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Scheible K, Beblavy R, Sohn MB, Qui X, Gill AL, Narvaez-Miranda J, Brunner J, Miller RK, Barrett ES, O’Connor TG, Gill SR. Affective Symptoms in Pregnancy are Associated with the Vaginal Microbiome. bioRxiv 2024:2024.04.12.589254. [PMID: 38645042 PMCID: PMC11030453 DOI: 10.1101/2024.04.12.589254] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Composition of the vaginal microbiome in pregnancy is associated with adverse maternal, obstetric, and child health outcomes. Identifying the sources of individual differences in the vaginal microbiome is therefore of considerable clinical and public health interest. The current study tested the hypothesis that vaginal microbiome composition during pregnancy is associated with an individual's experience of affective symptoms and stress exposure. Data were based on a prospective longitudinal study of a diverse and medically healthy community sample of 275 mother-infant pairs. Affective symptoms and stress exposure and select measures of associated biomarkers (diurnal salivary cortisol, serum measures of sex hormones) were collected at each trimester; self-report, clinical, and medical records were used to collect detailed data on socio-demographic factors and health behavior, including diet and sleep. Vaginal microbiome samples were collected in the third trimester (34-40 weeks) and characterized by 16S rRNA sequencing. Identified taxa were clustered into three community state types (CST1-3) based on dissimilarity of vaginal microbiota composition. Results indicate that depressive symptoms during pregnancy were reliably associated with individual taxa and CST3 in the third trimester. Prediction of functional potential from 16S taxonomy revealed a differential abundance of metabolic pathways in CST1-3 and individual taxa, including biosynthetic pathways for the neuroactive metabolites, serotonin and dopamine. With the exception of bioavailable testosterone, no significant associations were found between symptoms- and stress-related biomarkers and CSTs. Our results provide further evidence of how prenatal psychological distress during pregnancy alters the maternal-fetal microbiome ecosystem that may be important for understanding maternal and child health outcomes.
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Affiliation(s)
- Kristin Scheible
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Robert Beblavy
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Michael B. Sohn
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Xing Qui
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Ann L. Gill
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Janiret Narvaez-Miranda
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Jessica Brunner
- Department of Obstetrics and Gynecology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Richard K. Miller
- Department of Obstetrics and Gynecology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Emily S. Barrett
- Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey, USA
- Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, New Jersey, USA
| | - Tom G. O’Connor
- Department of Psychiatry, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Department of Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Wynne Center for Family Research, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Steven R. Gill
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
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Kopycka-Kedzierawski DT, Feng C, Billings RJ, Watson GE, Ragusa PG, Flint K, Wong CL, Gill SR, Manning S, O'Connor TG. Psychosocial Risk Exposure Limits Routine Pediatric Oral Health Care. AJPM Focus 2024; 3:100191. [PMID: 38357551 PMCID: PMC10864889 DOI: 10.1016/j.focus.2024.100191] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Introduction This study aimed to identify social, psychological, and contextual factors that influenced attendance at routine oral health visits in a cohort of 189 preschool children who were followed over a 2-year period. Methods Generalized estimating equation was used to examine the association between clinic attendance and the predictors. ORs and 95% CIs were reported in the multiple logistic regression models. The study was conducted in Rochester, New York, between February 2016 and February 2021. Results Prior to the COVID-19 pandemic declaration, the rate of canceled and no-show appointments was greater for routine clinic visits (20% and 24%, respectively) than for research visits (14% and 9%, respectively) for the same participants; these rates increased during the pandemic. After adjusting for sociodemographic factors, the likelihood of a canceled or no-show appointment was associated with parental depression (OR=1.06, CI=1.03, 1.09), regardless of the type or occurrence of the visit. Conclusions Findings from this study demonstrate that attendance to oral health care in young children is reliably reduced with parental depression and that this may provide one mechanism for early emerging health inequalities of oral health.
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Affiliation(s)
| | - Changyong Feng
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, New York
- Department of Anesthesiology and Perioperative Medicine, University of Rochester, Rochester, New York
| | - Ronald J. Billings
- Department of Dentistry, Eastman Institute for Oral Health, University of Rochester, Rochester, New York
| | - Gene E. Watson
- Department of Dentistry, Eastman Institute for Oral Health, University of Rochester, Rochester, New York
- Department of Pharmacology & Physiology, University of Rochester, Rochester, New York
- Department of Environmental Medicine, University of Rochester, Rochester, New York
| | - Patricia G. Ragusa
- Department of Dentistry, Eastman Institute for Oral Health, University of Rochester, Rochester, New York
| | - Kimberly Flint
- Department of Dentistry, Eastman Institute for Oral Health, University of Rochester, Rochester, New York
| | - Cynthia L. Wong
- Department of Pediatric Dentistry, Eastman Institute for Oral Health, University of Rochester, Rochester, New York
- Department of Pediatrics, Eastman Institute for Oral Health, University of Rochester, Rochester, New York
| | - Steven R. Gill
- Department of Pediatric Dentistry, Eastman Institute for Oral Health, University of Rochester, Rochester, New York
- Department of Pediatrics, Eastman Institute for Oral Health, University of Rochester, Rochester, New York
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York
| | - Samantha Manning
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, New York
| | - Thomas G. O'Connor
- Department of Psychiatry, University of Rochester, Rochester, New York
- Department of Psychology, University of Rochester, Rochester, New York
- Department of Neuroscience, University of Rochester, Rochester, New York
- Department of Obstetrics and Gynecology, University of Rochester, Rochester, New York
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Schwarz EM, Archer NK, Atkins GJ, Bentley KLDM, Botros M, Cassat JE, Chisari E, Coraça-Huber DC, Daiss JL, Gill SR, Goodman SB, Harro J, Hernandez CJ, Ivashkiv LB, Kates SL, Marques CNH, Masters EA, Muthukrishnan G, Owen JR, Raafat D, Saito M, Veis DJ, Xie C. The 2023 Orthopaedic Research Society's International Consensus Meeting on musculoskeletal infection: Summary from the host immunity section. J Orthop Res 2024; 42:518-530. [PMID: 38102985 DOI: 10.1002/jor.25758] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/18/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023]
Abstract
Musculoskeletal infections (MSKI), which are a major problem in orthopedics, occur when the pathogen eludes or overwhelms the host immune system. While effective vaccines and immunotherapies to prevent and treat MSKI should be possible, fundamental knowledge gaps in our understanding of protective, nonprotective, and pathogenic host immunity are prohibitive. We also lack critical knowledge of how host immunity is affected by the microbiome, implants, prior infection, nutrition, antibiotics, and concomitant therapies, autoimmunity, and other comorbidities. To define our current knowledge of these critical topics, a Host Immunity Section of the 2023 Orthopaedic Research Society MSKI International Consensus Meeting (ICM) proposed 78 questions. Systematic reviews were performed on 15 of these questions, upon which recommendations with level of evidence were voted on by the 72 ICM delegates, and another 12 questions were voted on with a recommendation of "Unknown" without systematic reviews. Two questions were transferred to another ICM Section, and the other 45 were tabled for future consideration due to limitations of available human resources. Here we report the results of the voting with internet access to the questions, recommendations, and rationale from the systematic reviews. Eighteen questions received a consensus vote of ≥90%, while nine recommendations failed to achieve this threshold. Commentary on why consensus was not achieved on these questions and potential ways forward are provided to stimulate specific funding mechanisms and research on these critical MSKI host defense questions.
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Affiliation(s)
- Edward M Schwarz
- Department of Orthopaedics, University of Rochester, Rochester, New York, USA
| | - Nathan K Archer
- Department of Dermatology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Gerald J Atkins
- Centre for Orthopaedic and Trauma Research, University of Adelaide, Adelaide, South Australia, Australia
| | - Karen L de Mesy Bentley
- Department of Orthopaedics and Pathology and Laboratory Medicine, University of Rochester, Rochester, New York, USA
| | - Mina Botros
- Department of Orthopaedics, University of Rochester, Rochester, New York, USA
| | - James E Cassat
- Departments of Pediatrics, Pathology, Microbiology, and Immunology, and Biomedical Engineering, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Emanuele Chisari
- Department of Adult Hip and Knee Joint Reconstruction, Rothman Orthopaedic Institute, Philadelphia, Pennsylvania, USA
| | - Débora C Coraça-Huber
- ResearchLaboratory for Implant Associated Infections (Biofilm Lab) - University Hospital for Orthopedics and Traumatology, Medical University of Innsbruck, Innsbruck, Austria
| | - John L Daiss
- Department of Orthopaedics, University of Rochester, Rochester, New York, USA
| | - Steven R Gill
- Department of Microbiology & Immunology, University of Rochester, Rochester, New York, USA
| | - Stuart B Goodman
- Department of Orthopaedic Surgery, Stanford University, Redwood City, California, USA
| | - Janette Harro
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, Maryland, USA
| | - Christopher J Hernandez
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, California, USA
| | - Lionel B Ivashkiv
- Department of Medicine and Immunology, Weill Cornell Medicine, Hospital for Special Surgery, New York, New York, USA
| | - Stephen L Kates
- Department of Orthopaedic Surgery, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Cláudia N H Marques
- Department of Biological Sciences, Binghamton Biofilm Research Center, Binghamton University, Binghamton, New York, USA
| | - Elysia A Masters
- Department of Biomedical Engineering, University of Rochester, Rochester, New York, USA
| | | | - John R Owen
- Department of Orthopaedic Surgery, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Dina Raafat
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
- Institute of Immunology, University Medicine Greifswald, Greifswald, Germany
| | - Motoo Saito
- Department of Orthopaedics, University of Rochester, Rochester, New York, USA
| | - Deborah J Veis
- Departments of Medicine, Pathology & Immunology, Washington University, St. Louis, Missouri, USA
| | - Chao Xie
- Department of Orthopaedics, University of Rochester, Rochester, New York, USA
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Xie C, Ren Y, Weeks J, Rainbolt J, Kenney HM, Xue T, Allen F, Shu Y, Tay AJH, Lekkala S, Yeh SCA, Muthukrishnan G, Gill AL, Gill SR, Kim M, Kates SL, Schwarz EM. Longitudinal intravital imaging of the bone marrow for analysis of the race for the surface in a murine osteomyelitis model. J Orthop Res 2024; 42:531-538. [PMID: 37812184 DOI: 10.1002/jor.25716] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/08/2023] [Accepted: 10/05/2023] [Indexed: 10/10/2023]
Abstract
Critical knowledge gaps of orthopedic infections pertain to bacterial colonization. The established dogma termed the Race for the Surface posits that contaminating bacteria compete with host cells for the implant post-op, which remains unproven without real-time in vivo evidence. Thus, we modified the murine longitudinal intravital imaging of the bone marrow (LIMB) system to allow real-time quantification of green fluorescent protein (GFP+) host cells and enhanced cyan fluorescent protein (ECFP+) or red fluorescent protein (RFP+) methicillin-resistant Staphylococcus aureus (MRSA) proximal to a transfemoral implant. Following inoculation with ~105 CFU, an L-shaped metal implant was press-fit through the lateral cortex at a 90° angle ~0.150 mm below a gradient refractive index (GRIN) lens. We empirically derived a volume of interest (VOI) = 0.0161 ± 0.000675 mm3 during each imaging session by aggregating the Z-stacks between the first (superior) and last (inferior) in-focus LIMB slice. LIMB postimplantation revealed very limited bacteria detection at 1 h, but by 3 h, 56.8% of the implant surface was covered by ECFP+ bacteria, and the rest were covered by GFP+ host cells. 3D volumetric rendering of the GFP+ and ECFP+ or RFP+ voxels demonstrated exponential MRSA growth between 3 and 6 h in the Z-plane, which was validated with cross-sectional ex vivo bacterial burden analyses demonstrating significant growth by ~2 × 104 CFU/h on the implant from 2 to 12 h post-op (p < 0.05; r2 > 0.98). Collectively, these results show the competition at the surface is completed by 3 h in this model and demonstrate the potential of LIMB to elucidate mechanisms of bacterial colonization, the host immune response, and the efficacy of antimicrobials.
