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Berkson JD, Wate CE, Allen GB, Schubert AM, Dunbar KE, Coryell MP, Sava RL, Gao Y, Hastie JL, Smith EM, Kenneally CR, Zimmermann SK, Carlson PE. Phage-specific immunity impairs efficacy of bacteriophage targeting Vancomycin Resistant Enterococcus in a murine model. Nat Commun 2024; 15:2993. [PMID: 38582763 PMCID: PMC10998888 DOI: 10.1038/s41467-024-47192-w] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/22/2024] [Indexed: 04/08/2024] Open
Abstract
Bacteriophage therapy is a promising approach to address antimicrobial infections though questions remain regarding the impact of the immune response on clinical effectiveness. Here, we develop a mouse model to assess phage treatment using a cocktail of five phages from the Myoviridae and Siphoviridae families that target Vancomycin-Resistant Enterococcus gut colonization. Phage treatment significantly reduces fecal bacterial loads of Vancomycin-Resistant Enterococcus. We also characterize immune responses elicited following administration of the phage cocktail. While minimal innate responses are observed after phage administration, two rounds of treatment induces phage-specific neutralizing antibodies and accelerate phage clearance from tissues. Interestingly, the myophages in our cocktail induce a more robust neutralizing antibody response than the siphophages. This anti-phage immunity reduces the effectiveness of the phage cocktail in our murine model. Collectively, this study shows phage-specific immune responses may be an important consideration in the development of phage cocktails for therapeutic use.
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Affiliation(s)
- Julia D Berkson
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Claire E Wate
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Garrison B Allen
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Alyxandria M Schubert
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Kristin E Dunbar
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Michael P Coryell
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Rosa L Sava
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Yamei Gao
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Viral Products, Laboratory of Pediatric and Respiratory Viral Diseases, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Jessica L Hastie
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Emily M Smith
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Charlotte R Kenneally
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Sally K Zimmermann
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA
| | - Paul E Carlson
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, 10903 New Hampshire Ave, Silver Spring, MD, 20832, USA.
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Hastie JL, Carmichael HL, Werner BM, Dunbar KE, Carlson PE. Clostridioides difficile utilizes siderophores as an iron source and FhuDBGC contributes to ferrichrome uptake. J Bacteriol 2023; 205:e0032423. [PMID: 37971230 PMCID: PMC10729759 DOI: 10.1128/jb.00324-23] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE This study is the first example of C. difficile growing with siderophores as the sole iron source and describes the characterization of the ferric hydroxamate uptake ABC transporter (FhuDBGC). This transporter shows specificity to the siderophore ferrichrome. While not required for pathogenesis, this transporter highlights the redundancy in iron acquisition mechanisms that C. difficile uses to compete for iron during an infection.
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Affiliation(s)
- Jessica L. Hastie
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, Silver Spring, Maryland, USA
| | - Hannah L. Carmichael
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, Silver Spring, Maryland, USA
| | - Bailey M. Werner
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, Silver Spring, Maryland, USA
| | - Kristin E. Dunbar
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, Silver Spring, Maryland, USA
| | - Paul E. Carlson
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, Silver Spring, Maryland, USA
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3
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Coryell MP, Sava RL, Hastie JL, Carlson PE. Application of MALDI-TOF MS for enumerating bacterial constituents of defined consortia. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12558-5. [PMID: 37148337 DOI: 10.1007/s00253-023-12558-5] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/08/2023]
Abstract
Characterization of live biotherapeutic product (LBP) batches typically includes a measurement of viability, such as colony forming units (CFU). However, strain-specific CFU enumeration assays can be complicated by the presence of multiple organisms in a single product with similar growth requirements. To overcome specific challenges associated with obtaining strain-specific CFU values from multi-strain mixtures, we developed a method combining mass spectrometry-based colony identification with a traditional CFU assay. This method was assessed using defined consortia made from up to eight bacterial strains. Among four replicate batches of an eight-strain mixture, observed values differed from expected values by less than 0.4 log10 CFU among all strains measured (range of differences, -0.318 to + 0.267). The average difference between observed and expected values was + 0.0308 log10 CFU, with 95% limits of agreement from -0.347 to 0.408 (Bland-Altman analysis). To estimate precision, a single batch of eight-strain mixture was assayed in triplicate by three different users, for a total of nine measurements. Pooled standard deviation values ranged from 0.067 to 0.195 log10 CFU for the eight strains measured, and user averages did not differ significantly. Leveraging emerging mass-spectrometry-based colony identification tools, a novel method for simultaneous enumeration and identification of viable bacteria from mixed-strain consortia was developed and tested. This study demonstrates the potential for this approach to generate accurate and consistent measurements of up to eight bacterial strains simultaneously and may provide a flexible platform for future refinements and modifications. KEY POINTS: • Enumeration of live biotherapeutics is essential for product quality and safety. • Conventional CFU counting may not differentiate between strains in microbial products. • This approach was developed for direct enumeration of mixed bacterial strains simultaneously.
