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Hong G, Daniel SG, Lee JJ, Bittinger K, Glaser L, Mattei LM, Dorgan DJ, Hadjiliadis D, Kawut SM, Collman RG. Distinct community structures of the fungal microbiome and respiratory health in adults with cystic fibrosis. J Cyst Fibros 2023; 22:636-643. [PMID: 36822979 PMCID: PMC10440372 DOI: 10.1016/j.jcf.2023.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 10/12/2022] [Revised: 01/05/2023] [Accepted: 02/06/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND The respiratory tract fungal microbiome in cystic fibrosis (CF) has been understudied despite increasing recognition of fungal pathogens in CF lung disease. We sought to better understand the fungal communities in adults with CF, and to define relationships between fungal profiles and clinical characteristics. METHODS We enrolled 66 adults with CF and collected expectorated sputum, spirometry, Cystic Fibrosis Questionnaire-revised, and clinical data. Fungi were molecularly profiled by sequencing of the internal transcribed spacer (ITS) region. Total fungal abundance was measured by quantitative PCR. Relative abundance and qPCR-corrected abundances were determined. Selective fungus culture identified cultivable fungi. Alpha diversity and beta diversity were measured and relationships with clinical parameters were interrogated. RESULTS Median age was 29 years and median FEV1 percent predicted 58%. Members of the Candida genus were the most frequent dominant taxa in CF sputum. Apiotrichum, Trichosporon, Saccharomyces cerevisiae, and Scedosporium were present in high relative abundance in few samples; whereas, Aspergillus species were detected at low levels. Higher FEV1% predicted and CFTR modulator use were associated with greater alpha-diversity. Chronic azithromycin use was associated with lower alpha-diversity. Patients with acute pulmonary had distinct fungal community composition compared to clinically stable subjects. Differing yeast species were mainly responsible for the community differences. CONCLUSION The respiratory tract fungal microbiome in adults with CF is associated with lung function, pulmonary exacerbation status, macrolide use, and CFTR modulator use. Future work to better understand fungal diversity in the CF airway and its impact on lung health is necessary.
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Affiliation(s)
- Gina Hong
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of.
| | - Scott G Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia 19104
| | - Jung-Jin Lee
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia 19104
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia 19104
| | - Laurel Glaser
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Lisa M Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia 19104
| | - Daniel J Dorgan
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of
| | - Denis Hadjiliadis
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of
| | - Steven M Kawut
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of
| | - Ronald G Collman
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Palestine, State of
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2
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Mukhopadhyay S, Lee JJ, Hartman E, Woodford E, Dhudasia MB, Mattei LM, Daniel SG, Wade KC, Underwood MA, Bittinger K. Preterm infants at low risk for early-onset sepsis differ in early fecal microbiome assembly. Gut Microbes 2022; 14:2154091. [PMID: 36474348 PMCID: PMC9733690 DOI: 10.1080/19490976.2022.2154091] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Antibiotics are administered near-universally to very low birth weight (VLBW) infants after birth for suspected early-onset sepsis (EOS). We previously identified a phenotypic group of VLBW infants, referred to as low-risk for EOS (LRE), whose risk of EOS is low enough to avoid routine antibiotic initiation. In this cohort study, we compared 18 such infants with 30 infants categorized as non-LRE to determine if the lower risk of pathogen transmission at birth is accompanied by differences in microbiome acquisition and development. We did shotgun metagenomic sequencing of 361 fecal samples obtained serially. LRE infants had a higher human-to-bacterial DNA ratio than non-LRE infants in fecal samples on days 1-3 after birth, confirming lower bacterial acquisition among LRE infants. The microbial diversity and composition in samples from days 4-7 differed between the groups with a predominance of Staphylococcus epidermidis in LRE infants and Enterobacteriaceae sp. in non-LRE infants. Compositional differences were congruent with the distribution of virulence factors and antibiotic resistant genes. After the first week, the overall composition was similar, but changes in relative abundance for several taxa with increasing age differed between groups. Of the nine late-onset bacteremia episodes, eight occurred in non-LRE infants. Species isolated from the blood culture was detected in the pre-antibiotic fecal samples of the infant for all episodes, though these species were also found in infants without bacteremia. In conclusion, LRE infants present a distinct pattern of microbiome development that is aligned with their low risk for EOS. Further investigation to determine the impact of these differences on later outcomes such as late-onset bacteremia is warranted.
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Affiliation(s)
- Sagori Mukhopadhyay
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States,Center for Pediatric Clinical Effectiveness, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States,Sagori Mukhopadhyay Center for Pediatric Clinical Effectiveness, Children’s Hospital of Philadelphia, Roberts Center for Pediatric Research, 2716 South Street, Office 19-322, Philadelphia, PA19146, United States
| | - Jung-Jin Lee
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Erica Hartman
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States,Center for Pediatric Clinical Effectiveness, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Emily Woodford
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Miren B. Dhudasia
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States,Center for Pediatric Clinical Effectiveness, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Lisa M. Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Scott G. Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Kelly C. Wade
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States
| | - Mark A. Underwood
- Department of Pediatrics, University of California Davis, Sacramento, California, United States
| | - Kyle Bittinger
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States,Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States,CONTACT Kyle Bittinger CHOP Microbiome Center, Children’s Hospital of Philadelphia, Roberts Center for Pediatric Research, 2716 South Street, Philadelphia, PA19146, United States
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3
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Mahalak KK, Firrman J, Bobokalonov J, Narrowe AB, Bittinger K, Daniel S, Tanes C, Mattei LM, Zeng WB, Soares JW, Kobori M, Lemons JMS, Tomasula PM, Liu L. Persistence of the Probiotic Lacticaseibacillus rhamnosus Strain GG (LGG) in an In Vitro Model of the Gut Microbiome. Int J Mol Sci 2022; 23:12973. [PMID: 36361763 PMCID: PMC9657340 DOI: 10.3390/ijms232112973] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/26/2023] Open
Abstract
The consumption of probiotics is widely encouraged due to reports of their positive effects on human health. In particular, Lacticaseibacillus rhamnosus strain GG (LGG) is an approved probiotic that has been reported to improve health outcomes, especially for gastrointestinal disorders. However, how LGG cooperates with the gut microbiome has not been fully explored. To understand the interaction between LGG and its ability to survive and grow within the gut microbiome, this study introduced LGG into established microbial communities using an in vitro model of the colon. LGG was inoculated into the simulated ascending colon and its persistence in, and transit through the subsequent transverse and descending colon regions was monitored over two weeks. The impact of LGG on the existing bacterial communities was investigated using 16S rRNA sequencing and short-chain fatty acid analysis. LGG was able to engraft and proliferate in the ascending region for at least 10 days but was diminished in the transverse and descending colon regions with little effect on short-chain fatty acid abundance. These data suggest that the health benefits of the probiotic LGG rely on its ability to transiently engraft and modulate the host microbial community.