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Affiliation(s)
- Chao Xie
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, New York, USA
- Department of Orthopaedics and Rehabilitation, University of Rochester Medical Center, Rochester, New York, USA
| | - Youliang Ren
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, New York, USA
- Department of Orthopaedics and Rehabilitation, University of Rochester Medical Center, Rochester, New York, USA
| | - Jason Weeks
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, New York, USA
- Department of Orthopaedics and Rehabilitation, University of Rochester Medical Center, Rochester, New York, USA
| | - Joshua Rainbolt
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, New York, USA
| | - Howard M Kenney
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, New York, USA
| | - Thomas Xue
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, New York, USA
| | - Faith Allen
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, New York, USA
| | - Ye Shu
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, New York, USA
| | - Allie J H Tay
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, New York, USA
| | - Sashank Lekkala
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, New York, USA
| | - Shu-Chi A Yeh
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, New York, USA
- Department of Orthopaedics and Rehabilitation, University of Rochester Medical Center, Rochester, New York, USA
| | - Gowrishankar Muthukrishnan
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, New York, USA
- Department of Orthopaedics and Rehabilitation, University of Rochester Medical Center, Rochester, New York, USA
| | - Ann L Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Steven R Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Minsoo Kim
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Stephen L Kates
- Department of Orthopaedic Surgery, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Edward M Schwarz
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, New York, USA
- Department of Orthopaedics and Rehabilitation, University of Rochester Medical Center, Rochester, New York, USA
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Stolarczyk A, Perez-Nazario N, Knowlden SA, Chinchilli E, Grier A, Paller A, Gill SR, De Benedetto A, Yoshida T, Beck LA. Bleach baths enhance skin barrier, reduce itch but do not normalize skin dysbiosis in atopic dermatitis. Arch Dermatol Res 2023; 315:2883-2892. [PMID: 37755506 PMCID: PMC10615920 DOI: 10.1007/s00403-023-02723-1] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/02/2023] [Accepted: 09/06/2023] [Indexed: 09/28/2023]
Abstract
Studies have demonstrated that bleach baths improve atopic dermatitis (AD) severity; however, the effects on itch, skin barrier, and cutaneous microbial composition are less clear. We examined whether bleach baths reduce itch, normalize skin barrier function, reduce S. aureus absolute abundance, and increase microbial diversity in adults with AD who were colonized with S. aureus on their non-lesional skin. This was an open label, non-randomized, controlled trial performed at a single academic center. Fifteen AD and five non-atopic healthy controls (NA) were instructed to take two bleach baths (0.005% NaClO; 5-10 min duration) per week for a total of 12 weeks as add-on therapy. Adults 18 to 65 years (inclusive) with mild to severe AD were recruited with EASI score > 6.0, S. aureus culture positivity, access to a bathtub, and ability and willingness to maintain current topical or systemic treatments. They were evaluated at baseline (before bleach baths), 6 weeks, and 12 weeks after the intervention of twice-weekly bleach baths. Efficacy measurements included EASI as well as 5-D Pruritus and ItchyQoL™. Transepidermal water loss (TEWL) and stratum corneum (SC) integrity assay were performed to assess the skin barrier. Skin dysbiosis was measured by S. aureus cultivation, S. aureus abundance (qPCR of thermonuclease gene), and V1-V3 16S rRNA gene sequencing on non-lesional and lesional AD skin. After 12 weeks of bleach baths, 8/15 (53.3%) AD subjects achieved an EASI50 and a significant reduction in itch as measured by 5-D pruritus and Itchy QoL. Eighty-seven percent reported improvements in sleep quality. At study entry, AD subjects had higher non-lesional TEWL values than NA subjects, and only AD subjects experienced a reduction with bleach baths (p = 0.006). Similarly, SC integrity improved as early as 6 weeks after bleach baths in AD subjects. Notably, bleach baths had no significant effect on S. aureus culture-positivity, qPCR absolute abundance, or microbial diversity. The addition of twice-weekly bleach baths improves investigator-assessed AD severity, patient-reported pruritus and sleep as well as physiological measures of skin barrier function in adult AD subjects while having no effect on qualitative and quantitative measures of cutaneous S. aureus. Trial Registration: ClinicalTrials.gov Identifier: NCT01996150, Date of registration: November 27th, 2013.
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Affiliation(s)
- Ania Stolarczyk
- Department of Dermatology, University of Rochester Medical Center, 601 Elmwood Ave, Box 697, Rochester, NY, 14642, USA
| | - Nelissa Perez-Nazario
- Department of Dermatology, University of Rochester Medical Center, 601 Elmwood Ave, Box 697, Rochester, NY, 14642, USA
| | - Sara A Knowlden
- Department of Dermatology, University of Rochester Medical Center, 601 Elmwood Ave, Box 697, Rochester, NY, 14642, USA
| | - Ellen Chinchilli
- Department of Dermatology, University of Rochester Medical Center, 601 Elmwood Ave, Box 697, Rochester, NY, 14642, USA
| | - Alex Grier
- University of Rochester Genomics Research Center, University of Rochester Medical Center, Rochester, NY, USA
| | - Amy Paller
- Department of Dermatology, Northwestern University, Chicago, IL, USA
| | - Steven R Gill
- University of Rochester Genomics Research Center, University of Rochester Medical Center, Rochester, NY, USA
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Anna De Benedetto
- Department of Dermatology, University of Rochester Medical Center, 601 Elmwood Ave, Box 697, Rochester, NY, 14642, USA
| | - Takeshi Yoshida
- Department of Dermatology, University of Rochester Medical Center, 601 Elmwood Ave, Box 697, Rochester, NY, 14642, USA
| | - Lisa A Beck
- Department of Dermatology, University of Rochester Medical Center, 601 Elmwood Ave, Box 697, Rochester, NY, 14642, USA.
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Simpson EL, Schlievert PM, Yoshida T, Lussier S, Boguniewicz M, Hata T, Fuxench Z, De Benedetto A, Ong PY, Ko J, Calatroni A, Rudman Spergel AK, Plaut M, Quataert SA, Kilgore SH, Peterson L, Gill AL, David G, Mosmann T, Gill SR, Leung DYM, Beck LA. Rapid reduction in Staphylococcus aureus in atopic dermatitis subjects following dupilumab treatment. J Allergy Clin Immunol 2023; 152:1179-1195. [PMID: 37315812 PMCID: PMC10716365 DOI: 10.1016/j.jaci.2023.05.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 11/07/2022] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND Atopic dermatitis (AD) is an inflammatory disorder characterized by dominant type 2 inflammation leading to chronic pruritic skin lesions, allergic comorbidities, and Staphylococcus aureus skin colonization and infections. S aureus is thought to play a role in AD severity. OBJECTIVES This study characterized the changes in the host-microbial interface in subjects with AD following type 2 blockade with dupilumab. METHODS Participants (n = 71) with moderate-severe AD were enrolled in a randomized (dupilumab vs placebo; 2:1), double-blind study at Atopic Dermatitis Research Network centers. Bioassays were performed at multiple time points: S aureus and virulence factor quantification, 16s ribosomal RNA microbiome, serum biomarkers, skin transcriptomic analyses, and peripheral blood T-cell phenotyping. RESULTS At baseline, 100% of participants were S aureus colonized on the skin surface. Dupilumab treatment resulted in significant reductions in S aureus after only 3 days (compared to placebo), which was 11 days before clinical improvement. Participants with the greatest S aureus reductions had the best clinical outcomes, and these reductions correlated with reductions in serum CCL17 and disease severity. Reductions (10-fold) in S aureus cytotoxins (day 7), perturbations in TH17-cell subsets (day 14), and increased expression of genes relevant for IL-17, neutrophil, and complement pathways (day 7) were also observed. CONCLUSIONS Blockade of IL-4 and IL-13 signaling, very rapidly (day 3) reduces S aureus abundance in subjects with AD, and this reduction correlates with reductions in the type 2 biomarker, CCL17, and measures of AD severity (excluding itch). Immunoprofiling and/or transcriptomics suggest a role for TH17 cells, neutrophils, and complement activation as potential mechanisms to explain these findings.
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Affiliation(s)
- Eric L Simpson
- Department of Dermatology, Oregon Health and Science University, Portland, Ore
| | | | - Takeshi Yoshida
- Department of Dermatology, University of Rochester School of Medicine and Dentistry, Rochester, NY
| | | | - Mark Boguniewicz
- Division of Allergy-Immunology, Department of Pediatrics, National Jewish Health and University of Colorado School of Medicine, Denver, Colo
| | - Tissa Hata
- Department of Dermatology, University of California, San Diego, Calif
| | - Zelma Fuxench
- Department of Dermatology, University of Pennsylvania, Philadelphia, Pa
| | - Anna De Benedetto
- Department of Dermatology, University of Rochester School of Medicine and Dentistry, Rochester, NY
| | - Peck Y Ong
- Department of Pediatrics, University Southern California, Los Angeles, Calif
| | - Justin Ko
- Department of Dermatology, Stanford University, Stanford, Calif
| | | | - Amanda K Rudman Spergel
- Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Marshall Plaut
- Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Sally A Quataert
- Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY
| | - Samuel H Kilgore
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa
| | - Liam Peterson
- Department of Dermatology, University of Rochester School of Medicine and Dentistry, Rochester, NY
| | - Ann L Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY
| | | | - Tim Mosmann
- Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY
| | - Steven R Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY
| | - Donald Y M Leung
- Division of Allergy-Immunology, Department of Pediatrics, National Jewish Health and University of Colorado School of Medicine, Denver, Colo.
| | - Lisa A Beck
- Department of Dermatology, University of Rochester School of Medicine and Dentistry, Rochester, NY.
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Gill SR, O'Connor TG, Kopycka-Kedzierawski DT. Early childhood caries prevention through a developmental origins model of the oral microbiome, host and oral environment, and sociodemographic influences. Quintessence Int 2023; 54:610-611. [PMID: 37724759 DOI: 10.3290/j.qi.b4417923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
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Bui TI, Gill AL, Mooney RA, Gill SR. Modulation of Gut Microbiota Metabolism in Obesity-Related Type 2 Diabetes Reduces Osteomyelitis Severity. Microbiol Spectr 2022; 10:e0017022. [PMID: 35315698 PMCID: PMC9045376 DOI: 10.1128/spectrum.00170-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/03/2022] [Indexed: 12/01/2022] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen causing osteomyelitis through hematogenous seeding or contamination of implants and open wounds following orthopedic surgeries. The severity of S. aureus-mediated osteomyelitis is enhanced in obesity-related type 2 diabetes (obesity/T2D) due to chronic inflammation impairing both adaptive and innate immunity. Obesity-induced inflammation is linked to gut dysbiosis, with modification of the gut microbiota by high-fiber diets leading to a reduction in the symptoms and complications of obesity/T2D. However, our understanding of the mechanisms by which modifications of the gut microbiota alter host infection responses is limited. To address this gap, we monitored tibial S. aureus infections in obese/T2D mice treated with the inulin-like fructan fiber oligofructose. Treatment with oligofructose significantly decreased S. aureus colonization and lowered proinflammatory signaling postinfection in obese/T2D mice, as observed by decreased circulating inflammatory cytokines (tumor necrosis factor-α [TNF-α]) and chemokines (interferon-γ-induced protein 10 kDa [IP-10], keratinocyte-derived chemokine [KC], monokine induced by interferon-γ [MIG], monocyte chemoattractant protein-1 [MCP-1], and regulated upon activation, normal T cell expressed and presumably secreted [RANTES]), indicating partial reduction in inflammation. Oligofructose markedly shifted diversity in the gut microbiota of obese/T2D mice, with notable increases in the anti-inflammatory bacterium Bifidobacterium pseudolongum. Analysis of the cecum and plasma metabolome suggested that polyamine production was increased, specifically spermine and spermidine. Oral administration of these polyamines to obese/T2D mice resulted in reduced infection severity similar to oligofructose supplementation, suggesting that polyamines can mediate the beneficial effects of fiber on osteomyelitis severity. These results demonstrate the contribution of gut microbiota metabolites to the control of bacterial infections distal to the gut and polyamines as an adjunct therapeutic for osteomyelitis in obesity/T2D. IMPORTANCE Individuals with obesity-related type 2 diabetes (obesity/T2D) are at a five times increased risk for invasive Staphylococcus aureus osteomyelitis (bone infection) following orthopedic surgeries. With increasing antibiotic resistance and limited discoveries of novel antibiotics, it is imperative that we explore other avenues for therapeutics. In this study, we demonstrated that the dietary fiber oligofructose markedly reduced osteomyelitis severity and hyperinflammation following acute prosthetic joint infections in obese/T2D mice. Reduced infection severity was associated with changes in gut microbiota composition and metabolism, as indicated by increased production of natural polyamines in the gut and circulating plasma. This work identifies a novel role for the gut microbiome in mediating control of bacterial infections and polyamines as beneficial metabolites involved in improving the obesity/T2D host response to osteomyelitis. Understanding the impact of polyamines on host immunity and mechanisms behind decreasing susceptibility to severe implant-associated osteomyelitis is crucial to improving treatment strategies for this patient population.