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Affiliation(s)
- Michael P Coryell
- Division of Bacterial, Parasitic, and Allergenic Products; Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Rosa L Sava
- Division of Bacterial, Parasitic, and Allergenic Products; Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Jessica L Hastie
- Division of Bacterial, Parasitic, and Allergenic Products; Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Paul E Carlson
- Division of Bacterial, Parasitic, and Allergenic Products; Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA.
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4
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Coryell MP, Iakiviak M, Pereira N, Murugkar PP, Rippe J, Williams DB, Heald-Sargent T, Sanchez-Pinto LN, Chavez J, Hastie JL, Sava RL, Lien CZ, Wang TT, Muller WJ, Fischbach MA, Carlson PE. A method for detection of SARS-CoV-2 RNA in healthy human stool: a validation study. Lancet Microbe 2021; 2:e259-e266. [PMID: 33821247 PMCID: PMC8012028 DOI: 10.1016/s2666-5247(21)00059-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background Faecal shedding of SARS-CoV-2 has raised concerns about transmission through faecal microbiota transplantation procedures. Validation parameters of authorised tests for SARS-CoV-2 RNA detection in respiratory samples are described in product labelling, whereas the published methods for SARS-CoV-2 detection from faecal samples have not permitted a robust description of the assay parameters. We aimed to develop and validate a test specifically for detection of SARS-CoV-2 in human stool. Methods In this validation study, we evaluated performance characteristics of a reverse transcriptase real-time PCR (RT-rtPCR) test for detection of SARS-CoV-2 in human stool specimens by spiking stool with inactivated SARS-CoV-2 material. A modified version of the US Centers for Disease Control and Prevention RT-rtPCR SARS-CoV-2 test was used for detection of viral RNA. Analytical sensitivity was evaluated in freshly spiked stool by testing two-fold dilutions in replicates of 20. Masked samples were tested by a second laboratory to evaluate interlaboratory reproducibility. Short-term (7-day) stability of viral RNA in stool samples was assessed with four different stool storage buffers (phosphate-buffered saline, Cary-Blair medium, Stool Transport and Recovery [STAR] buffer, and DNA/RNA Shield) kept at −80°C, 4°C, and ambient temperature (approximately 21°C). We also tested clinical stool and anal swab specimens from patients who were SARS-CoV-2 positive by nasopharyngeal testing. Findings The lower limit of detection of the assay was found to be 3000 viral RNA copies per g of original stool sample, with 100% detection across 20 replicates assessed at this concentration. Analytical sensitivity was diminished by approximately two times after a single freeze-thaw cycle at −80°C. At 100 times the limit of detection, spiked samples were generally stable in all four stool storage buffers tested for up to 7 days, with maximum changes in mean threshold cycle values observed at −80°C storage in Cary-Blair medium (from 29·4 [SD 0·27] at baseline to 30·8 [0·17] at day 7; p<0·0001), at 4°C storage in DNA/RNA Shield (from 28·5 [0·15] to 29·8 [0·09]; p=0·0019), and at ambient temperature in STAR buffer (from 30·4 [0·24] to 32·4 [0·62]; p=0·0083). 30 contrived SARS-CoV-2 samples were tested by a second laboratory and were correctly identified as positive or negative in at least one of two rounds of testing. Additionally, SARS-CoV-2 RNA was detected using this assay in the stool and anal swab specimens of 11 of 23 individuals known to be positive for SARS-CoV-2. Interpretation This is a sensitive and reproducible assay for detection of SARS-CoV-2 RNA in human stool, with potential uses in faecal microbiota transplantation donor screening, sewage monitoring, and further research into the effects of faecal shedding on the epidemiology of the COVID-19 pandemic. Funding National Institute of Allergy and Infectious Diseases, US National Institutes of Health; Center for Biologics Evaluation and Research, US Food and Drug Administration.
