and active, biological fluids. In this work, we detail the procedure for applying the technique to new materials and discuss the critical considerations for implementing the technique, including a custom analysis script for analyzing data output. We focus on the advantages of applying DLSμR to biologically relevant materials: breast cancer cells encapsulated in a collagen gel and cystic fibrosis sputum. DLSμR is an easy, efficient, and economical rheological technique that can guide the design of new polymeric materials and facilitate the understanding of the underlying physics governing behavior of naturally derived materials.
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Affiliation(s)
- Pamela C Cai
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
| | - Brad A Krajina
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
| | - Michael J Kratochvil
- Department of Materials Science, Stanford University, Stanford, CA 94305, USA. and Stanford Immunology, Stanford University, Stanford, CA 94305, USA
| | - Lei Zou
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Audrey Zhu
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
| | - Elizabeth B Burgener
- Center for Excellence in Pulmonary Biology, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Paul L Bollyky
- Stanford Immunology, Stanford University, Stanford, CA 94305, USA
| | - Carlos E Milla
- Center for Excellence in Pulmonary Biology, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Matthew J Webber
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Andrew J Spakowitz
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA. and Department of Materials Science, Stanford University, Stanford, CA 94305, USA. and Department of Applied Physics, Stanford University, Stanford, CA 94305, USA and Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Sarah C Heilshorn
- Department of Materials Science, Stanford University, Stanford, CA 94305, USA.
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12
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Brockmeyer JM, Wise RT, Burgener EB, Milla C, Frymoyer A. Area under the curve achievement of once daily tobramycin in children with cystic fibrosis during clinical care. Pediatr Pulmonol 2020; 55:3343-3350. [PMID: 32827334 DOI: 10.1002/ppul.25037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/17/2020] [Accepted: 08/19/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND The area under the concentration-time curve over 24 hours (AUC24 ) is frequently utilized to monitor tobramycin exposure in children with cystic fibrosis (CF). An understanding of exposure target achievement during clinical implementation of an AUC24 based approach in children is limited. METHODS A retrospective chart review was performed in children with CF treated with once daily tobramycin and drug concentration monitoring at a pediatric CF center. During clinical care AUC24 was estimated using a traditional log-linear regression approach (LLR). AUC24 was also estimated retrospectively using a pharmacokinetic model-based Bayesian forecasting approach (BF). AUC24 achievement after both approaches were compared. RESULTS In 77 treatment courses (mean age, 12.7 ± 5.0 years), a target AUC24 100 to 125 mg h/L was achieved after starting dose in 21 (27%) and after initial dose adjustment in 35 (45%). In the first 7 days of treatment, 24 (32%) required ≥3 dose adjustments, and the mean number of drug concentrations measured was 7.1 ± 3.2. Examination of a BF approach demonstrated adequate prediction of measured tobramycin concentrations (median bias -2.1% [95% CI -3.1 to -1.4]; median precision 7.6% [95% CI, 7.1%-8.2%]). AUC24 estimates utilizing the BF approach were higher than the LLR approach with a mean difference of 6.4 mg h/L (95% CI, 4.8 to 8.0 mg h/L). CONCLUSIONS Achievement of a narrow AUC24 target is challenging during clinical care, and dose individualization is needed in most children with CF. Implementing a BF approach for estimating AUC24 in children with CF is supported.
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Affiliation(s)
- Jake M Brockmeyer
- Department of Pharmacy, Lucile Packard Children's Hospital Stanford, Palo Alto, California
| | - Russell T Wise
- Department of Pharmacy, Lucile Packard Children's Hospital Stanford, Palo Alto, California
| | - Elizabeth B Burgener
- Division of Pediatric Pulmonary Medicine, Stanford University, Stanford, California
| | - Carlos Milla
- Division of Pediatric Pulmonary Medicine, Stanford University, Stanford, California
| | - Adam Frymoyer
- Department of Pediatrics, Stanford University, Stanford, California
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13
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Kaber G, Kratochvil MJ, Burgener EB, Peltan EL, Barlow G, Yang S, Nicolls MR, de Jesus Perez V, Rosser JI, Wardle AJ, Kalinowski A, Ozawa MG, Regula DP, Nagy N, Heilshorn SC, Milla CE, Rogers AJ, Bollyky PL. Hyaluronan is abundant in COVID-19 respiratory secretions. medRxiv 2020. [PMID: 32935110 DOI: 10.1101/2020.09.11.20191692] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
COVID-19 respiratory infections are associated with copious, adherent respiratory secretions that prolong chronic ventilation and contribute to the morbidity and mortality caused by the disease. We hypothesized that hyaluronan, an extracellular matrix glycosaminoglycan produced at sites of active inflammation that promotes edema in other settings, might be a component of these secretions. To interrogate this, we examined the respiratory secretions collected from eight intubated patients with COVID-19, six control patients with cystic fibrosis (CF), a different respiratory disease also associated with thick adherent secretions, and eight healthy controls. In this sample set we found that hyaluronan content is increased approximately 20-fold in both CF and COVID-19 patients compared to healthy controls. The hyaluronan in COVID-19 samples was comprised of low-molecular weight fragments, the hyaluronan form most strongly linked with pro-inflammatory functions. Hyaluronan is similarly abundant in histologic sections from cadaveric lung tissue from COVID-19 patients. These findings implicate hyaluronan in the thick respiratory secretions characteristic of COVID-19 infection. Therapeutic strategies targeting hyaluronan should be investigated further for potential use in patients with COVID-19.