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Affiliation(s)
- Tina I. Bui
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Ann Lindley Gill
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Robert A. Mooney
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Center for Musculoskeletal Research, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Steven R. Gill
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Center for Musculoskeletal Research, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
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9
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McDavid A, Laniewski N, Grier A, Gill AL, Kessler HA, Huyck H, Carbonell E, Holden-Wiltse J, Bandyopadhyay S, Carnahan J, Dylag AM, Topham DJ, Falsey AR, Caserta MT, Pryhuber GS, Gill SR, Scheible KM. Aberrant newborn T cell and microbiota developmental trajectories predict respiratory compromise during infancy. iScience 2022; 25:104007. [PMID: 35310935 PMCID: PMC8931366 DOI: 10.1016/j.isci.2022.104007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/30/2021] [Accepted: 02/25/2022] [Indexed: 11/11/2022] Open
Abstract
Neonatal immune-microbiota co-development is poorly understood, yet age-appropriate recognition of – and response to – pathogens and commensal microbiota is critical to health. In this longitudinal study of 148 preterm and 119 full-term infants from birth through one year of age, we found that postmenstrual age or weeks from conception is a central factor influencing T cell and mucosal microbiota development. Numerous features of the T cell and microbiota functional development remain unexplained; however, by either age metric and are instead shaped by discrete perinatal and postnatal events. Most strikingly, we establish that prenatal antibiotics or infection disrupt the normal T cell population developmental trajectory, influencing subsequent respiratory microbial colonization and predicting respiratory morbidity. In this way, early exposures predict the postnatal immune-microbiota axis trajectory, placing infants at later risk for respiratory morbidity in early childhood. T cells and microbiota in the first year of life advance in sync with infant age Perinatal events can disrupt T cell and microbiota developmental trajectories Atypical T cell and microbiota co-development predicts poor respiratory outcome
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10
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Herman KE, Yoshida T, Hughson A, Grier A, Gill SR, Beck LA, Fowell DJ. IL-17-Dependent Dysregulated Cutaneous Immune Homeostasis in the Absence of the Wiskott-Aldrich Syndrome Protein. Front Immunol 2022; 13:817427. [PMID: 35265075 PMCID: PMC8900519 DOI: 10.3389/fimmu.2022.817427] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
Wiskott-Aldrich Syndrome (WAS) is characterized by recurrent infections, thrombocytopenia, and eczema. Here, we show that WASp-deficient mice on a BALB/c background have dysregulated cutaneous immune homeostasis with increased leukocyte accumulation in the skin, 1 week after birth. Increased cutaneous inflammation was associated with epithelial abnormalities, namely, altered keratinization, abnormal epidermal tight junctional morphology and increased trans-epidermal water loss; consistent with epidermal barrier dysfunction. Immune and physical barrier disruption was accompanied by progressive skin dysbiosis, highlighting the functional significance of the disrupted cutaneous homeostasis. Interestingly, the dysregulated immunity in the skin preceded the systemic elevation in IgE and lymphocytic infiltration of the colonic lamina propria associated with WASp deficiency. Mechanistically, the enhanced immune cell accumulation in the skin was lymphocyte dependent. Elevated levels of both Type 2 (IL-4, IL-5) and Type 17 (IL-17, IL-22, IL-23) cytokines were present in the skin, as well as the 'itch' factor IL-31. Unexpectedly, the canonical WAS-associated cytokine IL-4 did not play a role in the immune dysfunction. Instead, IL-17 was critical for skin immune infiltration and elevation of both Type 2 and Type 17 cytokines. Our findings reveal a previously unrecognized IL-17-dependent breakdown in immune homeostasis and cutaneous barrier integrity in the absence of WASp, targeting of which may provide new therapeutic possibilities for the treatment of skin pathologies in WAS patients.
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Affiliation(s)
- Katherine E. Herman
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, University of Rochester Medical Center, Rochester, NY, United States
| | - Takeshi Yoshida
- Department of Dermatology, University of Rochester Medical Center, Rochester, NY, United States
| | - Angela Hughson
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, University of Rochester Medical Center, Rochester, NY, United States
| | - Alex Grier
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
| | - Steven R. Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
| | - Lisa A. Beck
- Department of Dermatology, University of Rochester Medical Center, Rochester, NY, United States
| | - Deborah J. Fowell
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, University of Rochester Medical Center, Rochester, NY, United States,Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States,*Correspondence: Deborah J. Fowell,
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11
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Bui TI, Britt EA, Muthukrishnan G, Gill SR. Probiotic induced synthesis of microbiota polyamine as a nutraceutical for metabolic syndrome and obesity-related type 2 diabetes. Front Endocrinol (Lausanne) 2022; 13:1094258. [PMID: 36714575 PMCID: PMC9880209 DOI: 10.3389/fendo.2022.1094258] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/16/2022] [Indexed: 01/15/2023] Open
Abstract
The gut microbiota regulates multiple facets of host metabolism and immunity through the production of signaling metabolites, such as polyamines which are small organic compounds that are essential to host cell growth and lymphocyte activation. Polyamines are most abundant in the intestinal lumen, where their synthesis by the gut microbiota is influenced by microbiome composition and host diet. Disruption of the host gut microbiome in metabolic syndrome and obesity-related type 2 diabetes (obesity/T2D) results in potential dysregulation of polyamine synthesis. A growing body of evidence suggests that restoration of the dysbiotic gut microbiota and polyamine synthesis is effective in ameliorating metabolic syndrome and strengthening the impaired immune responses of obesity/T2D. In this review, we discuss existing studies on gut microbiome determinants of polyamine synthesis, polyamine production in obesity/T2D, and evidence that demonstrates the potential of polyamines as a nutraceutical in obesity/T2D hosts.
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Affiliation(s)
- Tina I. Bui
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
| | - Emily A. Britt
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
| | - Gowrishankar Muthukrishnan
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States
- Department of Orthopedics, University of Rochester Medical Center, Rochester, NY, United States
| | - Steven R. Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States
- *Correspondence: Steven R. Gill,
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12
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McCall MN, Chu CY, Wang L, Benoodt L, Thakar J, Corbett A, Holden-Wiltse J, Slaunwhite C, Grier A, Gill SR, Falsey AR, Topham DJ, Caserta MT, Walsh EE, Qiu X, Mariani TJ. A systems genomics approach uncovers molecular associates of RSV severity. PLoS Comput Biol 2021; 17:e1009617. [PMID: 34962914 PMCID: PMC8746750 DOI: 10.1371/journal.pcbi.1009617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 03/25/2021] [Revised: 01/10/2022] [Accepted: 11/05/2021] [Indexed: 01/06/2023] Open
Abstract
Respiratory syncytial virus (RSV) infection results in millions of hospitalizations and thousands of deaths each year. Variations in the adaptive and innate immune response appear to be associated with RSV severity. To investigate the host response to RSV infection in infants, we performed a systems-level study of RSV pathophysiology, incorporating high-throughput measurements of the peripheral innate and adaptive immune systems and the airway epithelium and microbiota. We implemented a novel multi-omic data integration method based on multilayered principal component analysis, penalized regression, and feature weight back-propagation, which enabled us to identify cellular pathways associated with RSV severity. In both airway and immune cells, we found an association between RSV severity and activation of pathways controlling Th17 and acute phase response signaling, as well as inhibition of B cell receptor signaling. Dysregulation of both the humoral and mucosal response to RSV may play a critical role in determining illness severity. This paper presents a novel approach to understanding the localized molecular responses to respiratory syncytial virus (RSV) and the system-level correlates of clinical outcomes. To do this, we developed a novel statistical method able to integrate high dimensional molecular data characterizing the host airway microbota and immune and nasal gene expression. We show that this integrative approach facilitates superior performance in estimating clinical outcome as opposed to any single data type. Using this approach, we identified both cell type-specific and shared biomarkers and regulatory pathways associated with RSV severity. Specifically, we identified an association between RSV severity, activation of pathways controlling Th17, and inhibition of B cell receptor signaling, which were present in both the site of infection airway and in peripheral immune cells. These results can guide future efforts to identify biomarkers for identifying or predicting illness severity following infant RSV infection. They may also be useful as biomarkers to inform the efficacy of future interventions (e.g., therapies) or preventative measures to suppress the rate of severe disease (e.g., vaccines).
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Affiliation(s)
- Matthew N McCall
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester New York, United States of America.,Department of Biomedical Genetics, University of Rochester Medical Center, Rochester New York, United States of America
| | - Chin-Yi Chu
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, University of Rochester Medical Center, Rochester New York, United States of America.,Department of Pediatrics, University of Rochester Medical Center, Rochester New York, United States of America
| | - Lu Wang
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester New York, United States of America
| | - Lauren Benoodt
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester New York, United States of America
| | - Juilee Thakar
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester New York, United States of America.,Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester New York, United States of America
| | - Anthony Corbett
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester New York, United States of America.,Clinical and Translational Science Institute, University of Rochester Medical Center, Rochester New York, United States of America
| | - Jeanne Holden-Wiltse
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester New York, United States of America.,Clinical and Translational Science Institute, University of Rochester Medical Center, Rochester New York, United States of America
| | - Christopher Slaunwhite
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, University of Rochester Medical Center, Rochester New York, United States of America.,Department of Pediatrics, University of Rochester Medical Center, Rochester New York, United States of America
| | - Alex Grier
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester New York, United States of America
| | - Steven R Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester New York, United States of America
| | - Ann R Falsey
- Department of Medicine, University of Rochester Medical Center, Rochester New York, United States of America.,Department of Medicine, Rochester General Hospital, Rochester New York, United States of America
| | - David J Topham
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester New York, United States of America.,David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester New York, United States of America
| | - Mary T Caserta
- Department of Pediatrics, University of Rochester Medical Center, Rochester New York, United States of America
| | - Edward E Walsh
- Department of Medicine, University of Rochester Medical Center, Rochester New York, United States of America.,Department of Medicine, Rochester General Hospital, Rochester New York, United States of America
| | - Xing Qiu
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester New York, United States of America
| | - Thomas J Mariani
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, University of Rochester Medical Center, Rochester New York, United States of America.,Department of Pediatrics, University of Rochester Medical Center, Rochester New York, United States of America
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13
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Masters EA, Muthukrishnan G, Ho L, Gill AL, de Mesy Bentley KL, Galloway CA, McGrath JL, Awad HA, Gill SR, Schwarz EM. Staphylococcus aureus Cell Wall Biosynthesis Modulates Bone Invasion and Osteomyelitis Pathogenesis. Front Microbiol 2021; 12:723498. [PMID: 34484165 PMCID: PMC8415456 DOI: 10.3389/fmicb.2021.723498] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/15/2021] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus aureus invasion of the osteocyte lacuno-canalicular network (OLCN) is a novel mechanism of bacterial persistence and immune evasion in chronic osteomyelitis. Previous work highlighted S. aureus cell wall transpeptidase, penicillin binding protein 4 (PBP4), and surface adhesin, S. aureus surface protein C (SasC), as critical factors for bacterial deformation and propagation through nanopores in vitro, representative of the confined canaliculi in vivo. Given these findings, we hypothesized that cell wall synthesis machinery and surface adhesins enable durotaxis- and haptotaxis-guided invasion of the OLCN, respectively. Here, we investigated select S. aureus cell wall synthesis mutants (Δpbp3, Δatl, and ΔmreC) and surface adhesin mutants (ΔclfA and ΔsasC) for nanopore propagation in vitro and osteomyelitis pathogenesis in vivo. In vitro evaluation in the microfluidic silicon membrane-canalicular array (μSiM-CA) showed pbp3, atl, clfA, and sasC deletion reduced nanopore propagation. Using a murine model for implant-associated osteomyelitis, S. aureus cell wall synthesis proteins were found to be key modulators of S. aureus osteomyelitis pathogenesis, while surface adhesins had minimal effects. Specifically, deletion of pbp3 and atl decreased septic implant loosening and S. aureus abscess formation in the medullary cavity, while deletion of surface adhesins showed no significant differences. Further, peri-implant osteolysis, osteoclast activity, and receptor activator of nuclear factor kappa-B ligand (RANKL) production were decreased following pbp3 deletion. Most notably, transmission electron microscopy (TEM) imaging of infected bone showed that pbp3 was the only gene herein associated with decreased submicron invasion of canaliculi in vivo. Together, these results demonstrate that S. aureus cell wall synthesis enzymes are critical for OLCN invasion and osteomyelitis pathogenesis in vivo.