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Affiliation(s)
- Michael P Coryell
- Division of Bacterial, Parasitic and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Mikhail Iakiviak
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA, USA
| | - Nicole Pereira
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA, USA
| | - Pallavi P Murugkar
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA, USA
| | - Jason Rippe
- Division of Infectious Diseases, Department of Pediatrics, Ann & Robert H Lurie Children's Hospital, Chicago, IL, USA
| | - David B Williams
- Division of Infectious Diseases, Department of Pediatrics, Ann & Robert H Lurie Children's Hospital, Chicago, IL, USA
| | - Taylor Heald-Sargent
- Division of Infectious Diseases, Department of Pediatrics, Ann & Robert H Lurie Children's Hospital, Chicago, IL, USA.,Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - L Nelson Sanchez-Pinto
- Division of Infectious Diseases, Department of Pediatrics, Ann & Robert H Lurie Children's Hospital, Chicago, IL, USA.,Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jairo Chavez
- Division of Infectious Diseases, Department of Pediatrics, Ann & Robert H Lurie Children's Hospital, Chicago, IL, USA.,Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jessica L Hastie
- Division of Bacterial, Parasitic and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Rosa L Sava
- Division of Bacterial, Parasitic and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Christopher Z Lien
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Tony T Wang
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - William J Muller
- Division of Infectious Diseases, Department of Pediatrics, Ann & Robert H Lurie Children's Hospital, Chicago, IL, USA.,Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Michael A Fischbach
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA, USA
| | - Paul E Carlson
- Division of Bacterial, Parasitic and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
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5
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Smith AD, Foss ED, Zhang I, Hastie JL, Giordano NP, Gasparyan L, VinhNguyen LP, Schubert AM, Prasad D, McMichael HL, Sun J, Beger RD, Simonyan V, Cowley SC, Carlson PE. Microbiota of MR1 deficient mice confer resistance against Clostridium difficile infection. PLoS One 2019; 14:e0223025. [PMID: 31560732 PMCID: PMC6764671 DOI: 10.1371/journal.pone.0223025] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 09/11/2019] [Indexed: 12/19/2022] Open
Abstract
Clostridium difficile (Cd) infection (CDI) typically occurs after antibiotic usage perturbs the gut microbiota. Mucosa-associated invariant T cells (MAIT) are found in the gut and their development is dependent on Major histocompatibility complex-related protein 1 (MR1) and the host microbiome. Here we were interested in determining whether the absence of MR1 impacts resistance to CDI. To this end, wild-type (WT) and MR1-/- mice were treated with antibiotics and then infected with Cd spores. Surprisingly, MR1-/- mice exhibited resistance to Cd colonization. 16S rRNA gene sequencing of feces revealed inherent differences in microbial composition. This colonization resistance was transferred from MR1-/- to WT mice via fecal microbiota transplantation, suggesting that MR1-dependent factors influence the microbiota, leading to CDI susceptibility.
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Affiliation(s)
- Ashley D Smith
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial Pathogens and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Elissa D Foss
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial Pathogens and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Irma Zhang
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial Pathogens and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Jessica L Hastie
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial Pathogens and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Nicole P Giordano
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial Pathogens and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Lusine Gasparyan
- High-performance Integrated Personal Environment, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Lam Phuc VinhNguyen
- High-performance Integrated Personal Environment, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Alyxandria M Schubert
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial Pathogens and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Deepika Prasad
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial Pathogens and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America.,High-performance Integrated Personal Environment, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Hannah L McMichael
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial Pathogens and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Jinchun Sun
- Division of Systems Biology, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Richard D Beger
- Division of Systems Biology, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Vahan Simonyan
- High-performance Integrated Personal Environment, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Siobhán C Cowley
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial Pathogens and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Paul E Carlson
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial Pathogens and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
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Hastie JL, Hanna PC, Carlson PE. Transcriptional response of Clostridium difficile to low iron conditions. Pathog Dis 2018; 76:4830099. [PMID: 29390127 DOI: 10.1093/femspd/fty009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/25/2018] [Indexed: 12/14/2022] Open
Abstract
Clostridium difficile (Cd) is the leading cause of antibiotic-associated diarrhea. During an infection, Cd must compete with both the host and other commensal bacteria to acquire iron. Iron is essential for many cell processes, but it can also cause damage if allowed to form reactive hydroxyl radicals. In all organisms, levels of free iron are tightly regulated as are processes utilizing iron molecules. Genome-wide transcriptional analysis of Cd grown in iron-depleted conditions revealed significant changes in expression of genes involved in iron transport, metabolism and virulence. These data will aid future studies examining Cd colonization and the requirements for growth in vivo during an infection.