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Affiliation(s)
- Karley K. Mahalak
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Jamshed Bobokalonov
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Adrienne B. Narrowe
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Scott Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lisa M. Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Wei-Bin Zeng
- Department of Mathematics, University of Louisville, Louisville, KY 40292, USA
| | - Jason W. Soares
- Bioprocessing and Bioengineering Group, US Army Combat Capabilities Development Command Soldier Center (CCDC-SC), Natick, MA 01760, USA
| | - Masuko Kobori
- Institute of Food Research, National Agriculture and Food Research Organization, Tsukuba 305-8642, Ibaraki, Japan
| | - Johanna M. S. Lemons
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Peggy M. Tomasula
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA
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4
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Payne E, Harrington K, Richard P, Brackin R, Davis R, Couture S, Liff J, Asmus F, Mutina E, Fisher A, Giuvelis D, Sannajust S, Rostama B, King T, Mattei LM, Lee JJ, Friedman ES, Bittinger K, May M, Stevenson GW. Effects of Vancomycin on Persistent Pain-Stimulated and Pain-Depressed Behaviors in Female Fischer Rats With or Without Voluntary Access to Running Wheels. J Pain 2021; 22:1530-1544. [PMID: 34029686 PMCID: PMC8578155 DOI: 10.1016/j.jpain.2021.05.003] [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] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/02/2021] [Accepted: 05/15/2021] [Indexed: 10/21/2022]
Abstract
The present experiments determined the effects of the narrow-spectrum antibiotic vancomycin on inflammatory pain-stimulated and pain-depressed behaviors in rats. Persistent inflammatory pain was modeled using dilute formalin (0.5%). Two weeks of oral vancomycin administered in drinking water attenuated Phase II formalin pain-stimulated behavior, and prevented formalin pain-depressed wheel running. Fecal microbiota transplantation produced a non-significant trend toward reversal of the vancomycin effect on pain-stimulated behavior. Vancomycin depleted Firmicutes and Bacteroidetes populations in the gut while having a partial sparing effect on Lactobacillus species and Clostridiales. The vancomycin treatment effect was associated with an altered profile in amino acid concentrations in the gut with increases in arginine, glycine, alanine, proline, valine, leucine, and decreases in tyrosine and methionine. These results indicate that vancomycin may have therapeutic effects against persistent inflammatory pain conditions that are distal to the gut. PERSPECTIVE: The narrow-spectrum antibiotic vancomycin reduces pain-related behaviors in the formalin model of inflammatory pain. These data suggest that manipulation of the gut microbiome may be one method to attenuate inflammatory pain amplitude.
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Affiliation(s)
- Emily Payne
- Department of Psychology, University of New England, Biddeford, ME, 04005
| | - Kylee Harrington
- Department of Psychology, University of New England, Biddeford, ME, 04005
| | - Philomena Richard
- Department of Psychology, University of New England, Biddeford, ME, 04005
| | - Rebecca Brackin
- Department of Psychology, University of New England, Biddeford, ME, 04005
| | - Ravin Davis
- Department of Psychology, University of New England, Biddeford, ME, 04005
| | - Sarah Couture
- Department of Psychology, University of New England, Biddeford, ME, 04005
| | - Jacob Liff
- Department of Psychology, University of New England, Biddeford, ME, 04005
| | - Francesca Asmus
- Department of Psychology, University of New England, Biddeford, ME, 04005
| | - Elizabeth Mutina
- Department of Psychology, University of New England, Biddeford, ME, 04005
| | - Anyssa Fisher
- Department of Psychology, University of New England, Biddeford, ME, 04005
| | - Denise Giuvelis
- Department of Biomedical Sciences, University of New England College of Osteopathic Medicine, Biddeford, ME, 04005
| | - Sebastien Sannajust
- Department of Biomedical Sciences, University of New England College of Osteopathic Medicine, Biddeford, ME, 04005
| | - Bahman Rostama
- Department of Biomedical Sciences, University of New England College of Osteopathic Medicine, Biddeford, ME, 04005; Center for Excellence in the Neurosciences, University of New England, Biddeford, ME, 04005
| | - Tamara King
- Department of Biomedical Sciences, University of New England College of Osteopathic Medicine, Biddeford, ME, 04005; Center for Excellence in the Neurosciences, University of New England, Biddeford, ME, 04005
| | - Lisa M Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104
| | - Jung-Jin Lee
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104
| | - Elliot S Friedman
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104
| | - Meghan May
- Department of Biomedical Sciences, University of New England College of Osteopathic Medicine, Biddeford, ME, 04005; Center for Excellence in the Neurosciences, University of New England, Biddeford, ME, 04005
| | - Glenn W Stevenson
- Department of Psychology, University of New England, Biddeford, ME, 04005; Center for Excellence in the Neurosciences, University of New England, Biddeford, ME, 04005.