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Affiliation(s)
- Elysia A Masters
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States.,Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY, United States
| | - Gowrishankar Muthukrishnan
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States.,Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY, United States
| | - Lananh Ho
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States.,Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY, United States
| | - Ann Lindley Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
| | - Karen L de Mesy Bentley
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States.,Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY, United States.,Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Chad A Galloway
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States.,Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - James L McGrath
- Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY, United States
| | - Hani A Awad
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States.,Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY, United States
| | - Steven R Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
| | - Edward M Schwarz
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States.,Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY, United States.,Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY, United States.,Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States
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14
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Quivey RG, O'Connor TG, Gill SR, Kopycka-Kedzierawski DT. Prediction of early childhood caries onset and oral microbiota. Mol Oral Microbiol 2021; 36:255-257. [PMID: 34314578 DOI: 10.1111/omi.12349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 07/21/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Robert G Quivey
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA.,Center for Oral Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Thomas G O'Connor
- Department of Psychiatry, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA.,Department of Obstetrics and Gynecology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA.,Department of Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Steven R Gill
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA.,Genomics Research Center, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Dorota T Kopycka-Kedzierawski
- Center for Oral Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA.,Department of Dentistry, Eastman Institute for Oral Health, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
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15
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Chu CY, Qiu X, McCall MN, Wang L, Corbett A, Holden-Wiltse J, Slaunwhite C, Grier A, Gill SR, Pryhuber GS, Falsey AR, Topham DJ, Caserta MT, Walsh EE, Mariani TJ. Airway Gene Expression Correlates of Respiratory Syncytial Virus Disease Severity and Microbiome Composition in Infants. J Infect Dis 2021; 223:1639-1649. [PMID: 32926149 PMCID: PMC8136980 DOI: 10.1093/infdis/jiaa576] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 05/11/2020] [Accepted: 09/09/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is the leading cause of severe respiratory disease in infants. The causes and correlates of severe illness in the majority of infants are poorly defined. METHODS We recruited a cohort of RSV-infected infants and simultaneously assayed the molecular status of their airways and the presence of airway microbiota. We used rigorous statistical approaches to identify gene expression patterns associated with disease severity and microbiota composition, separately and in combination. RESULTS We measured comprehensive airway gene expression patterns in 106 infants with primary RSV infection. We identified an airway gene expression signature of severe illness dominated by excessive chemokine expression. We also found an association between Haemophilus influenzae, disease severity, and airway lymphocyte accumulation. Exploring the time of onset of clinical symptoms revealed acute activation of interferon signaling following RSV infection in infants with mild or moderate illness, which was absent in subjects with severe illness. CONCLUSIONS Our data reveal that airway gene expression patterns distinguish mild/moderate from severe illness. Furthermore, our data identify biomarkers that may be therapeutic targets or useful for measuring efficacy of intervention responses.
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Affiliation(s)
- Chin-Yi Chu
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, University of Rochester Medical Center, Rochester, New York, USA
- Departments of Pediatrics, University of Rochester Medical Center, Rochester, New York, USA
| | - Xing Qiu
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York, USA
| | - Matthew N McCall
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York, USA
| | - Lu Wang
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York, USA
| | - Anthony Corbett
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York, USA
- Clinical and Translational Science Institute, University of Rochester Medical Center, Rochester, New York, USA
| | - Jeanne Holden-Wiltse
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York, USA
- Clinical and Translational Science Institute, University of Rochester Medical Center, Rochester, New York, USA
| | - Christopher Slaunwhite
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, University of Rochester Medical Center, Rochester, New York, USA
- Departments of Pediatrics, University of Rochester Medical Center, Rochester, New York, USA
| | - Alex Grier
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Steven R Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Gloria S Pryhuber
- Departments of Pediatrics, University of Rochester Medical Center, Rochester, New York, USA
| | - Ann R Falsey
- Department of Medicine, University of Rochester Medical Center, Rochester, New York, USA
- Department of Medicine, Rochester General Hospital, Rochester, New York, USA
| | - David J Topham
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Mary T Caserta
- Departments of Pediatrics, University of Rochester Medical Center, Rochester, New York, USA
| | - Edward E Walsh
- Department of Medicine, University of Rochester Medical Center, Rochester, New York, USA
- Department of Medicine, Rochester General Hospital, Rochester, New York, USA
| | - Thomas J Mariani
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, University of Rochester Medical Center, Rochester, New York, USA
- Departments of Pediatrics, University of Rochester Medical Center, Rochester, New York, USA
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16
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Grier A, Gill AL, Kessler HA, Corbett A, Bandyopadhyay S, Java J, Holden-Wiltse J, Falsey AR, Topham DJ, Mariani TJ, Caserta MT, Walsh EE, Gill SR. Temporal Dysbiosis of Infant Nasal Microbiota Relative to Respiratory Syncytial Virus Infection. J Infect Dis 2021; 223:1650-1658. [PMID: 32926147 PMCID: PMC8136976 DOI: 10.1093/infdis/jiaa577] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 05/12/2020] [Accepted: 09/08/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is a leading cause of infant respiratory disease. Infant airway microbiota has been associated with respiratory disease risk and severity. The extent to which interactions between RSV and microbiota occur in the airway, and their impact on respiratory disease susceptibility and severity, are unknown. METHODS We carried out 16S rRNA microbiota profiling of infants in the first year of life from (1) a cross-sectional cohort of 89 RSV-infected infants sampled during illness and 102 matched healthy controls, and (2) a matched longitudinal cohort of 12 infants who developed RSV infection and 12 who did not, sampled before, during, and after infection. RESULTS We identified 12 taxa significantly associated with RSV infection. All 12 taxa were differentially abundant during infection, with 8 associated with disease severity. Nasal microbiota composition was more discriminative of healthy vs infected than of disease severity. CONCLUSIONS Our findings elucidate the chronology of nasal microbiota dysbiosis and suggest an altered developmental trajectory associated with RSV infection. Microbial temporal dynamics reveal indicators of disease risk, correlates of illness and severity, and impact of RSV infection on microbiota composition.
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Affiliation(s)
- Alex Grier
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Genomics Research Center, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Ann L Gill
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Haeja A Kessler
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Anthony Corbett
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Sanjukta Bandyopadhyay
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - James Java
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Jeanne Holden-Wiltse
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Ann R Falsey
- Department of Medicine, Rochester General Hospital, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - David J Topham
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Thomas J Mariani
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Mary T Caserta
- Division of Pediatric Infectious Diseases, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Edward E Walsh
- Department of Medicine, Rochester General Hospital, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Steven R Gill
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Genomics Research Center, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
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17
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Lambert PA, Gill AL, Gill SR, Allen PD, Man L. Microbiomics of irrigation with xylitol or Lactococcus lactis in chronic rhinosinusitis. Laryngoscope Investig Otolaryngol 2021; 6:64-70. [PMID: 33614931 PMCID: PMC7883620 DOI: 10.1002/lio2.524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/11/2021] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Topical sinonasal rinse therapies may alter the local microbiome and improve disease control in chronic rhinosinusitis (CRS). The objective of this study was to examine microbiome changes in post-surgical CRS patients when rinsing with commercially available products containing xylitol or Lactococcus lactis. METHODS A crossover-type protocol with a washout period was designed. Swab samples from anterior ethmoid cavities of CRS patients were collected prospectively at baseline. Subjects were provided packets containing either L. lactis W136 or xylitol in non-blinded fashion and instructed to add it to their rinse bottles daily for 28 days, after which another swab was taken. A saline wash-out period was completed and a third swab taken. A final 28-day regimen of the opposite product was followed by a final swab. DNA extraction and sequencing of the 16S rRNA gene allowed for global microbiome analysis. RESULTS We enrolled 25 subjects with CRS and 10 controls resulting in 70 adequate samples. Increased detection of Lactococcus was observed after use of L. lactis. No significant trends in alpha or beta diversity as a result of treatment were observed. SNOT-22 score did not change significantly following treatment with xylitol, L. lactis, or saline. CONCLUSION We did not detect any major clinical or microbiome-level effect due to treatment with two topical rinse products. Further research is needed to elucidate their clinical utility and possible probiotic effect. LEVEL OF EVIDENCE 3.
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Affiliation(s)
- Paul A. Lambert
- Department of Otolaryngology Head and Neck SurgeryUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - Ann L. Gill
- Department of Microbiology and ImmunologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - Steven R. Gill
- Department of Microbiology and ImmunologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - Paul D. Allen
- Department of Otolaryngology Head and Neck SurgeryUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - Li‐Xing Man
- Department of Otolaryngology Head and Neck SurgeryUniversity of Rochester Medical CenterRochesterNew YorkUSA
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18
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Snell SB, Gill AL, Haidaris CG, Foster TH, Baran TM, Gill SR. Staphylococcus aureus Tolerance and Genomic Response to Photodynamic Inactivation. mSphere 2021; 6:e00762-20. [PMID: 33408223 PMCID: PMC7845598 DOI: 10.1128/msphere.00762-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/08/2020] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen with a clinical spectrum ranging from asymptomatic skin colonization to invasive infections. While traditional antibiotic therapies can be effective against S. aureus, the increasing prevalence of antibiotic-resistant strains results in treatment failures and high mortality rates. Photodynamic inactivation (PDI) is an innovative and promising alternative to antibiotics. While progress has been made in our understanding of the bacterial response to PDI, major gaps remain in our knowledge of PDI tolerance, the global cellular response, and adaptive genomic mutations acquired as a result of PDI. To address these gaps, S. aureus HG003 and isogenic mutants with mutations in agr, mutS, mutL, and mutY exposed to single or multiple doses of PDI were assessed for survival and tolerance and examined by global transcriptome and genome analyses to identify regulatory and genetic adaptations that contribute to tolerance. Pathways in inorganic ion transport, oxidative response, DNA replication recombination and repair, and cell wall and membrane biogenesis were identified in a global cellular response to PDI. Tolerance to PDI was associated with superoxide dismutase and the S. aureus global methylhydroquinone (MHQ)-quinone transcriptome network. Genome analysis of PDI-tolerant HG003 identified a nonsynonymous mutation in the quinone binding domain of the transcriptional repressor QsrR, which mediates quinone sensing and oxidant response. Acquisition of a heritable QsrR mutation through repeated PDI treatment demonstrates selective adaption of S. aureus to PDI. PDI tolerance of a qsrR gene deletion in HG003 confirmed that QsrR regulates the S. aureus response to PDI.IMPORTANCEStaphylococcus aureus can cause disease at most body sites, with illness ranging from asymptomatic infection to death. The increasing prevalence of antibiotic-resistant strains results in treatment failures and high mortality rates. S. aureus acquires resistance to antibiotics through multiple mechanisms, often by genetic variation that alters antimicrobial targets. Photodynamic inactivation (PDI), which employs a combination of a nontoxic dye and low-intensity visible light, is a promising alternative to antibiotics that effectively eradicates S. aureus in human infections when antibiotics are no longer effective. In this study, we demonstrate that repeated exposure to PDI results in resistance of S. aureus to further PDI treatment and identify the underlying bacterial mechanisms that contribute to resistance. This work supports further analysis of these mechanisms and refinement of this novel technology as an adjunctive treatment for S. aureus infections.