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Affiliation(s)
- Jessica L Hastie
- Division of Bacterial, Parasitic and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Phillip C Hanna
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Paul E Carlson
- Division of Bacterial, Parasitic and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
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7
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Giordano N, Hastie JL, Carlson PE. Transcriptomic profiling of Clostridium difficile grown under microaerophillic conditions. Pathog Dis 2018; 76:4830101. [DOI: 10.1093/femspd/fty010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/25/2018] [Indexed: 12/17/2022] Open
Affiliation(s)
- Nicole Giordano
- Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial, Parasitic and Allergenic Products, US Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Jessica L Hastie
- Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial, Parasitic and Allergenic Products, US Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Paul E Carlson
- Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial, Parasitic and Allergenic Products, US Food and Drug Administration, Silver Spring, MD 20993, USA
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8
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Kochan TJ, Somers MJ, Kaiser AM, Shoshiev MS, Hagan AK, Hastie JL, Giordano NP, Smith AD, Schubert AM, Carlson PE, Hanna PC. Intestinal calcium and bile salts facilitate germination of Clostridium difficile spores. PLoS Pathog 2017; 13:e1006443. [PMID: 28704538 PMCID: PMC5509370 DOI: 10.1371/journal.ppat.1006443] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 06/03/2017] [Indexed: 12/26/2022] Open
Abstract
Clostridium difficile (C. difficile) is an anaerobic gram-positive pathogen that is the leading cause of nosocomial bacterial infection globally. C. difficile infection (CDI) typically occurs after ingestion of infectious spores by a patient that has been treated with broad-spectrum antibiotics. While CDI is a toxin-mediated disease, transmission and pathogenesis are dependent on the ability to produce viable spores. These spores must become metabolically active (germinate) in order to cause disease. C. difficile spore germination occurs when spores encounter bile salts and other co-germinants within the small intestine, however, the germination signaling cascade is unclear. Here we describe a signaling role for Ca2+ during C. difficile spore germination and provide direct evidence that intestinal Ca2+ coordinates with bile salts to stimulate germination. Endogenous Ca2+ (released from within the spore) and a putative AAA+ ATPase, encoded by Cd630_32980, are both essential for taurocholate-glycine induced germination in the absence of exogenous Ca2+. However, environmental Ca2+ replaces glycine as a co-germinant and circumvents the need for endogenous Ca2+ fluxes. Cd630_32980 is dispensable for colonization in a murine model of C. difficile infection and ex vivo germination in mouse ileal contents. Calcium-depletion of the ileal contents prevented mutant spore germination and reduced WT spore germination by 90%, indicating that Ca2+ present within the gastrointestinal tract plays a critical role in C. difficile germination, colonization, and pathogenesis. These data provide a biological mechanism that may explain why individuals with inefficient intestinal calcium absorption (e.g., vitamin D deficiency, proton pump inhibitor use) are more prone to CDI and suggest that modulating free intestinal calcium is a potential strategy to curb the incidence of CDI. The anaerobic, spore-forming bacterium Clostridium difficile (C. difficile) is a prominent pathogen in hospitals worldwide and the leading cause of nosocomial diarrhea. Numerous risk factors are associated with C. difficile infections (CDIs) including: antibiotics, advanced age, vitamin D deficiency, and proton pump inhibitors. Antibiotic use disrupts the intestinal microbiota allowing for C. difficile to colonize, however, why these other risk factors increase CDI incidence is unclear. Notably, deficient intestinal calcium absorption (i.e., increased calcium levels) is associated with these risk factors. In this work, we investigate the role of calcium in C. difficile spore germination. C. difficile spores are the infectious particles and they must become metabolically active (germinate) to cause disease. Here, we show that calcium is required for C. difficile germination, specifically activating the key step of cortex hydrolysis, and that this calcium can be derived from either within the spore or the environment. We also demonstrate that intestinal calcium is required for efficient spore germination in vivo, suggesting that intestinal concentrations of other co-germinants are insufficient to induce C. difficile germination. Collectively, these data provide a mechanism that explains the strong clinical correlations between increased intestinal calcium levels and risk of CDI.