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5
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Rhee RL, Lu J, Bittinger K, Lee JJ, Mattei LM, Sreih AG, Chou S, Miner JJ, Cohen NA, Kelly BJ, Lee H, Grayson PC, Collman RG, Merkel PA. Dynamic Changes in the Nasal Microbiome Associated With Disease Activity in Patients With Granulomatosis With Polyangiitis. Arthritis Rheumatol 2021; 73:1703-1712. [PMID: 33682371 DOI: 10.1002/art.41723] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/02/2021] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Little is known about temporal changes in nasal bacteria in granulomatosis with polyangiitis (GPA). This study was undertaken to examine longitudinal changes in the nasal microbiome in association with relapse in GPA patients. METHODS Bacterial 16S ribosomal RNA gene sequencing was performed on nasal swabs from 19 patients with GPA who were followed up longitudinally for a total of 78 visits, including 9 patients who experienced a relapse and 10 patients who remained in remission. Relative abundance of bacteria and ratios between bacteria were examined. Generalized estimating equation models were used to evaluate the association between bacterial composition and 1) disease activity and 2) levels of antineutrophil cytoplasmic antibody (ANCA) with specificity for proteinase 3 (PR3), adjusted for medication. RESULTS Corynebacterium and Staphylococcus were the most abundant bacterial genera across all nasal samples. Patients with quiescent disease maintained a stable ratio of Corynebacterium to Staphylococcus across visits. In contrast, in patients who experienced a relapse, a significantly lower ratio was observed at the visit prior to relapse, followed by a higher ratio at the time of relapse (adjusted P < 0.01). Species-level analysis identified an association between a higher abundance of nasal Corynebacterium tuberculostearicum and 1) relapse (adjusted P = 0.04) and 2) higher PR3-ANCA levels (adjusted P = 0.02). CONCLUSION In GPA, significant changes occur in the nasal microbiome over time and are associated with disease activity. The occurrence of these changes months prior to the onset of relapse supports a pathogenic role of nasal bacteria in GPA. Our results uphold existing hypotheses implicating Staphylococcus as an instigator of disease and have generated a novel finding involving Corynebacterium as a potential mediator of disease in GPA.
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Affiliation(s)
| | - Jiarui Lu
- University of Pennsylvania, Philadelphia
| | - Kyle Bittinger
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jung-Jin Lee
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Lisa M Mattei
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | | | | | | | | | | | - Peter C Grayson
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland
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Maslanka JR, Gu CH, Zarin I, Denny JE, Broadaway S, Fett B, Mattei LM, Walk ST, Abt MC. Detection and elimination of a novel non-toxigenic Clostridioides difficile strain from the microbiota of a mouse colony. Gut Microbes 2020; 12:1-15. [PMID: 33305657 PMCID: PMC7734020 DOI: 10.1080/19490976.2020.1851999] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Clostridioides difficile is an enteric bacterial pathogen that can a cause nosocomial infection leading to debilitating colitis. The development of a murine model of C. difficile infection has led to fundamental discoveries in disease pathogenesis and the host immune response to infection. Recently, C. difficile endogenously present in the microbiota of mice has been reported and was found to complicate interpretation of mouse studies. Here, we report a novel C. difficile strain, named NTCD-035, isolated from the microbiota of our mouse colony. The presence of NTCD-035 in mice prior to challenge with a highly pathogenic C. difficile strain (VPI10463) led to significantly reduced disease severity. Phylogenetic characterization derived from whole genome sequencing and PCR ribotyping identified the isolate as a novel clade 1, ribotype 035 strain that lacks the pathogenicity locus required to produce toxins. Deficiency in toxin production along with sporulation capacity and secondary bile acid sensitivity was confirmed using in vitro assays. Inoculation of germ-free mice with NTCD-035 did not cause morbidity despite the strain readily colonizing the large intestine. Implementation of a culture-based screening procedure enabled the identification of mice harboring C. difficile in their microbiota, the establishment of a C. difficile-free mouse colony, and a monitoring system to prevent future contamination. Taken together, these data provide a framework for screening mice for endogenously harbored C. difficile and support clinical findings that demonstrate the therapeutic potential of non-toxigenic strains in preventing C. difficile associated disease. Abbreviations: PaLoc - Pathogenicity locus, CFUs - Colony forming units, TcdA - toxin-A, TcdB - toxin-B, CdtA - binary toxin A, CdtB - binary toxin B, CdtR - binary toxin R, NTCD - non-toxigenic C. difficile.
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Affiliation(s)
- Jeffrey R. Maslanka
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher H. Gu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Isma Zarin
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joshua E. Denny
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Susan Broadaway
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Bryton Fett
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lisa M. Mattei
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Seth T. Walk
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Michael C. Abt
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA,CONTACT Michael C Abt Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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7
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Gu CH, Zhao C, Hofstaedter C, Tebas P, Glaser L, Baldassano R, Bittinger K, Mattei LM, Bushman FD. Investigating hospital Mycobacterium chelonae infection using whole genome sequencing and hybrid assembly. PLoS One 2020; 15:e0236533. [PMID: 33166284 PMCID: PMC7652343 DOI: 10.1371/journal.pone.0236533] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 07/03/2020] [Accepted: 10/20/2020] [Indexed: 11/21/2022] Open
Abstract
Mycobacterium chelonae is a rapidly growing nontuberculous mycobacterium that is a common cause of nosocomial infections. Here we describe investigation of a possible nosocomial transmission of M. chelonae at the Hospital of the University of Pennsylvania (HUP). M. chelonae strains with similar high-level antibiotic resistance patterns were isolated from two patients who developed post-operative infections at HUP in 2017, suggesting a possible point source infection. The isolates, along with other clinical isolates from other patients, were sequenced using the Illumina and Oxford Nanopore technologies. The resulting short and long reads were hybrid assembled into draft genomes. The genomes were compared by quantifying single nucleotide variants in the core genome and assessed using a control dataset to quantify error rates in comparisons of identical genomes. We show that all M. chelonae isolates tested were highly dissimilar, as indicated by high pairwise SNV values, consistent with environmental acquisition and not a nosocomial point source. Our control dataset determined a threshold for evaluating identity between strains while controlling for sequencing error. Finally, antibiotic resistance genes were predicted for our isolates, and several single nucleotide variants were identified that have the potential to modulated drug resistance.