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Affiliation(s)
- Sara B Snell
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Ann Lindley Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Constantine G Haidaris
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
- Center for Oral Biology, University of Rochester Medical Center, Rochester, New York, USA
| | - Thomas H Foster
- Department of Imaging Sciences, University of Rochester Medical Center, Rochester, New York, USA
| | - Timothy M Baran
- Department of Imaging Sciences, University of Rochester Medical Center, Rochester, New York, USA
| | - Steven R Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
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19
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Grier A, Myers JA, O'Connor TG, Quivey RG, Gill SR, Kopycka-Kedzierawski DT. Oral Microbiota Composition Predicts Early Childhood Caries Onset. J Dent Res 2020; 100:599-607. [PMID: 33356775 DOI: 10.1177/0022034520979926] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
As the most common chronic disease in preschool children in the United States, early childhood caries (ECC) has a profound impact on a child's quality of life, represents a tremendous human and economic burden to society, and disproportionately affects those living in poverty. Caries risk assessment (CRA) is a critical component of ECC management, yet the accuracy, consistency, reproducibility, and longitudinal validation of the available risk assessment techniques are lacking. Molecular and microbial biomarkers represent a potential source for accurate and reliable dental caries risk and onset. Next-generation nucleotide-sequencing technology has made it feasible to profile the composition of the oral microbiota. In the present study, 16S ribosomal RNA (rRNA) gene sequencing was applied to saliva samples that were collected at 6-mo intervals for 24 mo from a subset of 56 initially caries-free children from an ongoing cohort of 189 children, aged 1 to 3 y, over the 2-y study period; 36 children developed ECC and 20 remained caries free. Analyses from machine learning models of microbiota composition, across the study period, distinguished between affected and nonaffected groups at the time of their initial study visits with an area under the receiver operating characteristic curve (AUC) of 0.71 and discriminated ECC-converted from healthy controls at the visit immediately preceding ECC diagnosis with an AUC of 0.89, as assessed by nested cross-validation. Rothia mucilaginosa, Streptococcus sp., and Veillonella parvula were selected as important discriminatory features in all models and represent biomarkers of risk for ECC onset. These findings indicate that oral microbiota as profiled by high-throughput 16S rRNA gene sequencing is predictive of ECC onset.
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Affiliation(s)
- A Grier
- Genomics Research Center, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - J A Myers
- Genomics Research Center, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - T G O'Connor
- Department of Psychiatry, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.,Department of Obstetrics and Gynecology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.,Department of Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - R G Quivey
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.,Center for Oral Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - S R Gill
- Genomics Research Center, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.,Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - D T Kopycka-Kedzierawski
- Center for Oral Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.,Department of Dentistry, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
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20
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Quinones Tavarez Z, Li D, Croft DP, Gill SR, Ossip DJ, Rahman I. The Interplay Between Respiratory Microbiota and Innate Immunity in Flavor E-Cigarette Vaping Induced Lung Dysfunction. Front Microbiol 2020; 11:589501. [PMID: 33391205 PMCID: PMC7772214 DOI: 10.3389/fmicb.2020.589501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/24/2020] [Indexed: 12/11/2022] Open
Abstract
Global usage of electronic nicotine delivery systems (ENDS) has been increasing in the last decade. ENDS are non-combustible tobacco products that heat and aerosolize a liquid containing humectants, with added flavorings and often nicotine. Though ENDS are promoted as a less harmful alternative to smoking, current evidence links their use to a wide range of deleterious health effects including acute and chronic lung damage. ENDS can elicit an inflammatory response and impair the innate immune response in the lungs. Exposure to ENDS flavorings results in abnormal activation of the lung epithelial cells and β-defensins, dysfunction of the macrophage phagocytic activity, increased levels of mucin (MUC5AC) and abnormal activation of the neutrophilic response (NETosis). ENDS menthol flavorings disrupt innate immunity and might be associated with allergies and asthma through activation of transient receptor potential ankyrin 1 (TRAP1). Recent studies have expanded our understanding of the relationship between the homeostasis of lung innate immunity and the immunomodulatory effect of the host-microbiota interaction. Alterations of the normal respiratory microbiota have been associated with chronic obstructive pulmonary disease (COPD), asthma, atopy and cystic fibrosis complications which are strongly associated with smoking and potentially with ENDS use. Little is known about the short-and long-term effects of ENDS on the respiratory microbiota, their impact on the innate immune response and their link to pulmonary health and disease. Here we review the interaction between the innate immune system and the respiratory microbiota in the pathogenesis of ENDS-induced pulmonary dysfunction and identify future areas of research.
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Affiliation(s)
- Zahira Quinones Tavarez
- Department of Clinical and Translational Research, University of Rochester Medical Center, Rochester, NY, United States
| | - Dongmei Li
- Department of Clinical and Translational Research, University of Rochester Medical Center, Rochester, NY, United States
| | - Daniel P Croft
- Department of Medicine, Pulmonary Diseases and Critical Care, University of Rochester, Rochester, NY, United States
| | - Steven R Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
| | - Deborah J Ossip
- Department of Public Health Sciences, University of Rochester Medical Center, Rochester, NY, United States
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, United States
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21
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Masters EA, de Mesy Bentley KL, Gill AL, Hao SP, Galloway CA, Salminen AT, Guy DR, McGrath JL, Awad HA, Gill SR, Schwarz EM. Identification of Penicillin Binding Protein 4 (PBP4) as a critical factor for Staphylococcus aureus bone invasion during osteomyelitis in mice. PLoS Pathog 2020; 16:e1008988. [PMID: 33091079 PMCID: PMC7608983 DOI: 10.1371/journal.ppat.1008988] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/03/2020] [Accepted: 09/17/2020] [Indexed: 12/03/2022] Open
Abstract
Staphylococcus aureus infection of bone is challenging to treat because it colonizes the osteocyte lacuno-canalicular network (OLCN) of cortical bone. To elucidate factors involved in OLCN invasion and identify novel drug targets, we completed a hypothesis-driven screen of 24 S. aureus transposon insertion mutant strains for their ability to propagate through 0.5 μm-sized pores in the Microfluidic Silicon Membrane Canalicular Arrays (μSiM-CA), developed to model S. aureus invasion of the OLCN. This screen identified the uncanonical S. aureus transpeptidase, penicillin binding protein 4 (PBP4), as a necessary gene for S. aureus deformation and propagation through nanopores. In vivo studies revealed that Δpbp4 infected tibiae treated with vancomycin showed a significant 12-fold reduction in bacterial load compared to WT infected tibiae treated with vancomycin (p<0.05). Additionally, Δpbp4 infected tibiae displayed a remarkable decrease in pathogenic bone-loss at the implant site with and without vancomycin therapy. Most importantly, Δpbp4 S. aureus failed to invade and colonize the OLCN despite high bacterial loads on the implant and in adjacent tissues. Together, these results demonstrate that PBP4 is required for S. aureus colonization of the OLCN and suggest that inhibitors may be synergistic with standard of care antibiotics ineffective against bacteria within the OLCN. Staphylococcus aureus is the most prevalent pathogen in osteomyelitis, and its infection of bone is difficult to cure. S. aureus colonization of the osteocyte lacuno-canalicular network (OLCN) of cortical bone has been identified as a novel pathogenetic mechanism in chronic osteomyelitis. To elucidate factors involved in OLCN invasion, we conducted an in vitro genetic screen that identified pbp4 as a critical gene for S. aureus cell deformation and propagation through nanopores and demonstrated that PBP4 is critical for OLCN colonization in murine osteomyelitis. Thus, PBP4 inhibitors may be novel drugs to treat osteomyelitis in combination with standard of care antibiotics.
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Affiliation(s)
- Elysia A. Masters
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States of America
- Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Karen L. de Mesy Bentley
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States of America
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States of America
- Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Ann Lindley Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Stephanie P. Hao
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Chad A. Galloway
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States of America
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Alec T. Salminen
- Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Diamond R. Guy
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States of America
| | - James L. McGrath
- Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Hani A. Awad
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States of America
- Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Steven R. Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Edward M. Schwarz
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, United States of America
- Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY, United States of America
- Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY, United States of America
- * E-mail:
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22
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McDavid A, Corbett AM, Dutra JL, Straw AG, Topham DJ, Pryhuber GS, Caserta MT, Gill SR, Scheible KM, Holden-Wiltse J. Eight practices for data management to enable team data science. J Clin Transl Sci 2020; 5:e14. [PMID: 33948240 PMCID: PMC8057476 DOI: 10.1017/cts.2020.501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 12/16/2022] Open
Abstract
INTRODUCTION In clinical and translational research, data science is often and fortuitously integrated with data collection. This contrasts to the typical position of data scientists in other settings, where they are isolated from data collectors. Because of this, effective use of data science techniques to resolve translational questions requires innovation in the organization and management of these data. METHODS We propose an operational framework that respects this important difference in how research teams are organized. To maximize the accuracy and speed of the clinical and translational data science enterprise under this framework, we define a set of eight best practices for data management. RESULTS In our own work at the University of Rochester, we have strived to utilize these practices in a customized version of the open source LabKey platform for integrated data management and collaboration. We have applied this platform to cohorts that longitudinally track multidomain data from over 3000 subjects. CONCLUSIONS We argue that this has made analytical datasets more readily available and lowered the bar to interdisciplinary collaboration, enabling a team-based data science that is unique to the clinical and translational setting.
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Affiliation(s)
- Andrew McDavid
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, USA
| | - Anthony M. Corbett
- Clinical and Translational Science Institute, University of Rochester, Rochester, NY, USA
| | - Jennifer L. Dutra
- Clinical and Translational Science Institute, University of Rochester, Rochester, NY, USA
| | - Andrew G. Straw
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, USA
| | - David J. Topham
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, USA
| | | | - Mary T. Caserta
- Department of Pediatrics, University of Rochester, Rochester, NY, USA
| | - Steven R. Gill
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, USA
| | | | - Jeanne Holden-Wiltse
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, USA
- Clinical and Translational Science Institute, University of Rochester, Rochester, NY, USA
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23
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Caserta MT, Yang H, Bandyopadhyay S, Qiu X, Gill SR, Java J, McDavid A, Falsey AR, Topham DJ, Holden-Wiltse J, Scheible K, Pryhuber G. Measuring the Severity of Respiratory Illness in the First 2 Years of Life in Preterm and Term Infants. J Pediatr 2019; 214:12-19.e3. [PMID: 31377041 PMCID: PMC6815715 DOI: 10.1016/j.jpeds.2019.06.061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/10/2019] [Accepted: 06/25/2019] [Indexed: 11/05/2022]
Abstract
OBJECTIVE To develop a valid research tool to measure infant respiratory illness severity using parent-reported symptoms. STUDY DESIGN Nose and throat swabs were collected monthly for 1 year and during respiratory illnesses for 2 years in a prospective study of term and preterm infants in the Prematurity, Respiratory Outcomes, Immune System and Microbiome study. Viral pathogens were detected using Taqman Array Cards. Parents recorded symptoms during respiratory illnesses using a Childhood Origins of Asthma (COAST) scorecard. The COAST score was validated using linear mixed effects regression modeling to evaluate associations with hospitalization and specific infections. A data-driven method was also used to compute symptom weights and derive a new score, the Infant Research Respiratory Infection Severity Score (IRRISS). Linear mixed effects regression modeling was repeated with the IRRISS illness data. RESULTS From April 2013 to April 2017, 50 term, 40 late preterm, and 28 extremely low gestational age (<29 weeks of gestation) infants had 303 respiratory illness visits with viral testing and parent-reported symptoms. A range of illness severity was described with 39% of illness scores suggestive of severe disease. Both the COAST score and IRRISS were associated with respiratory syncytial virus infection and hospitalization. Gestational age and human rhinovirus infection were inversely associated with both scoring systems. The IRRISS and COAST scores were highly correlated (r = 0.93; P < .0001). CONCLUSIONS Using parent-reported symptoms, we validated the COAST score as a measure of respiratory illness severity in infants. The new IRRISS score performed as well as the COAST score.