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Affiliation(s)
- Travis J. Kochan
- University of Michigan Medical School, Department of Microbiology and Immunology. Ann Arbor, Michigan, United States of America
| | - Madeline J. Somers
- University of Michigan Medical School, Department of Microbiology and Immunology. Ann Arbor, Michigan, United States of America
| | - Alyssa M. Kaiser
- University of Michigan Medical School, Department of Microbiology and Immunology. Ann Arbor, Michigan, United States of America
| | - Michelle S. Shoshiev
- University of Michigan Medical School, Department of Microbiology and Immunology. Ann Arbor, Michigan, United States of America
| | - Ada K. Hagan
- University of Michigan Medical School, Department of Microbiology and Immunology. Ann Arbor, Michigan, United States of America
| | - Jessica L. Hastie
- Center for Biologics Evaluation and Research, US Food and Drug Administration. Silver Spring, Maryland, United States of America
| | - Nicole P. Giordano
- Center for Biologics Evaluation and Research, US Food and Drug Administration. Silver Spring, Maryland, United States of America
| | - Ashley D. Smith
- Center for Biologics Evaluation and Research, US Food and Drug Administration. Silver Spring, Maryland, United States of America
| | - Alyxandria M. Schubert
- Center for Biologics Evaluation and Research, US Food and Drug Administration. Silver Spring, Maryland, United States of America
| | - Paul E. Carlson
- Center for Biologics Evaluation and Research, US Food and Drug Administration. Silver Spring, Maryland, United States of America
| | - Philip C. Hanna
- University of Michigan Medical School, Department of Microbiology and Immunology. Ann Arbor, Michigan, United States of America
- * E-mail:
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Hastie JL, Williams KB, Bohr LL, Houtman JC, Gakhar L, Ellermeier CD. The Anti-sigma Factor RsiV Is a Bacterial Receptor for Lysozyme: Co-crystal Structure Determination and Demonstration That Binding of Lysozyme to RsiV Is Required for σV Activation. PLoS Genet 2016; 12:e1006287. [PMID: 27602573 PMCID: PMC5014341 DOI: 10.1371/journal.pgen.1006287] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/09/2016] [Indexed: 01/25/2023] Open
Abstract
σ factors provide RNA polymerase with promoter specificity in bacteria. Some σ factors require activation in order to interact with RNA polymerase and transcribe target genes. The Extra-Cytoplasmic Function (ECF) σ factor, σV, is encoded by several Gram-positive bacteria and is specifically activated by lysozyme. This activation requires the proteolytic destruction of the anti-σ factor RsiV via a process of regulated intramembrane proteolysis (RIP). In many cases proteases that cleave at site-1 are thought to directly sense a signal and initiate the RIP process. We previously suggested binding of lysozyme to RsiV initiated the proteolytic destruction of RsiV and activation of σV. Here we determined the X-ray crystal structure of the RsiV-lysozyme complex at 2.3 Å which revealed that RsiV and lysozyme make extensive contacts. We constructed RsiV mutants with altered abilities to bind lysozyme. We find that mutants that are unable to bind lysozyme block site-1 cleavage of RsiV and σV activation in response to lysozyme. Taken together these data demonstrate that RsiV is a receptor for lysozyme and binding of RsiV to lysozyme is required for σV activation. In addition, the co-structure revealed that RsiV binds to the lysozyme active site pocket. We provide evidence that in addition to acting as a sensor for the presence of lysozyme, RsiV also inhibits lysozyme activity. Thus we have demonstrated that RsiV is a protein with multiple functions. RsiV inhibits σV activity in the absence of lysozyme, RsiV binds lysozyme triggering σV activation and RsiV inhibits the enzymatic activity of lysozyme. The exposed cell wall of Gram-positive bacteria renders them particularly susceptible to the innate immune defense enzyme lysozyme. Several Gram-positive bacteria activate lysozyme resistance via a signal transduction system, σV, which is induced by lysozyme. Here we report the co-structure of lysozyme with its bacterial receptor the anti-σ factor RsiV. In the absence of lysozyme, RsiV inhibits activity of σV. In the presence of lysozyme, RsiV is destroyed via proteolytic cascade. We demonstrate that binding of lysozyme to RsiV triggers the proteolytic destruction of the anti-σ factor RsiV and thus activation of σV. In addition, we demonstrate that RsiV also acts as an inhibitor of lysozyme activity. Thus, the anti-σ factor RsiV allows for the cell to sense lysozyme and inhibit its activity as well as inducing additional lysozyme resistance mechanisms.