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Affiliation(s)
- Christopher H. Gu
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Chunyu Zhao
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Casey Hofstaedter
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Pablo Tebas
- Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Laurel Glaser
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Robert Baldassano
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Lisa M. Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
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8
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Bushman FD, Conrad M, Ren Y, Zhao C, Gu C, Petucci C, Kim MS, Abbas A, Downes KJ, Devas N, Mattei LM, Breton J, Kelsen J, Marakos S, Galgano A, Kachelries K, Erlichman J, Hart JL, Moraskie M, Kim D, Zhang H, Hofstaedter CE, Wu GD, Lewis JD, Zackular JP, Li H, Bittinger K, Baldassano R. Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease. Cell Host Microbe 2020; 28:422-433.e7. [PMID: 32822584 DOI: 10.1016/j.chom.2020.07.020] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [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: 08/28/2019] [Revised: 06/09/2020] [Accepted: 07/28/2020] [Indexed: 12/21/2022]
Abstract
Children with inflammatory bowel diseases (IBD) are particularly vulnerable to infection with Clostridioides difficile (CDI). IBD and IBD + CDI have overlapping symptoms but respond to distinctive treatments, highlighting the need for diagnostic biomarkers. Here, we studied pediatric patients with IBD and IBD + CDI, comparing longitudinal data on the gut microbiome, metabolome, and other measures. The microbiome is dysbiotic and heterogeneous in both disease states, but the metabolome reveals disease-specific patterns. The IBD group shows increased concentrations of markers of inflammation and tissue damage compared with healthy controls, and metabolic changes associate with susceptibility to CDI. In IBD + CDI, we detect both metabolites associated with inflammation/tissue damage and fermentation products produced by C. difficile. The most discriminating metabolite found is isocaproyltaurine, a covalent conjugate of a distinctive C. difficile fermentation product (isocaproate) and an amino acid associated with tissue damage (taurine), which may be useful as a joint marker of the two disease processes.
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Affiliation(s)
- Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Maire Conrad
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yue Ren
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chunyu Zhao
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Christopher Gu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher Petucci
- Metabolomics Core, Cardiovascular Institute, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Min-Soo Kim
- Metabolomics Core, Cardiovascular Institute, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Arwa Abbas
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kevin J Downes
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nina Devas
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lisa M Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jessica Breton
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Judith Kelsen
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah Marakos
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alissa Galgano
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kelly Kachelries
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jessi Erlichman
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jessica L Hart
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Michael Moraskie
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Dorothy Kim
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Huanjia Zhang
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Casey E Hofstaedter
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Gary D Wu
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James D Lewis
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joseph P Zackular
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hongzhe Li
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Robert Baldassano
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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9
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Mahalak KK, Firrman J, Lee JJ, Bittinger K, Nuñez A, Mattei LM, Zhang H, Fett B, Bobokalonov J, Arango-Argoty G, Zhang L, Zhang G, Liu LS. Triclosan has a robust, yet reversible impact on human gut microbial composition in vitro. PLoS One 2020; 15:e0234046. [PMID: 32585680 PMCID: PMC7316517 DOI: 10.1371/journal.pone.0234046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 12/13/2019] [Accepted: 05/17/2020] [Indexed: 12/17/2022] Open
Abstract
The recent ban of the antimicrobial compound triclosan from use in consumer soaps followed research that showcased the risk it poses to the environment and to human health. Triclosan has been found in human plasma, urine and milk, demonstrating that it is present in human tissues. Previous work has also demonstrated that consumption of triclosan disrupts the gut microbial community of mice and zebrafish. Due to the widespread use of triclosan and ubiquity in the environment, it is imperative to understand the impact this chemical has on the human body and its symbiotic resident microbes. To that end, this study is the first to explore how triclosan impacts the human gut microbial community in vitro both during and after treatment. Through our in vitro system simulating three regions of the human gut; the ascending colon, transverse colon, and descending colon regions, we found that treatment with triclosan significantly impacted the community structure in terms of reduced population, diversity, and metabolite production, most notably in the ascending colon region. Given a 2 week recovery period, most of the population levels, community structure, and diversity levels were recovered for all colon regions. Our results demonstrate that the human gut microbial community diversity and population size is significantly impacted by triclosan at a high dose in vitro, and that the community is recoverable within this system.
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Affiliation(s)
- Karley K. Mahalak
- United States Department of Agriculture, Dairy and Functional Foods Research Unit, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, United States of America
| | - Jenni Firrman
- United States Department of Agriculture, Dairy and Functional Foods Research Unit, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, United States of America
| | - Jung-Jin Lee
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Alberto Nuñez
- United States Department of Agriculture, Dairy and Functional Foods Research Unit, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, United States of America
| | - Lisa M. Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Huanjia Zhang
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Bryton Fett
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Jamshed Bobokalonov
- United States Department of Agriculture, Dairy and Functional Foods Research Unit, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, United States of America
| | - Gustavo Arango-Argoty
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Guodong Zhang
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, United States of America
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Lin Shu Liu
- United States Department of Agriculture, Dairy and Functional Foods Research Unit, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, United States of America
- * E-mail:
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10
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Tang AT, Sullivan KR, Hong CC, Goddard LM, Mahadevan A, Ren A, Pardo H, Peiper A, Griffin E, Tanes C, Mattei LM, Yang J, Li L, Mericko-Ishizuka P, Shen L, Hobson N, Girard R, Lightle R, Moore T, Shenkar R, Polster SP, Rödel CJ, Li N, Zhu Q, Whitehead KJ, Zheng X, Akers A, Morrison L, Kim H, Bittinger K, Lengner CJ, Schwaninger M, Velcich A, Augenlicht L, Abdelilah-Seyfried S, Min W, Marchuk DA, Awad IA, Kahn ML. Distinct cellular roles for PDCD10 define a gut-brain axis in cerebral cavernous malformation. Sci Transl Med 2019; 11:eaaw3521. [PMID: 31776290 PMCID: PMC6937779 DOI: 10.1126/scitranslmed.aaw3521] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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: 12/14/2018] [Revised: 07/17/2019] [Accepted: 10/09/2019] [Indexed: 12/11/2022]
Abstract
Cerebral cavernous malformation (CCM) is a genetic, cerebrovascular disease. Familial CCM is caused by genetic mutations in KRIT1, CCM2, or PDCD10 Disease onset is earlier and more severe in individuals with PDCD10 mutations. Recent studies have shown that lesions arise from excess mitogen-activated protein kinase kinase kinase 3 (MEKK3) signaling downstream of Toll-like receptor 4 (TLR4) stimulation by lipopolysaccharide derived from the gut microbiome. These findings suggest a gut-brain CCM disease axis but fail to define it or explain the poor prognosis of patients with PDCD10 mutations. Here, we demonstrate that the gut barrier is a primary determinant of CCM disease course, independent of microbiome configuration, that explains the increased severity of CCM disease associated with PDCD10 deficiency. Chemical disruption of the gut barrier with dextran sulfate sodium augments CCM formation in a mouse model, as does genetic loss of Pdcd10, but not Krit1, in gut epithelial cells. Loss of gut epithelial Pdcd10 results in disruption of the colonic mucosal barrier. Accordingly, loss of Mucin-2 or exposure to dietary emulsifiers that reduce the mucus barrier increases CCM burden analogous to loss of Pdcd10 in the gut epithelium. Last, we show that treatment with dexamethasone potently inhibits CCM formation in mice because of the combined effect of action at both brain endothelial cells and gut epithelial cells. These studies define a gut-brain disease axis in an experimental model of CCM in which a single gene is required for two critical components: gut epithelial function and brain endothelial signaling.