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Key Words
- auc, area under the curve
- coast, childhood origins of asthma study
- ed, emergency department
- elgans, extremely low gestational age newborns
- hrv, human rhinovirus
- irriss, infant research respiratory infection severity score
- lmer, linear mixed effects regression modeling
- prism, prematurity, respiratory outcomes, immune system and microbiome
- rsv, respiratory syncytial virus
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Affiliation(s)
- Mary T. Caserta
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY,Reprint requests: Mary T. Caserta, MD, Division of Pediatric Infectious Diseases, 601 Elmwood Ave, Box 690, Rochester, NY 14642
| | - Hongmei Yang
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY
| | - Sanjukta Bandyopadhyay
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY
| | - Xing Qiu
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY
| | - Steven R. Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY
| | - James Java
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY
| | - Andrew McDavid
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY
| | - Ann R. Falsey
- Department of Medicine-Infectious Diseases, University of Rochester Medical Center, Rochester, NY
| | - David J. Topham
- Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY
| | - Jeanne Holden-Wiltse
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY,UR Clinical and Translational Science Institute, University of Rochester Medical Center, Rochester, NY
| | - Kristin Scheible
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY
| | - Gloria Pryhuber
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY,Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY
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24
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Masters EA, Trombetta RP, de Mesy Bentley KL, Boyce BF, Gill AL, Gill SR, Nishitani K, Ishikawa M, Morita Y, Ito H, Bello-Irizarry SN, Ninomiya M, Brodell JD, Lee CC, Hao SP, Oh I, Xie C, Awad HA, Daiss JL, Owen JR, Kates SL, Schwarz EM, Muthukrishnan G. Evolving concepts in bone infection: redefining "biofilm", "acute vs. chronic osteomyelitis", "the immune proteome" and "local antibiotic therapy". Bone Res 2019; 7:20. [PMID: 31646012 PMCID: PMC6804538 DOI: 10.1038/s41413-019-0061-z] [Citation(s) in RCA: 245] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/17/2019] [Accepted: 06/21/2019] [Indexed: 02/08/2023] Open
Abstract
Osteomyelitis is a devastating disease caused by microbial infection of bone. While the frequency of infection following elective orthopedic surgery is low, rates of reinfection are disturbingly high. Staphylococcus aureus is responsible for the majority of chronic osteomyelitis cases and is often considered to be incurable due to bacterial persistence deep within bone. Unfortunately, there is no consensus on clinical classifications of osteomyelitis and the ensuing treatment algorithm. Given the high patient morbidity, mortality, and economic burden caused by osteomyelitis, it is important to elucidate mechanisms of bone infection to inform novel strategies for prevention and curative treatment. Recent discoveries in this field have identified three distinct reservoirs of bacterial biofilm including: Staphylococcal abscess communities in the local soft tissue and bone marrow, glycocalyx formation on implant hardware and necrotic tissue, and colonization of the osteocyte-lacuno canalicular network (OLCN) of cortical bone. In contrast, S. aureus intracellular persistence in bone cells has not been substantiated in vivo, which challenges this mode of chronic osteomyelitis. There have also been major advances in our understanding of the immune proteome against S. aureus, from clinical studies of serum antibodies and media enriched for newly synthesized antibodies (MENSA), which may provide new opportunities for osteomyelitis diagnosis, prognosis, and vaccine development. Finally, novel therapies such as antimicrobial implant coatings and antibiotic impregnated 3D-printed scaffolds represent promising strategies for preventing and managing this devastating disease. Here, we review these recent advances and highlight translational opportunities towards a cure.
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Affiliation(s)
- Elysia A Masters
- 1Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY USA.,2Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY USA
| | - Ryan P Trombetta
- 1Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY USA.,2Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY USA
| | - Karen L de Mesy Bentley
- 1Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY USA.,3Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY USA.,4Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY USA
| | - Brendan F Boyce
- 1Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY USA.,3Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY USA
| | - Ann Lindley Gill
- 5Department of Microbiology & Immunology, University of Rochester Medical Center, Rochester, NY USA
| | - Steven R Gill
- 5Department of Microbiology & Immunology, University of Rochester Medical Center, Rochester, NY USA
| | - Kohei Nishitani
- 1Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY USA.,6Department of Orthopaedic Surgery, Kyoto University, Kyoto, Japan
| | - Masahiro Ishikawa
- 1Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY USA.,6Department of Orthopaedic Surgery, Kyoto University, Kyoto, Japan
| | - Yugo Morita
- 1Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY USA.,6Department of Orthopaedic Surgery, Kyoto University, Kyoto, Japan
| | - Hiromu Ito
- 6Department of Orthopaedic Surgery, Kyoto University, Kyoto, Japan
| | - Sheila N Bello-Irizarry
- 1Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY USA
| | - Mark Ninomiya
- 1Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY USA
| | - James D Brodell
- 1Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY USA
| | - Charles C Lee
- 1Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY USA
| | - Stephanie P Hao
- 1Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY USA
| | - Irvin Oh
- 1Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY USA.,4Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY USA
| | - Chao Xie
- 1Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY USA.,4Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY USA
| | - Hani A Awad
- 1Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY USA.,2Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY USA.,4Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY USA
| | - John L Daiss
- 1Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY USA.,4Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY USA
| | - John R Owen
- 7Department of Orthopaedic Surgery, Virginia Commonwealth University Medical Center, Richmond, VA USA
| | - Stephen L Kates
- 7Department of Orthopaedic Surgery, Virginia Commonwealth University Medical Center, Richmond, VA USA
| | - Edward M Schwarz
- 1Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY USA.,2Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY USA.,3Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY USA.,4Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY USA.,5Department of Microbiology & Immunology, University of Rochester Medical Center, Rochester, NY USA
| | - Gowrishankar Muthukrishnan
- 1Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY USA.,4Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY USA
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25
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Masters EA, Salminen AT, Begolo S, Luke EN, Barrett SC, Overby CT, Gill AL, de Mesy Bentley KL, Awad HA, Gill SR, Schwarz EM, McGrath JL. An in vitro platform for elucidating the molecular genetics of S. aureus invasion of the osteocyte lacuno-canalicular network during chronic osteomyelitis. Nanomedicine 2019; 21:102039. [PMID: 31247310 DOI: 10.1016/j.nano.2019.102039] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/11/2019] [Accepted: 06/11/2019] [Indexed: 11/30/2022]
Abstract
Staphylococcus aureus osteomyelitis is a devasting disease that often leads to amputation. Recent findings have shown that S. aureus is capable of invading the osteocyte lacuno-canalicular network (OLCN) of cortical bone during chronic osteomyelitis. Normally a 1 μm non-motile cocci, S. aureus deforms smaller than 0.5 μm in the sub-micron channels of the OLCN. Here we present the μSiM-CA (Microfluidic - Silicon Membrane - Canalicular Array) as an in vitro screening platform for the genetic mechanisms of S. aureus invasion. The μSiM-CA platform features an ultrathin silicon membrane with defined pores that mimic the openings of canaliculi. While we anticipated that S. aureus lacking the accessory gene regulator (agr) quorum-sensing system would not be capable of invading the OLCN, we found no differences in propagation compared to wild type in the μSiM-CA. However the μSiM-CA proved predictive as we also found that the agr mutant strain invaded the OLCN of murine tibiae.
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Affiliation(s)
- Elysia A Masters
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY; Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY
| | - Alec T Salminen
- Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY
| | | | - Emma N Luke
- Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY
| | - Sydney C Barrett
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY
| | - Clyde T Overby
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY; Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY
| | - Ann Lindley Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY
| | - Karen L de Mesy Bentley
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY; Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY; Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY
| | - Hani A Awad
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY; Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY
| | - Steven R Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY
| | - Edward M Schwarz
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY; Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY; Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY; Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY
| | - James L McGrath
- Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY.
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26
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Walsh EE, Mariani TJ, Chu C, Grier A, Gill SR, Qiu X, Wang L, Holden-Wiltse J, Corbett A, Thakar J, Benoodt L, McCall MN, Topham DJ, Falsey AR, Caserta MT. Aims, Study Design, and Enrollment Results From the Assessing Predictors of Infant Respiratory Syncytial Virus Effects and Severity Study. JMIR Res Protoc 2019; 8:e12907. [PMID: 31199303 PMCID: PMC6595944 DOI: 10.2196/12907] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 03/01/2019] [Accepted: 03/03/2019] [Indexed: 01/04/2023] Open
Abstract
Background The majority of infants hospitalized with primary respiratory syncytial virus (RSV) infection have no obvious risk factors for severe disease. Objective The aim of this study (Assessing Predictors of Infant RSV Effects and Severity, AsPIRES) was to identify factors associated with severe disease in full-term healthy infants younger than 10 months with primary RSV infection. Methods RSV infected infants were enrolled from 3 cohorts during consecutive winters from August 2012 to April 2016 in Rochester, New York. A birth cohort was prospectively enrolled and followed through their first winter for development of RSV infection. An outpatient supplemental cohort was enrolled in the emergency department or pediatric offices, and a hospital cohort was enrolled on admission with RSV infection. RSV was diagnosed by reverse transcriptase-polymerase chain reaction. Demographic and clinical data were recorded and samples collected for assays: buccal swab (cytomegalovirus polymerase chain reaction, PCR), nasal swab (RSV qualitative PCR, complete viral gene sequence, 16S ribosomal ribonucleic acid [RNA] amplicon microbiota analysis), nasal wash (chemokine and cytokine assays), nasal brush (nasal respiratory epithelial cell gene expression using RNA sequencing [RNAseq]), and 2 to 3 ml of heparinized blood (flow cytometry, RNAseq analysis of purified cluster of differentiation [CD]4+, CD8+, B cells and natural killer cells, and RSV-specific antibody). Cord blood (RSV-specific antibody) was also collected for the birth cohort. Univariate and multivariate logistic regression will be used for analysis of data using a continuous Global Respiratory Severity Score (GRSS) as the outcome variable. Novel statistical methods will be developed for integration of the large complex datasets. Results A total of 453 infants were enrolled into the 3 cohorts; 226 in the birth cohort, 60 in the supplemental cohort, and 78 in the hospital cohort. A total of 126 birth cohort infants remained in the study and were evaluated for 150 respiratory illnesses. Of the 60 RSV positive infants in the supplemental cohort, 42 completed the study, whereas all 78 of the RSV positive hospital cohort infants completed the study. A GRSS was calculated for each RSV-infected infant and is being used to analyze each of the complex datasets by correlation with disease severity in univariate and multivariate methods. Conclusions The AsPIRES study will provide insights into the complex pathogenesis of RSV infection in healthy full-term infants with primary RSV infection. The analysis will allow assessment of multiple factors potentially influencing the severity of RSV infection including the level of RSV specific antibodies, the innate immune response of nasal epithelial cells, the adaptive response by various lymphocyte subsets, the resident airway microbiota, and viral factors. Results of this study will inform disease interventions such as vaccines and antiviral therapies.
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Affiliation(s)
- Edward E Walsh
- University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Thomas J Mariani
- University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - ChinYi Chu
- University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Alex Grier
- University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Steven R Gill
- University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Xing Qiu
- University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Lu Wang
- University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Jeanne Holden-Wiltse
- University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Anthony Corbett
- University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Juilee Thakar
- University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Lauren Benoodt
- University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Matthew N McCall
- University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - David J Topham
- University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Ann R Falsey
- University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Mary T Caserta
- University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
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27
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Caito SW, Jackson BP, Punshon T, Scrimale T, Grier A, Gill SR, Love TM, Watson GE, van Wijngaarden E, Rand MD. Editor's Highlight: Variation in Methylmercury Metabolism and Elimination Status in Humans Following Fish Consumption. Toxicol Sci 2019; 161:443-453. [PMID: 29145616 DOI: 10.1093/toxsci/kfx226] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Evaluating the potential for methylmercury (MeHg) toxicity relies on accurately predicting the mercury (Hg) body burden that results from eating fish. Hg body burden is directly determined by the slow elimination kinetics of MeHg in the human body (kel = 0.014 days-1 or t1/2 =50 days). Existing studies on MeHg half-life in humans demonstrate a wide range values (t1/2 = 30 to >150 days) and has lead to uncertainty in the derivation of a regulatory standard for acceptable daily oral intake. The causes of variation in MeHg toxicokinetics in humans remain little explored. Here we characterize variation in human MeHg metabolism and elimination rate (kel) in 37 adult volunteers who consumed 3 fish meals. We determined MeHg elimination rates via longitudinal Hg analysis in single hairs using laser ablation inductively coupled plasma mass spectrometry. We also measured MeHg metabolism (biotransformation) via speciation of fecal Hg. We find an average kel = 0.0157 days-1 (t1/2 = 44 days) amongst a more than 2-fold variation in kel across the cohort (0.0248-0.0112 days-1; t1/2 = 28-62 days). Although MeHg biotransformation varied widely between individuals, it showed a positive association with elimination rates across the cohort. A more than 2-fold change in kel over a period of 2 years was seen in some individuals. In 2 individuals, who received antibiotic for unrelated health issues, elimination rate was seen to slow significantly. Associations of kel with age, body mass index, gender, and fish eating habits were not observed. We establish that a measure of methylmercury metabolism and eliminaiton status (MerMES) can reduce uncertainty in determining an individual's MeHg toxicokinetics subsequent to eating fish.