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Affiliation(s)
- Jessica L. Hastie
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Kyle B. Williams
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Lindsey L. Bohr
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Jon C. Houtman
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Lokesh Gakhar
- Department of Biochemistry & Protein Crystallography Facility, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Craig D. Ellermeier
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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Hastie JL, Williams KB, Sepúlveda C, Houtman JC, Forest KT, Ellermeier CD. Evidence of a bacterial receptor for lysozyme: binding of lysozyme to the anti-σ factor RsiV controls activation of the ecf σ factor σV. PLoS Genet 2014; 10:e1004643. [PMID: 25275625 PMCID: PMC4183432 DOI: 10.1371/journal.pgen.1004643] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 07/31/2014] [Indexed: 02/02/2023] Open
Abstract
σ factors endow RNA polymerase with promoter specificity in bacteria. Extra-Cytoplasmic Function (ECF) σ factors represent the largest and most diverse family of σ factors. Most ECF σ factors must be activated in response to an external signal. One mechanism of activation is the stepwise proteolytic destruction of an anti-σ factor via Regulated Intramembrane Proteolysis (RIP). In most cases, the site-1 protease required to initiate the RIP process directly senses the signal. Here we report a new mechanism in which the anti-σ factor rather than the site-1 protease is the sensor. We provide evidence suggesting that the anti-σ factor RsiV is the bacterial receptor for the innate immune defense enzyme, lysozyme. The site-1 cleavage site is similar to the recognition site of signal peptidase and cleavage at this site is required for σV activation in Bacillus subtilis. We reconstitute site-1 cleavage in vitro and demonstrate that it requires both signal peptidase and lysozyme. We demonstrate that the anti-σ factor RsiV directly binds to lysozyme and muramidase activity is not required for σV activation. We propose a model in which the binding of lysozyme to RsiV activates RsiV for signal peptidase cleavage at site-1, initiating proteolytic destruction of RsiV and activation of σV. This suggests a novel mechanism in which conformational change in a substrate controls the cleavage susceptibility for signal peptidase. Thus, unlike other ECF σ factors which require regulated intramembrane proteolysis for activation, the sensor for σV activation is not the site-1 protease but the anti-σ factor. All cells sense and respond to changes in their environments by transmitting information across the membrane. In bacteria, σ factors provide promoter specificity to RNA polymerase. Bacteria encode Extra-Cytoplasmic Function (ECF) σ factors, which often respond to extracellular signals. Activation of some ECF σ factors is controlled by stepwise proteolytic destruction of an anti-σ factor which is initiated by a site-1 protease. In most cases, the site-1 protease required to initiate the RIP process is thought to be the signal sensor. Here we report that the anti-σ factor RsiV, and not the site-1 protease, is the sensor for σV activation. Activation of the ECF σ factor σV is induced by lysozyme, an innate immune defense enzyme. We identify the site-1 protease as signal peptidase, which is required for general protein secretion. The anti-σ factor RsiV directly binds lysozyme. Binding of lysozyme to RsiV allows signal peptidase to cleave RsiV at site-1 and this leads to activation of σV. Thus, the anti-σ factor functions as a bacterial receptor for lysozyme. RsiV homologs from C. difficile and E. faecalis also bind lysozyme, suggesting they may utilize this receptor-ligand mechanism to control activation of σV to induce lysozyme resistance.
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Affiliation(s)
- Jessica L. Hastie
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Kyle B. Williams
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Carolina Sepúlveda
- Department of Bacteriology, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Jon C. Houtman
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Katrina T. Forest
- Department of Bacteriology, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Craig D. Ellermeier
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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