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Affiliation(s)
- Alan T Tang
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Katie R Sullivan
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Courtney C Hong
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Lauren M Goddard
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Aparna Mahadevan
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Aileen Ren
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Heidy Pardo
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Amy Peiper
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Erin Griffin
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lisa M Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jisheng Yang
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Li Li
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Patricia Mericko-Ishizuka
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Le Shen
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, University of Chicago School of Medicine and Biological Sciences, Chicago, IL 60637, USA
| | - Nicholas Hobson
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, University of Chicago School of Medicine and Biological Sciences, Chicago, IL 60637, USA
| | - Romuald Girard
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, University of Chicago School of Medicine and Biological Sciences, Chicago, IL 60637, USA
| | - Rhonda Lightle
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, University of Chicago School of Medicine and Biological Sciences, Chicago, IL 60637, USA
| | - Thomas Moore
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, University of Chicago School of Medicine and Biological Sciences, Chicago, IL 60637, USA
| | - Robert Shenkar
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, University of Chicago School of Medicine and Biological Sciences, Chicago, IL 60637, USA
| | - Sean P Polster
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, University of Chicago School of Medicine and Biological Sciences, Chicago, IL 60637, USA
| | - Claudia J Rödel
- Institute for Biochemistry and Biology, Department of Animal Physiology, Potsdam University, Karl-Liebknecht-Str. 24-25, Haus 26, 14476 Potsdam, Germany
| | - Ning Li
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qin Zhu
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kevin J Whitehead
- Division of Cardiovascular Medicine and the Program in Molecular Medicine, University of Utah, Salt Lake City, UT 84112, USA
| | - Xiangjian Zheng
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
- Centenary Institute, Sydney Medical School, University of Sydney, Sydney, NSW 2050, Australia
| | - Amy Akers
- Angioma Alliance, Norfolk, VA 23517, USA
| | - Leslie Morrison
- Department of Neurology and Pediatrics, University of New Mexico, Albuquerque, NM 87106, USA
| | - Helen Kim
- Center for Cerebrovascular Research, Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Christopher J Lengner
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Markus Schwaninger
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, 23562 Lübeck, Germany
| | - Anna Velcich
- Department of Cell Biology, Albert Einstein College of Medicine/Albert Einstein Cancer Center, NY 10461, USA
| | - Leonard Augenlicht
- Department of Cell Biology, Albert Einstein College of Medicine/Albert Einstein Cancer Center, NY 10461, USA
| | - Salim Abdelilah-Seyfried
- Institute for Biochemistry and Biology, Department of Animal Physiology, Potsdam University, Karl-Liebknecht-Str. 24-25, Haus 26, 14476 Potsdam, Germany
- Institute of Molecular Biology, Hannover Medical School, Carl-Neuberg Str. 1, D-30625 Hannover, Germany
| | - Wang Min
- Department of Pathology and the Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Douglas A Marchuk
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Issam A Awad
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, University of Chicago School of Medicine and Biological Sciences, Chicago, IL 60637, USA
| | - Mark L Kahn
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA.
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11
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Shi Z, Zou J, Zhang Z, Zhao X, Noriega J, Zhang B, Zhao C, Ingle H, Bittinger K, Mattei LM, Pruijssers AJ, Plemper RK, Nice TJ, Baldridge MT, Dermody TS, Chassaing B, Gewirtz AT. Segmented Filamentous Bacteria Prevent and Cure Rotavirus Infection. Cell 2019; 179:644-658.e13. [PMID: 31607511 PMCID: PMC7525827 DOI: 10.1016/j.cell.2019.09.028] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [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: 11/15/2018] [Revised: 05/23/2019] [Accepted: 09/23/2019] [Indexed: 12/21/2022]
Abstract
Rotavirus (RV) encounters intestinal epithelial cells amidst diverse microbiota, opening possibilities of microbes influencing RV infection. Although RV clearance typically requires adaptive immunity, we unintentionally generated RV-resistant immunodeficient mice, which, we hypothesized, reflected select microbes protecting against RV. Accordingly, such RV resistance was transferred by co-housing and fecal transplant. RV-protecting microbiota were interrogated by heat, filtration, and antimicrobial agents, followed by limiting dilution transplant to germ-free mice and microbiome analysis. This approach revealed that segmented filamentous bacteria (SFB) were sufficient to protect mice against RV infection and associated diarrhea. Such protection was independent of previously defined RV-impeding factors, including interferon, IL-17, and IL-22. Colonization of the ileum by SFB induced changes in host gene expression and accelerated epithelial cell turnover. Incubation of RV with SFB-containing feces reduced infectivity in vitro, suggesting direct neutralization of RV. Thus, independent of immune cells, SFB confer protection against certain enteric viral infections and associated diarrheal disease.
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Affiliation(s)
- Zhenda Shi
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Jun Zou
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Zhan Zhang
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Xu Zhao
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Juan Noriega
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Benyue Zhang
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Chunyu Zhao
- Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Harshad Ingle
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kyle Bittinger
- Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lisa M Mattei
- Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Andrea J Pruijssers
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Richard K Plemper
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Timothy J Nice
- Department of Microbiology and Immunology, Oregon Health Sciences University, Portland, OR, USA
| | - Megan T Baldridge
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Terence S Dermody
- Department of Pediatrics, University of Pittsburgh School of Medicine and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Benoit Chassaing
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA; Neuroscience Institute, GSU, Atlanta, GA, USA
| | - Andrew T Gewirtz
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA.