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Affiliation(s)
- Samuel W Caito
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Brian P Jackson
- Trace Element Analysis Laboratory, Dartmouth College, Hanover, New Hampshire 03755
| | - Tracy Punshon
- Trace Element Analysis Laboratory, Dartmouth College, Hanover, New Hampshire 03755
| | - Thomas Scrimale
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Alex Grier
- Department of Microbiology and Immunology
| | | | - Tanzy M Love
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642.,Department of Biostatistics and Computational Biology
| | - Gene E Watson
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642.,Eastman Institute for Oral Health.,Department of Pharmacology and Physiology
| | - Edwin van Wijngaarden
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642.,Eastman Institute for Oral Health.,Department of Pediatrics.,Department of Public Health Sciences, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Matthew D Rand
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
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28
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Grier A, McDavid A, Wang B, Qiu X, Java J, Bandyopadhyay S, Yang H, Holden-Wiltse J, Kessler HA, Gill AL, Huyck H, Falsey AR, Topham DJ, Scheible KM, Caserta MT, Pryhuber GS, Gill SR. Neonatal gut and respiratory microbiota: coordinated development through time and space. Microbiome 2018; 6:193. [PMID: 30367675 PMCID: PMC6204011 DOI: 10.1186/s40168-018-0566-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 09/28/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND Postnatal development of early life microbiota influences immunity, metabolism, neurodevelopment, and infant health. Microbiome development occurs at multiple body sites, with distinct community compositions and functions. Associations between microbiota at multiple sites represent an unexplored influence on the infant microbiome. Here, we examined co-occurrence patterns of gut and respiratory microbiota in pre- and full-term infants over the first year of life, a period critical to neonatal development. RESULTS Gut and respiratory microbiota collected as longitudinal rectal, throat, and nasal samples from 38 pre-term and 44 full-term infants were first clustered into community state types (CSTs) on the basis of their compositional profiles. Multiple methods were used to relate the occurrence of CSTs to temporal microbiota development and measures of infant maturity, including gestational age (GA) at birth, week of life (WOL), and post-menstrual age (PMA). Manifestation of CSTs followed one of three patterns with respect to infant maturity: (1) chronological, with CST occurrence frequency solely a function of post-natal age (WOL), (2) idiosyncratic to maturity at birth, with the interval of CST occurrence dependent on infant post-natal age but the frequency of occurrence dependent on GA at birth, and (3) convergent, in which CSTs appear first in infants of greater maturity at birth, with occurrence frequency in pre-terms converging after a post-natal interval proportional to pre-maturity. The composition of CSTs was highly dissimilar between different body sites, but the CST of any one body site was highly predictive of the CSTs at other body sites. There were significant associations between the abundance of individual taxa at each body site and the CSTs of the other body sites, which persisted after stringent control for the non-linear effects of infant maturity. Canonical correlations exist between the microbiota composition at each pair of body sites, with the strongest correlations between proximal locations. CONCLUSION These findings suggest that early microbiota is shaped by neonatal innate and adaptive developmental responses. Temporal progression of CST occurrence is influenced by infant maturity at birth and post-natal age. Significant associations of microbiota across body sites reveal distal connections and coordinated development of the infant microbial ecosystem.
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Affiliation(s)
- Alex Grier
- Genomics Research Center, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Andrew McDavid
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Bokai Wang
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Xing Qiu
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - James Java
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Sanjukta Bandyopadhyay
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Hongmei Yang
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Jeanne Holden-Wiltse
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Haeja A Kessler
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Ann L Gill
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Heidie Huyck
- Medicine-Infectious Disease, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Ann R Falsey
- Medicine-Infectious Disease, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - David J Topham
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA
- Center for Vaccine Biology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Kristin M Scheible
- Division of Neonatology, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Mary T Caserta
- Division of Infectious Disease, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Gloria S Pryhuber
- Division of Neonatology, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Steven R Gill
- Genomics Research Center, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA.
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29
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Xiao J, Grier A, Faustoferri RC, Alzoubi S, Gill AL, Feng C, Liu Y, Quivey RG, Kopycka-Kedzierawski DT, Koo H, Gill SR. Association between Oral Candida and Bacteriome in Children with Severe ECC. J Dent Res 2018; 97:1468-1476. [PMID: 30049240 DOI: 10.1177/0022034518790941] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Candida albicans is an opportunistic fungal organism frequently detected in the oral cavity of children with severe early childhood caries (S-ECC). Previous studies suggested the cariogenic potential of C. albicans, in vitro and in vivo, and further demonstrated its synergistic interactions with Streptococcus mutans. In combination, the 2 organisms are associated with higher caries severity in a rodent model. However, it remains unknown whether C. albicans influences the composition and diversity of the entire oral bacterial community to promote S-ECC onset. With 16s rRNA amplicon sequencing, this study analyzed the microbiota of saliva and supragingival plaque from 39 children (21 S-ECC and 18 caries-free [CF]) and 33 mothers (17 S-ECC and 16 CF). The results revealed that the presence of oral C. albicans is associated with a highly acidogenic and acid-tolerant bacterial community in S-ECC, with an increased abundance of plaque Streptococcus (particularly S. mutans) and certain Lactobacillus/Scardovia species and salivary/plaque Veillonella and Prevotella, as well as decreased levels of salivary/plaque Actinomyces. Concurrent with this microbial community assembly, the activity of glucosyltransferases (cariogenic virulence factors secreted by S. mutans) in plaque was significantly elevated when C. albicans was present. Moreover, the oral microbial community composition and diversity differed significantly by disease group (CF vs. S-ECC) and sample source (saliva vs. plaque). Children and mothers within the CF and S-ECC groups shared microbiota composition and diversity, suggesting a strong maternal influence on children's oral microbiota. Altogether, this study underscores the importance of C. albicans in association with the oral bacteriome in the context of S-ECC etiopathogenesis. Further longitudinal studies are warranted to examine how fungal-bacterial interactions modulate the onset and severity of S-ECC, potentially leading to novel anticaries treatments that address fungal contributions.
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Affiliation(s)
- J Xiao
- 1 Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY, USA
| | - A Grier
- 2 Genomics Research Center, University of Rochester Medical Center, Rochester, NY, USA
| | - R C Faustoferri
- 1 Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY, USA
| | - S Alzoubi
- 1 Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY, USA
| | - A L Gill
- 3 Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - C Feng
- 4 Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Y Liu
- 5 Divisions of Pediatric Dentistry and Community Oral Health, Department of Orthodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - R G Quivey
- 1 Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY, USA.,2 Genomics Research Center, University of Rochester Medical Center, Rochester, NY, USA
| | | | - H Koo
- 5 Divisions of Pediatric Dentistry and Community Oral Health, Department of Orthodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - S R Gill
- 2 Genomics Research Center, University of Rochester Medical Center, Rochester, NY, USA.,3 Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
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30
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Farnsworth CW, Schott EM, Benvie A, Zukoski J, Kates SL, Schwarz EM, Gill SR, Zuscik MJ, Mooney RA. Obesity/type 2 diabetes increases inflammation, periosteal reactive bone formation, and osteolysis during Staphylococcus aureus implant-associated bone infection. J Orthop Res 2018; 36:1614-1623. [PMID: 29227579 PMCID: PMC5995608 DOI: 10.1002/jor.23831] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 05/06/2017] [Accepted: 11/29/2017] [Indexed: 02/04/2023]
Abstract
Obese and type 2 diabetic (T2D) patients have a fivefold increased rate of infection following placement of an indwelling orthopaedic device. Though implant infections are associated with inflammation, periosteal reactive bone formation, and osteolysis, the effect of obesity/T2D on these complicating factors has not been studied. To address this question, C57BL/6J mice were fed a high fat diet (60% Kcal from fat) to induce obesity/T2D, or a control diet (10% Kcal from fat) for 3 months, and challenged with a transtibial pin coated with a bioluminescent USA300 strain of S. aureus. In the resulting infected bone, obesity/T2D was associated with increased S. aureus proliferation and colony forming units. RNA sequencing of the infected tibiae on days 7 and 14 revealed an increase in 635 genes in obese/T2D mice relative to controls. Pathways associated with ossification, angiogenesis, and immunity were enriched. MicroCT and histology on days 21 and 35 demonstrated significant increased periosteal reactive bone formation in infected obese/T2D mice versus infected controls (p < 0.05). The enhanced periosteal bone formation was associated with increased osteoblastic activity and robust endochondral ossification, with persistant cartilage on day 21 that was only observed in infected obesity/T2D. Osteolysis and osteoclast numbers in obesity/T2D were also significantly increased versus infected controls (p < 0.05). Consistent with an up-regulated immune transcriptome, macrophages were more abundant within both the periosteum and the new reactive bone of obese/T2D mice. In conclusion, we find that implant-associated S. aureus osteomyelitis in obesity/T2D is associated with increased inflammation, reactive bone formation, and osteolysis. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:1614-1623, 2018.
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Affiliation(s)
- Christopher W Farnsworth
- Department of Pathology and Laboratory Medicine, University of Rochester, Rochester New York, USA,Center for Musculoskeletal Research, University of Rochester, Rochester New York, USA
| | - Eric M Schott
- Department of Pathology and Laboratory Medicine, University of Rochester, Rochester New York, USA,Center for Musculoskeletal Research, University of Rochester, Rochester New York, USA
| | - Abigail Benvie
- Department of Pathology and Laboratory Medicine, University of Rochester, Rochester New York, USA,Center for Musculoskeletal Research, University of Rochester, Rochester New York, USA
| | - Jacob Zukoski
- Department of Pathology and Laboratory Medicine, University of Rochester, Rochester New York, USA,Center for Musculoskeletal Research, University of Rochester, Rochester New York, USA
| | - Stephen L Kates
- Department of Orthopaedic Surgery, Virginia Commonwealth University, Richmond Virginia, USA
| | - Edward M Schwarz
- Center for Musculoskeletal Research, University of Rochester, Rochester New York, USA
| | - Steven R Gill
- Department of Microbiology and Immunology, University of Rochester, Rochester New York, USA
| | - Michael J Zuscik
- Center for Musculoskeletal Research, University of Rochester, Rochester New York, USA
| | - Robert A Mooney
- Department of Pathology and Laboratory Medicine, University of Rochester, Rochester New York, USA,Center for Musculoskeletal Research, University of Rochester, Rochester New York, USA
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31
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Farnsworth CW, Schott EM, Benvie A, Kates SL, Schwarz EM, Gill SR, Zuscik MJ, Mooney RA. Exacerbated Staphylococcus aureus Foot Infections in Obese/Diabetic Mice Are Associated with Impaired Germinal Center Reactions, Ig Class Switching, and Humoral Immunity. J Immunol 2018; 201:560-572. [PMID: 29858265 DOI: 10.4049/jimmunol.1800253] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/07/2018] [Indexed: 12/14/2022]
Abstract
Obese patients with type 2 diabetes (T2D) are at an increased risk of foot infection, with impaired immune function believed to be a critical factor in the infectious process. In this study, we test the hypothesis that humoral immune defects contribute to exacerbated foot infection in a murine model of obesity/T2D. C57BL/6J mice were rendered obese and T2D by a high-fat diet for 3 mo and were compared with controls receiving a low-fat diet. Following injection of Staphylococcus aureus into the footpad, obese/T2D mice had greater foot swelling and reduced S. aureus clearance than controls. Obese/T2D mice also had impaired humoral immune responses as indicated by lower total IgG levels and lower anti-S. aureus Ab production. Within the draining popliteal lymph nodes of obese/T2D mice, germinal center formation was reduced, and the percentage of germinal center T and B cells was decreased by 40-50%. Activation of both T and B lymphocytes was similarly suppressed in obese/T2D mice. Impaired humoral immunity in obesity/T2D was independent of active S. aureus infection, as a similarly impaired humoral immune response was demonstrated when mice were administered an S. aureus digest. Isolated splenic B cells from obese/T2D mice activated normally but had markedly suppressed expression of Aicda, with diminished IgG and IgE responses. These results demonstrate impaired humoral immune responses in obesity/T2D, including B cell-specific defects in Ab production and class-switch recombination. Together, the defects in humoral immunity may contribute to the increased risk of foot infection in obese/T2D patients.