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14
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Burgener EB, Secor PR, Tracy MC, Sweere JM, Bik EM, Milla CE, Bollyky PL. Methods for Extraction and Detection of Pf Bacteriophage DNA from the Sputum of Patients with Cystic Fibrosis. Phage (New Rochelle) 2020; 1:100-108. [PMID: 32626852 PMCID: PMC7327540 DOI: 10.1089/phage.2020.0003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background: There is increasing interest in the pulmonary microbiome's bacterial and viral communities, particularly in the context of chronic airway infections in cystic fibrosis (CF). However, the isolation of microbial DNA from the sputum from patients with CF is technically challenging and the optimal protocols for the analysis of viral species, including bacteriophage, from clinical samples remains difficult. Materials and Methods: In this study, we evaluate a set of methods developed for processing and analyzing sputum from patients with CF with the goal of detecting Pf bacteriophage virion-derived nucleic acid. We evaluate the impact of bead beating, deoxyribonuclease digestion, and heating steps in these protocols focusing on the quantitative assessment of Pseudomonas aeruginosa and Pf bacteriophage in sputum. Results: Based on these comparative data, we describe an optimized protocol for processing sputum from patients with CF and isolating DNA for polymerase chain reaction or sequencing-based studies. Conclusion: These studies demonstrate the assessment of a specific bacteriophage and bacteria in sputum from patients with CF.
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Affiliation(s)
- Elizabeth B. Burgener
- Department of Pediatrics, Center for Excellence in Pulmonary Biology, Stanford University, Stanford, California, USA
| | - Patrick R. Secor
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Michael C. Tracy
- Department of Pediatrics, Center for Excellence in Pulmonary Biology, Stanford University, Stanford, California, USA
| | - Johanna M. Sweere
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, California, USA
| | | | - Carlos E. Milla
- Department of Pediatrics, Center for Excellence in Pulmonary Biology, Stanford University, Stanford, California, USA
| | - Paul L. Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, California, USA
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15
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Secor PR, Burgener EB, Kinnersley M, Jennings LK, Roman-Cruz V, Popescu M, Van Belleghem JD, Haddock N, Copeland C, Michaels LA, de Vries CR, Chen Q, Pourtois J, Wheeler TJ, Milla CE, Bollyky PL. Pf Bacteriophage and Their Impact on Pseudomonas Virulence, Mammalian Immunity, and Chronic Infections. Front Immunol 2020; 11:244. [PMID: 32153575 PMCID: PMC7047154 DOI: 10.3389/fimmu.2020.00244] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/30/2020] [Indexed: 12/11/2022] Open
Abstract
Pf bacteriophage are temperate phages that infect the bacterium Pseudomonas aeruginosa, a major cause of chronic lung infections in cystic fibrosis (CF) and other settings. Pf and other temperate phages have evolved complex, mutualistic relationships with their bacterial hosts that impact both bacterial phenotypes and chronic infection. We and others have reported that Pf phages are a virulence factor that promote the pathogenesis of P. aeruginosa infections in animal models and are associated with worse skin and lung infections in humans. Here we review the biology of Pf phage and what is known about its contributions to pathogenesis and clinical disease. First, we review the structure, genetics, and epidemiology of Pf phage. Next, we address the diverse and surprising ways that Pf phages contribute to P. aeruginosa phenotypes including effects on biofilm formation, antibiotic resistance, and motility. Then, we cover data indicating that Pf phages suppress mammalian immunity at sites of bacterial infection. Finally, we discuss recent literature implicating Pf in chronic P. aeruginosa infections in CF and other settings. Together, these reports suggest that Pf bacteriophage have direct effects on P. aeruginosa infections and that temperate phages are an exciting frontier in microbiology, immunology, and human health.