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12
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Yardeni T, Tanes CE, Bittinger K, Mattei LM, Schaefer PM, Singh LN, Wu GD, Murdock DG, Wallace DC. Host mitochondria influence gut microbiome diversity: A role for ROS. Sci Signal 2019; 12:12/588/eaaw3159. [PMID: 31266851 DOI: 10.1126/scisignal.aaw3159] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Changes in the gut microbiota and the mitochondrial genome are both linked with the development of disease. To investigate why, we examined the gut microbiota of mice harboring various mutations in genes that alter mitochondrial function. These studies revealed that mitochondrial genetic variations altered the composition of the gut microbiota community. In cross-fostering studies, we found that although the initial microbiota community of newborn mice was that obtained from the nursing mother, the microbiota community progressed toward that characteristic of the microbiome of unfostered pups of the same genotype within 2 months. Analysis of the mitochondrial DNA variants associated with altered gut microbiota suggested that microbiome species diversity correlated with host reactive oxygen species (ROS) production. To determine whether the abundance of ROS could alter the gut microbiota, mice were aged, treated with N-acetylcysteine, or engineered to express the ROS scavenger catalase specifically within the mitochondria. All three conditions altered the microbiota from that initially established. Thus, these data suggest that the mitochondrial genotype modulates both ROS production and the species diversity of the gut microbiome, implying that the connection between the gut microbiome and common disease phenotypes might be due to underlying changes in mitochondrial function.
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Affiliation(s)
- Tal Yardeni
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ceylan E Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lisa M Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Patrick M Schaefer
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Larry N Singh
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Gary D Wu
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Deborah G Murdock
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pediatrics, Division of Human Genetics and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
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13
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Leiby JS, McCormick K, Sherrill-Mix S, Clarke EL, Kessler LR, Taylor LJ, Hofstaedter CE, Roche AM, Mattei LM, Bittinger K, Elovitz MA, Leite R, Parry S, Bushman FD. Lack of detection of a human placenta microbiome in samples from preterm and term deliveries. Microbiome 2018; 6:196. [PMID: 30376898 PMCID: PMC6208038 DOI: 10.1186/s40168-018-0575-4] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 10/10/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Historically, the human womb has been thought to be sterile in healthy pregnancies, but this idea has been challenged by recent studies using DNA sequence-based methods, which have suggested that the womb is colonized with bacteria. For example, analysis of DNA from placenta samples yielded small proportions of microbial sequences which were proposed to represent normal bacterial colonization. However, an analysis by our group showed no distinction between background negative controls and placenta samples. Also supporting the idea that the womb is sterile is the observation that germ-free mammals can be generated by sterile delivery of neonates into a sterile isolator, after which neonates remain germ-free, which would seem to provide strong data in support of sterility of the womb. RESULTS To probe this further and to investigate possible placental colonization associated with spontaneous preterm birth, we carried out another study comparing microbiota in placenta samples from 20 term and 20 spontaneous preterm deliveries. Both 16S rRNA marker gene sequencing and shotgun metagenomic sequencing were used to characterize placenta and control samples. We first quantified absolute amounts of bacterial 16S rRNA gene sequences using 16S rRNA gene quantitative PCR (qPCR). As in our previous study, levels were found to be low in the placenta samples and indistinguishable from negative controls. Analysis by DNA sequencing did not yield a placenta microbiome distinct from negative controls, either using marker gene sequencing as in our previous work, or with shotgun metagenomic sequencing. Several types of artifacts, including erroneous read classifications and barcode misattribution, needed to be identified and removed from the data to clarify this point. CONCLUSIONS Our findings do not support the existence of a consistent placental microbiome, in either placenta from term deliveries or spontaneous preterm births.
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Affiliation(s)
- Jacob S Leiby
- Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Kevin McCormick
- Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Erik L Clarke
- Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Lyanna R Kessler
- Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Louis J Taylor
- Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Casey E Hofstaedter
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Aoife M Roche
- Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Lisa M Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Michal A Elovitz
- Maternal and Child Health Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania School of Medicine, 3400 Spruce Street, Philadelphia, PA, 19104, USA
| | - Rita Leite
- Maternal and Child Health Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania School of Medicine, 3400 Spruce Street, Philadelphia, PA, 19104, USA
| | - Samuel Parry
- Maternal and Child Health Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania School of Medicine, 3400 Spruce Street, Philadelphia, PA, 19104, USA.
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA.
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14
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Etienne-Mesmin L, Chassaing B, Adekunle O, Mattei LM, Bushman FD, Gewirtz AT. Toxin-positive Clostridium difficile latently infect mouse colonies and protect against highly pathogenic C. difficile. Gut 2018; 67:860-871. [PMID: 28219893 PMCID: PMC5941301 DOI: 10.1136/gutjnl-2016-313510] [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] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/26/2017] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Clostridium difficile is a toxin-producing bacterium and a leading cause of antibiotic-associated disease. The ability of C. difficile to form spores and infect antibiotic-treated persons at low multiplicity of infection (MOI) underlies its large disease burden. However, C. difficile-induced disease might also result from long-harboured C. difficile that blooms in individuals administered antibiotics. DESIGN Mice purchased from multiple vendors and repeatedly testing negative for this pathogen by quantitative PCR bloomed C. difficile following antibiotic treatment. This endogenous C. difficile strain, herein termed LEM1, which formed spores and produced toxin, was compared with highly pathogenic C. difficile strain VPI10463. RESULTS Whole-genome sequencing revealed that LEM1 and VPI10463 shared 95% of their genes, including all known virulence genes. In contrast to VPI10463, LEM1 did not induce overt disease when administered to antibiotic-treated or germ-free mice, even at high doses. Rather, blooms of LEM1 correlated with survival following VPI10463 inoculation, and exogenous administration of LEM1 before or shortly following VPI10463 inoculation prevented C. difficile-induced death. Accordingly, despite similar growth properties in vitro, LEM1 strongly outcompeted VPI10463 in mice even at 100-fold lower inocula. CONCLUSIONS These results highlight the difficulty of determining whether individual cases of C. difficile infection resulted from a bloom of endogenous C. difficile or a new exposure to this pathogen. In addition to impacting the design of studies using mouse models of C. difficile-induced disease, this study identified, isolated and characterised an endogenous murine spore-forming C. difficile strain able to decrease colonisation, associated disease and death induced by a pathogenic C. difficile strain.
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Affiliation(s)
- Lucie Etienne-Mesmin
- Center for Inflammation Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, USA
| | - Benoit Chassaing
- Center for Inflammation Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, USA
| | - Oluwaseyi Adekunle
- Immunology and Molecular Pathogenesis Graduate Program, Emory University, Atlanta, Georgia, USA
| | - Lisa M. Mattei
- PennCHOP Microbiome, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Andrew T. Gewirtz
- Center for Inflammation Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, USA.,Corresponding author: Andrew T. Gewirtz, PhD, Center for Inflammation, Immunity, and Infection, Georgia State University, Atlanta GA 30303, , Ph: 404-413-3586
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15
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Tanner K, Dromey C, Berardi ML, Mattei LM, Pierce JL, Wisco JJ, Hunter EJ, Smith ME. Effects of voice-sparing cricotracheal resection on phonation in women. Laryngoscope 2016; 127:2085-2092. [PMID: 27882558 DOI: 10.1002/lary.26429] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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: 04/29/2016] [Revised: 08/30/2016] [Accepted: 10/10/2016] [Indexed: 11/08/2022]
Abstract
INTRODUCTION Individuals with idiopathic subglottic stenosis (SGS) are at risk for voice disorders prior to and following surgical management. This study examined the nature and severity of voice disorders in patients with SGS before and after a revised cricotracheal resection (CTR) procedure designed to minimize adverse effects on voice function. METHOD Eleven women with idiopathic SGS provided presurgical and postsurgical audio recordings. Voice Handicap Index (VHI) scores were also collected. Cepstral, signal-to-noise, periodicity, and fundamental frequency (F0 ) analyses were undertaken for connected speech and sustained vowel samples. Listeners made auditory-perceptual ratings of overall quality and monotonicity. RESULTS Paired samples statistical analyses revealed that mean F0 decreased from 215 Hz (standard deviation [SD] = 40 Hz) to 201 Hz (SD = 65 Hz) following surgery. In general, VHI scores decreased after surgery. Voice disorder severity based on the Cepstral Spectral Index of Dysphonia (KayPentax, Montvale, NJ) for sustained vowels decreased (improved) from 41 (SD = 41) to 25 (SD = 21) points; no change was observed for connected speech. Semitone SD (2.2 semitones) did not change from pre- to posttreatment. Auditory-perceptual ratings demonstrated similar results. CONCLUSION These preliminary results indicate that this revised CTR procedure is promising in minimizing adverse voice effects while offering a longer-term surgical outcome for SGS. Further research is needed to determine causal factors for pretreatment voice disorders, as well as to optimize treatments in this population. LEVEL OF EVIDENCE 4. Laryngoscope, 127:2085-2092, 2017.
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Affiliation(s)
- Kristine Tanner
- Department of Communication Disorders, Brigham Young University, Provo, Utah, U.S.A
| | - Christopher Dromey
- Department of Communication Disorders, Brigham Young University, Provo, Utah, U.S.A
| | - Mark L Berardi
- the Department of Physics and Astronomy, Brigham Young University, Provo, Utah, U.S.A
| | - Lisa M Mattei
- Department of Communication Disorders, Brigham Young University, Provo, Utah, U.S.A
| | - Jenny L Pierce
- Department of Communication Sciences and Disorders, University of Utah, Salt Lake City, Utah, U.S.A
| | - Jonathan J Wisco
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, Utah, U.S.A
| | - Eric J Hunter
- Department of Communicative Sciences and Disorders, Michigan State University, East Lansing, Michigan, U.S.A
| | - Marshall E Smith
- Division of Otolaryngology, Head and Neck Surgery, The University of Utah School of Medicine, Salt Lake City, Utah, U.S.A
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16
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Mattei LM, Cotmore SF, Tattersall P, Iwasaki A. Parvovirus evades interferon-dependent viral control in primary mouse embryonic fibroblasts. Virology 2013; 442:20-7. [PMID: 23676303 DOI: 10.1016/j.virol.2013.03.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 03/01/2013] [Accepted: 03/21/2013] [Indexed: 12/24/2022]
Abstract
Engagement of innate viral sensors elicits a robust antiviral program via the induction of type I interferons (IFNs). Innate defense mechanisms against ssDNA viruses are not well defined. Here, we examine type I IFN induction and effectiveness in controlling a ssDNA virus. Using mouse embryonic fibroblasts (MEFs), we found that a murine parvovirus, minute virus of mice (MVMp), induced a delayed but significant IFN response. MEFs deficient in mitochondrial antiviral signaling protein (MAVS) mounted a wild-type IFN response to MVMp infection, indicating that RIG-I-dependent RNA intermediate recognition is not required for innate sensing of this virus. However, MVMp-induced IFNs, as well recombinant type I IFNs, were unable to inhibit viral replication. Finally, MVMp infected cells became unresponsive to Poly (I:C) stimulation. Together, these data suggest that the MVMp efficiently evades antiviral immune mechanisms imposed by type I IFNs, which may in part explain their efficient transmission between mice.
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Affiliation(s)
- Lisa M Mattei
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA
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17
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Lindsay RWB, Darrah PA, Quinn KM, Wille-Reece U, Mattei LM, Iwasaki A, Kasturi SP, Pulendran B, Gall JGD, Spies AG, Seder RA. CD8+ T cell responses following replication-defective adenovirus serotype 5 immunization are dependent on CD11c+ dendritic cells but show redundancy in their requirement of TLR and nucleotide-binding oligomerization domain-like receptor signaling. J Immunol 2010; 185:1513-21. [PMID: 20610651 DOI: 10.4049/jimmunol.1000338] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Replication-defective adenovirus serotype 5 (rAd5) is the most potent recombinant vector for eliciting CD8 T cell responses in humans. In this study, the innate mechanisms that influence T cell responses following rAd5 immunization were assessed in mice. Using rAd5 expressing enhanced GFP (eGFP-rAd5), we show that rAd5 transfects CD11c(+) dendritic cells (DCs) in draining lymph nodes in vivo following s.c. or i.m. immunization. Among distinct DC subsets, eGFP expression was highest in CD11c(+)CD8(-)B220(-) with a lower frequency detected in CD11c(+)CD8(+)B220(-) and CD11c(+)B220(+) plasmacytoid DCs. CD11c(+) DCs but not CD11c(-) cells from mice immunized with rAd5 encoding the SIINFEKL peptide induced proliferation of naive OT-I CD8 T cells. Furthermore, CD11c(+)CD8(+)B220(-) was the most potent DC subset for eliciting naive OT-I CD8 T cell proliferation. Of note, mice with pre-existing immunity to rAd5 had a substantial decrease in eGFP expression in DCs, which was associated with approximately 2-fold decrease in Th1 and complete inhibition of CD8 responses. Thus, pre-existing rAd5 immunity has a greater influence on CD8 compared with CD4 T cell responses. In terms of how innate cytokines and signaling pathways influenced T cell immunity following rAd5 immunization, we show that the magnitude and quality of CD8 T cell responses are partially dependent on MyD88 but independent of IL-12, type I IFN, apoptosis-associated speck-like protein, nucleotide-binding oligomerization domain-like receptor protein 3, and IL-1. Taken together, these data demonstrate a critical role for CD11c(+) DCs for CD8 responses but striking redundancy for innate cytokines and signaling by TLR and nucleotide-binding oligomerization domain-like receptor pathways.