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Affiliation(s)
- Patrick R. Secor
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
- Center for Translational Medicine, University of Montana, Missoula, MT, United States
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT, United States
| | - Elizabeth B. Burgener
- Department of Pediatrics, Center for Excellence in Pulmonary Biology, Stanford University, Stanford, CA, United States
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, United States
| | - M. Kinnersley
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Laura K. Jennings
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
- Center for Translational Medicine, University of Montana, Missoula, MT, United States
| | - Valery Roman-Cruz
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
- Center for Translational Medicine, University of Montana, Missoula, MT, United States
| | - Medeea Popescu
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, United States
| | - Jonas D. Van Belleghem
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, United States
| | - Naomi Haddock
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, United States
| | - Conner Copeland
- Department of Computer Science, University of Montana, Missoula, MT, United States
| | - Lia A. Michaels
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Christiaan R. de Vries
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, United States
| | - Qingquan Chen
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, United States
| | - Julie Pourtois
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, United States
| | - Travis J. Wheeler
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT, United States
- Department of Computer Science, University of Montana, Missoula, MT, United States
| | - Carlos E. Milla
- Department of Pediatrics, Center for Excellence in Pulmonary Biology, Stanford University, Stanford, CA, United States
| | - Paul L. Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, United States
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16
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Burgener EB, Sweere JM, Bach MS, Secor PR, Haddock N, Jennings LK, Marvig RL, Johansen HK, Rossi E, Cao X, Tian L, Nedelec L, Molin S, Bollyky PL, Milla CE. Filamentous bacteriophages are associated with chronic Pseudomonas lung infections and antibiotic resistance in cystic fibrosis. Sci Transl Med 2019; 11:eaau9748. [PMID: 30996083 PMCID: PMC7021451 DOI: 10.1126/scitranslmed.aau9748] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 01/14/2019] [Accepted: 03/27/2019] [Indexed: 12/31/2022]
Abstract
Filamentous bacteriophage (Pf phage) contribute to the virulence of Pseudomonas aeruginosa infections in animal models, but their relevance to human disease is unclear. We sought to interrogate the prevalence and clinical relevance of Pf phage in patients with cystic fibrosis (CF) using sputum samples from two well-characterized patient cohorts. Bacterial genomic analysis in a Danish longitudinal cohort of 34 patients with CF revealed that 26.5% (n = 9) were consistently Pf phage positive. In the second cohort, a prospective cross-sectional cohort of 58 patients with CF at Stanford, sputum qPCR analysis showed that 36.2% (n = 21) of patients were Pf phage positive. In both cohorts, patients positive for Pf phage were older, and in the Stanford CF cohort, patients positive for Pf phage were more likely to have chronic P. aeruginosa infection and had greater declines in pulmonary function during exacerbations than patients negative for Pf phage presence in the sputum. Last, P. aeruginosa strains carrying Pf phage exhibited increased resistance to antipseudomonal antibiotics. Mechanistically, in vitro analysis showed that Pf phage sequesters these same antibiotics, suggesting that this mechanism may thereby contribute to the selection of antibiotic resistance over time. These data provide evidence that Pf phage may contribute to clinical outcomes in P. aeruginosa infection in CF.
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Affiliation(s)
- Elizabeth B Burgener
- Center for Excellence in Pulmonary Biology, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
| | - Johanna M Sweere
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Stanford Immunology, Stanford University, Stanford, CA 94305, USA
| | - Michelle S Bach
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Patrick R Secor
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Naomi Haddock
- Stanford Immunology, Stanford University, Stanford, CA 94305, USA
| | - Laura K Jennings
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Rasmus L Marvig
- Center for Genomic Medicine, Rigshospitalet-Copenhagen University Hospital, Copenhagen, Denmark
| | - Helle Krogh Johansen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen Ø, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Elio Rossi
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen Ø, Denmark
| | - Xiou Cao
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Lu Tian
- Biomedical Data Science Administration and Statistics, Stanford University, Stanford, CA 94305, USA
| | - Laurence Nedelec
- Primary Care and Population Health, Stanford University, Stanford, CA 94305, USA
| | - Søren Molin
- Primary Care and Population Health, Stanford University, Stanford, CA 94305, USA
| | - Paul L Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Stanford Immunology, Stanford University, Stanford, CA 94305, USA
| | - Carlos E Milla
- Center for Excellence in Pulmonary Biology, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
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17
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Burgener EB, Waggoner J, Pinsky BA, Chen SF. Clinical characteristics and outcomes of pediatric patients with CMV DNA detection in bronchoalveolar lavage fluid. Pediatr Pulmonol 2017; 52:112-118. [PMID: 27280337 DOI: 10.1002/ppul.23494] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 04/01/2016] [Accepted: 05/06/2016] [Indexed: 11/06/2022]
Abstract
INTRODUCTION Cytomegalovirus (CMV) infection can cause severe pulmonary disease in immunocompromised patients. There are no standard diagnostic criteria for CMV pulmonary disease beyond histopathology findings on lung tissue, which is challenging to obtain in pediatric patients. Bronchoalveolar lavage (BAL) fluid is easier to obtain. Since CMV remains latent after primary infection and can potentially reactivate due to any inflammatory response, CMV detection in BAL specimen may not indicate acute CMV pulmonary disease. Thus, we describe the clinical manifestations and outcomes of pediatric patients with CMV detection in BAL fluid. METHODS We reviewed the clinical, radiologic, and laboratory data of patients <19 years old with a BAL specimen positive for CMV during a 5-year period. RESULTS Thirty-four encounters in 29 patients were found with CMV detected in their BAL specimen. Half (17/34) of the encounters were in immunocompromised patients. CMV, polymerase chain reaction (PCR) was the most common positive test. Forty-seven percent of the patients had other infections detected in BAL specimens. The majority of patients were never treated for CMV and resolved their acute respiratory illness. Only one patient had probable CMV pulmonary disease. DISCUSSION CMV is frequently recovered from BAL specimens but does not usually indicate acute CMV pulmonary disease. We would suggest that other diagnoses be considered first, even if CMV is recovered. Pediatr Pulmonol. 2017;52:112-118. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Elizabeth B Burgener
- Department of Pediatrics, Pulmonary Medicine, Stanford University School of Medicine, Palo Alto, 94304, California
| | - Jesse Waggoner
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Palo Alto, California
| | - Benjamin A Pinsky
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Palo Alto, California.,Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - Sharon F Chen
- Department of Pediatrics, Infectious Disease, Stanford University School of Medicine, Palo Alto, California
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18
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Tan SK, Burgener EB, Waggoner JJ, Gajurel K, Gonzalez S, Chen SF, Pinsky BA. Molecular and Culture-Based Bronchoalveolar Lavage Fluid Testing for the Diagnosis of Cytomegalovirus Pneumonitis. Open Forum Infect Dis 2016; 3:ofv212. [PMID: 26885542 PMCID: PMC4752011 DOI: 10.1093/ofid/ofv212] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 12/24/2015] [Indexed: 11/12/2022] Open
Abstract
Background. Cytomegalovirus (CMV) is a major cause of morbidity and mortality in immunocompromised patients, with CMV pneumonitis among the most severe manifestations of infection. Although bronchoalveolar lavage (BAL) samples are frequently tested for CMV, the clinical utility of such testing remains uncertain. Methods. Retrospective analysis of adult patients undergoing BAL testing via CMV polymerase chain reaction (PCR), shell vial culture, and conventional viral culture between August 2008 and May 2011 was performed. Cytomegalovirus diagnostic methods were compared with a comprehensive definition of CMV pneumonitis that takes into account signs and symptoms, underlying host immunodeficiency, radiographic findings, and laboratory results. Results. Seven hundred five patients underwent 1077 bronchoscopy episodes with 1090 BAL specimens sent for CMV testing. Cytomegalovirus-positive patients were more likely to be hematopoietic cell transplant recipients (26% vs 8%, P < .0001) and less likely to have an underlying condition not typically associated with lung disease (3% vs 20%, P < .0001). Histopathology was performed in only 17.3% of CMV-positive bronchoscopy episodes. When CMV diagnostic methods were evaluated against the comprehensive definition, the sensitivity and specificity of PCR, shell vial culture, and conventional culture were 91.3% and 94.6%, 54.4% and 97.4%, and 28.3% and 96.5%, respectively. Compared with culture, PCR provided significantly higher sensitivity and negative predictive value (P ≤ .001), without significantly lower positive predictive value. Cytomegalovirus quantitation did not improve test performance, resulting in a receiver operating characteristic curve with an area under the curve of 0.53. Conclusions. Cytomegalovirus PCR combined with a comprehensive clinical definition provides a pragmatic approach for the diagnosis of CMV pneumonitis.
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Affiliation(s)
- Susanna K Tan
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine
| | | | - Jesse J Waggoner
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine
| | - Kiran Gajurel
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine
| | - Sarah Gonzalez
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Sharon F Chen
- Department of Pediatrics, Division of Infectious Diseases
| | - Benjamin A Pinsky
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine; Department of Pathology, Stanford University School of Medicine, Stanford, California
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19
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Todd S, Arora R, Kannikeswaran N, Allarakhia I, Sivaswamy L, Wallenstein MB, Burgener EB, Klotz J, Kerner JA. Index of suspicion. Pediatr Rev 2014; 35:439-46. [PMID: 25274971 DOI: 10.1542/pir.35-10-439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
| | - Rajan Arora
- Children's Hospital of Michigan, Detroit, MI,* and
| | | | - Iqbal Allarakhia
- Department of Pediatrics, St John Hospital and Medical Center, Detroit, MI
| | | | | | | | - Jenna Klotz
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA
| | - John A Kerner
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA
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