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Affiliation(s)
- Ross W B Lindsay
- Cellular Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD 20892, USA
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Lee HK, Mattei LM, Steinberg BE, Alberts P, Lee YH, Chervonsky A, Mizushima N, Grinstein S, Iwasaki A. In vivo requirement for Atg5 in antigen presentation by dendritic cells. Immunity 2010; 32:227-39. [PMID: 20171125 DOI: 10.1016/j.immuni.2009.12.006] [Citation(s) in RCA: 374] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 10/09/2009] [Accepted: 12/10/2009] [Indexed: 12/24/2022]
Abstract
Autophagy is known to be important in presentation of cytosolic antigens on MHC class II (MHC II). However, the role of autophagic process in antigen presentation in vivo is unclear. Mice with dendritic cell (DC)-conditional deletion in Atg5, a key autophagy gene, showed impaired CD4(+) T cell priming after herpes simplex virus infection and succumbed to rapid disease. The most pronounced defect of Atg5(-/-) DCs was the processing and presentation of phagocytosed antigens containing Toll-like receptor stimuli for MHC class II. In contrast, cross-presentation of peptides on MHC I was intact in the absence of Atg5. Although induction of metabolic autophagy did not enhance MHC II presentation, autophagic machinery was required for optimal phagosome-to-lysosome fusion and subsequent processing of antigen for MHC II loading. Thus, our study revealed that DCs utilize autophagic machinery to optimally process and present extracellular microbial antigens for MHC II presentation.
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Affiliation(s)
- Heung Kyu Lee
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
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Sánchez MD, Pierson TC, Degrace MM, Mattei LM, Hanna SL, Del Piero F, Doms RW. The neutralizing antibody response against West Nile virus in naturally infected horses. Virology 2006; 359:336-48. [PMID: 17055550 DOI: 10.1016/j.virol.2006.08.047] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [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: 05/31/2006] [Revised: 07/21/2006] [Accepted: 08/29/2006] [Indexed: 11/22/2022]
Abstract
A major neutralizing epitope (here referred to as the T332 epitope) located on the lateral surface of domain III (DIII) of the West Nile virus (WNV) envelope protein has been identified based on the analysis of murine monoclonal antibodies. However, little is known about the humoral immune response against WNV in a natural host or whether DIII in general or the T332 epitope in particular are important targets of neutralizing antibodies in vivo. To characterize the types of antibodies produced during infection with WNV, we studied a group of naturally infected horses. Using immune adsorption assays coupled with the use of virus particles bearing mutations in the T332 epitope, we found that in some animals neutralizing activity against DIII and the T332 epitope was below the limit of detection. In contrast, some animals generated a significant fraction of neutralizing activity to DIII and the T332 epitope. Thus, while antibodies to the T332 epitope did not represent a significant fraction of the total antibody response in the infected animals studied, in some horses, they comprised a significant fraction of neutralizing activity, making this an important but far from dominant neutralizing epitope. Rather, the neutralizing response to WNV generated in infected horses is both variable and polyclonal in nature, with epitopes within and outside of DIII playing important roles.
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Affiliation(s)
- Melissa D Sánchez
- Department of Microbiology, University of Pennsylvania, 225 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA 19104, USA
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Davis CW, Mattei LM, Nguyen HY, Ansarah-Sobrinho C, Doms RW, Pierson TC. The location of asparagine-linked glycans on West Nile virions controls their interactions with CD209 (dendritic cell-specific ICAM-3 grabbing nonintegrin). J Biol Chem 2006; 281:37183-94. [PMID: 17001080 DOI: 10.1074/jbc.m605429200] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [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] [Indexed: 11/06/2022] Open
Abstract
Mammalian cell-derived West Nile virus preferentially infects cells expressing the C-type lectin CD209L (dendritic cellspecific ICAM-3 grabbing nonintegrin-related protein; liver- and lymph node-specific ICAM-3 grabbing nonintegrin) but not cells expressing CD209 (dendritic cell-specific ICAM-3 grabbing nonintegrin). In contrast, Dengue virus infection is enhanced in cells expressing either attachment factor. The West Nile virus envelope (E) protein contains a single N-linked glycosylation site at residue 154, whereas Dengue virus E contains sites at residues 153 and 67. We introduced a glycosylation site at position 67 into West Nile virus E. Reporter virus particles pseudotyped with this E protein infected cells using either CD209 or CD209L. We also introduced glycosylation sites at several novel positions. All sites allowed CD209L-mediated infection, but only a subset promoted CD209 use. As seen for other viruses, mannose-rich glycans on West Nile virus were required for its interactions with CD209. Surprisingly, however, mannose-rich glycans were not required for CD209L-mediated infection. Complex glycans, particularly N-acetylglucosamine-terminated structures, were able to mediate reporter virus particle interactions with CD209L. We propose that CD209L recognizes glycosylated flaviviruses with broad specificity, whereas CD209 is selective for flaviviruses bearing mannose-rich glycans. The location of the N-linked glycosylation sites on a virion determines the types of glycans incorporated, thus controlling viral tropism for CD209-expressing cells.
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Affiliation(s)
- Carl W Davis
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
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