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Affiliation(s)
- Christopher W Farnsworth
- Department of Pathology and Laboratory Medicine, University of Rochester, Rochester, NY 14642.,Center for Musculoskeletal Research, University of Rochester, Rochester, NY 14642
| | - Eric M Schott
- Department of Pathology and Laboratory Medicine, University of Rochester, Rochester, NY 14642.,Center for Musculoskeletal Research, University of Rochester, Rochester, NY 14642
| | - Abigail Benvie
- Department of Pathology and Laboratory Medicine, University of Rochester, Rochester, NY 14642.,Center for Musculoskeletal Research, University of Rochester, Rochester, NY 14642
| | - Stephen L Kates
- Department of Orthopaedic Surgery, Virginia Commonwealth University, Richmond, VA 23298; and
| | - Edward M Schwarz
- Center for Musculoskeletal Research, University of Rochester, Rochester, NY 14642
| | - Steven R Gill
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642
| | - Michael J Zuscik
- Center for Musculoskeletal Research, University of Rochester, Rochester, NY 14642
| | - Robert A Mooney
- Department of Pathology and Laboratory Medicine, University of Rochester, Rochester, NY 14642; .,Center for Musculoskeletal Research, University of Rochester, Rochester, NY 14642
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32
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Schott EM, Farnsworth CW, Grier A, Lillis JA, Soniwala S, Dadourian GH, Bell RD, Doolittle ML, Villani DA, Awad H, Ketz JP, Kamal F, Ackert-Bicknell C, Ashton JM, Gill SR, Mooney RA, Zuscik MJ. Targeting the gut microbiome to treat the osteoarthritis of obesity. JCI Insight 2018; 3:95997. [PMID: 29669931 DOI: 10.1172/jci.insight.95997] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [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: 06/28/2017] [Accepted: 03/14/2018] [Indexed: 01/07/2023] Open
Abstract
Obesity is a risk factor for osteoarthritis (OA), the greatest cause of disability in the US. The impact of obesity on OA is driven by systemic inflammation, and increased systemic inflammation is now understood to be caused by gut microbiome dysbiosis. Oligofructose, a nondigestible prebiotic fiber, can restore a lean gut microbial community profile in the context of obesity, suggesting a potentially novel approach to treat the OA of obesity. Here, we report that - compared with the lean murine gut - obesity is associated with loss of beneficial Bifidobacteria, while key proinflammatory species gain in abundance. A downstream systemic inflammatory signature culminates with macrophage migration to the synovium and accelerated knee OA. Oligofructose supplementation restores the lean gut microbiome in obese mice, in part, by supporting key commensal microflora, particularly Bifidobacterium pseudolongum. This is associated with reduced inflammation in the colon, circulation, and knee and protection from OA. This observation of a gut microbiome-OA connection sets the stage for discovery of potentially new OA therapeutics involving strategic manipulation of specific microbial species inhabiting the intestinal space.
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Affiliation(s)
- Eric M Schott
- Center for Musculoskeletal Research.,Department of Pathology & Laboratory Medicine, and
| | | | - Alex Grier
- Genomics Research Center, University of Rochester Medical Center, Rochester, New York, USA
| | - Jacquelyn A Lillis
- Genomics Research Center, University of Rochester Medical Center, Rochester, New York, USA
| | - Sarah Soniwala
- Center for Musculoskeletal Research.,Department of Biology and
| | - Gregory H Dadourian
- Department of Biomedical Engineering, University of Rochester, Rochester, New York, USA
| | - Richard D Bell
- Center for Musculoskeletal Research.,Department of Pathology & Laboratory Medicine, and
| | - Madison L Doolittle
- Center for Musculoskeletal Research.,Department of Pathology & Laboratory Medicine, and
| | - David A Villani
- Center for Musculoskeletal Research.,Department of Pathology & Laboratory Medicine, and
| | - Hani Awad
- Center for Musculoskeletal Research.,Department of Biomedical Engineering, University of Rochester, Rochester, New York, USA
| | - John P Ketz
- Center for Musculoskeletal Research.,Department of Orthopaedics & Rehabilitation and
| | - Fadia Kamal
- Center for Musculoskeletal Research.,Department of Orthopaedics & Rehabilitation and
| | | | - John M Ashton
- Genomics Research Center, University of Rochester Medical Center, Rochester, New York, USA
| | - Steven R Gill
- Department of Microbiology & Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Robert A Mooney
- Center for Musculoskeletal Research.,Department of Pathology & Laboratory Medicine, and
| | - Michael J Zuscik
- Center for Musculoskeletal Research.,Department of Orthopaedics & Rehabilitation and
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Rieth KKS, Gill SR, Lott-Limbach AA, Merkley MA, Botero N, Allen PD, Miller MC. Prevalence of High-Risk Human Papillomavirus in Tonsil Tissue in Healthy Adults and Colocalization in Biofilm of Tonsillar Crypts. JAMA Otolaryngol Head Neck Surg 2018; 144:231-237. [PMID: 29372248 PMCID: PMC5885877 DOI: 10.1001/jamaoto.2017.2916] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 11/05/2017] [Indexed: 11/14/2022]
Abstract
IMPORTANCE The pathogenesis of human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma is currently an important topic of elucidation. The presence of latent HPV infection in tonsil tissue of healthy adults may provide an explanation for a component of this process and contribute to the understanding of HPV-associated squamous cell carcinoma oncogenesis of the oropharynx. OBJECTIVE To determine the prevalence of oropharyngeal HPV and to determine the spatial relationship between the virus and crypt biofilm in tonsil tissue. DESIGN, SETTING, AND PARTICIPANTS A retrospective, cross-sectional study was carried out using samples obtained from tonsils that were archived at a university hospital following elective nononcologic tonsillectomy from 2012 to 2015. Samples consisted of formalin-fixed paraffin embedded samples of tumor-free tonsil tissue from 102 adults between the ages of 20 and 39 years. EXPOSURES Human papillomavirus status was assessed by polymerase chain reaction, and high-risk subtypes 16 and 18 were assessed with quantitative polymerase chain reaction assay. Samples that demonstrated presence of HPV were then analyzed by in situ hybridization to localize the viral capsid protein. These samples were then stained with concanavalin A to establish biofilm presence and morphology. These samples were also stained with diamidino-phenylindole (DAPI) to visualize location of the virus in relation to cell nuclei. These data were then assembled for aggregate analysis to colocalize HPV in the biofilm of the tonsillar crypts. MAIN OUTCOMES AND MEASURES Outcome measurements were determined prior to data collection and include prevalence of high-risk HPV types 16 and 18 in tonsil tissue of otherwise healthy adults, as well as demonstration with immunohistochemistry of HPV in tonsillar crypt biofilm. RESULTS In 102 otherwise healthy adults (55 [53.9%] female; age range, 20-39 years), the overall prevalence of HPV in tonsils was 4.9% (n = 5); and high-risk type 16 or 18, 3.9% (n = 4). In this sample population, in situ hybridization colocalized HPV virus to the biofilm of the tonsillar crypts. CONCLUSIONS AND RELEVANCE Biofilm is present in the tonsillar crypts in a considerable proportion of tonsil tissues and may be reproducibly identified. Human papillomavirus is demonstrated to colocalize to the crypt biofilm. This has important implications with respect to the determination of HPV prevalence rates in the oropharynx. It may also play a role in the pathogenesis of HPV-related oropharyngeal carcinoma.
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Affiliation(s)
- Katherine K. S. Rieth
- Department of Otolaryngology, University of Rochester Medical Center, Rochester, New York
| | - Steven R. Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York
| | | | - Mark A. Merkley
- Department of Otolaryngology, University of Rochester Medical Center, Rochester, New York
| | | | - Paul D. Allen
- Department of Otolaryngology, University of Rochester Medical Center, Rochester, New York
| | - Matthew C. Miller
- Department of Otolaryngology, University of Rochester Medical Center, Rochester, New York
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Yoshida T, Grier A, Gill A, Corbett A, Cahill MP, Lockhart A, Simpson EL, Boguniewicz M, Hanifin JM, De Benedetto A, David GL, Leung DY, Schlievert PM, Gill SR, Beck LA. Staphylococcus Aureus -Culture Positivity Observed In Adults With Atopic Dermatitis Is Most Indicative Of An Increased Absolute and Relative Abundance Of S. Aureus and Not Reduced Biodiversity. J Allergy Clin Immunol 2018. [DOI: 10.1016/j.jaci.2017.12.413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Nakatsuji T, Chen TH, Narala S, Chun KA, Two AM, Yun T, Shafiq F, Kotol PF, Bouslimani A, Melnik AV, Latif H, Kim JN, Lockhart A, Artis K, David G, Taylor P, Streib J, Dorrestein PC, Grier A, Gill SR, Zengler K, Hata TR, Leung DYM, Gallo RL. Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis. Sci Transl Med 2017; 9:9/378/eaah4680. [PMID: 28228596 DOI: 10.1126/scitranslmed.aah4680] [Citation(s) in RCA: 613] [Impact Index Per Article: 87.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/08/2016] [Accepted: 01/17/2017] [Indexed: 12/21/2022]
Abstract
The microbiome can promote or disrupt human health by influencing both adaptive and innate immune functions. We tested whether bacteria that normally reside on human skin participate in host defense by killing Staphylococcus aureus, a pathogen commonly found in patients with atopic dermatitis (AD) and an important factor that exacerbates this disease. High-throughput screening for antimicrobial activity against S. aureus was performed on isolates of coagulase-negative Staphylococcus (CoNS) collected from the skin of healthy and AD subjects. CoNS strains with antimicrobial activity were common on the normal population but rare on AD subjects. A low frequency of strains with antimicrobial activity correlated with colonization by S. aureus The antimicrobial activity was identified as previously unknown antimicrobial peptides (AMPs) produced by CoNS species including Staphylococcus epidermidis and Staphylococcus hominis These AMPs were strain-specific, highly potent, selectively killed S. aureus, and synergized with the human AMP LL-37. Application of these CoNS strains to mice confirmed their defense function in vivo relative to application of nonactive strains. Strikingly, reintroduction of antimicrobial CoNS strains to human subjects with AD decreased colonization by S. aureus These findings show how commensal skin bacteria protect against pathogens and demonstrate how dysbiosis of the skin microbiome can lead to disease.
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Affiliation(s)
- Teruaki Nakatsuji
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92092, USA
| | - Tiffany H Chen
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92092, USA
| | - Saisindhu Narala
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92092, USA
| | - Kimberly A Chun
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92092, USA
| | - Aimee M Two
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92092, USA
| | - Tong Yun
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92092, USA
| | - Faiza Shafiq
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92092, USA
| | - Paul F Kotol
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92092, USA
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92092, USA
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92092, USA
| | - Haythem Latif
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92092, USA
| | - Ji-Nu Kim
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92092, USA
| | | | - Keli Artis
- Rho Federal Systems Division Inc., Chapel Hill, NC 27517, USA
| | - Gloria David
- Rho Federal Systems Division Inc., Chapel Hill, NC 27517, USA
| | - Patricia Taylor
- Division of Allergy and Immunology, Department of Pediatrics, National Jewish Health, Denver, CO 80206, USA
| | - Joanne Streib
- Division of Allergy and Immunology, Department of Pediatrics, National Jewish Health, Denver, CO 80206, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92092, USA.,Departments of Chemistry, Biochemistry and Pharmacology, University of California, San Diego, La Jolla, CA 92092, USA
| | - Alex Grier
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14611, USA
| | - Steven R Gill
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14611, USA
| | - Karsten Zengler
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92092, USA
| | - Tissa R Hata
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92092, USA
| | - Donald Y M Leung
- Division of Allergy and Immunology, Department of Pediatrics, National Jewish Health, Denver, CO 80206, USA
| | - Richard L Gallo
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92092, USA.
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Grier A, Qiu X, Bandyopadhyay S, Holden-Wiltse J, Kessler HA, Gill AL, Hamilton B, Huyck H, Misra S, Mariani TJ, Ryan RM, Scholer L, Scheible KM, Lee YH, Caserta MT, Pryhuber GS, Gill SR. Impact of prematurity and nutrition on the developing gut microbiome and preterm infant growth. Microbiome 2017; 5:158. [PMID: 29228972 PMCID: PMC5725645 DOI: 10.1186/s40168-017-0377-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [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: 04/18/2017] [Accepted: 11/23/2017] [Indexed: 05/17/2023]
Abstract
BACKGROUND Identification of factors that influence the neonatal gut microbiome is urgently needed to guide clinical practices that support growth of healthy preterm infants. Here, we examined the influence of nutrition and common practices on the gut microbiota and growth in a cohort of preterm infants. RESULTS With weekly gut microbiota samples spanning postmenstrual age (PMA) 24 to 46 weeks, we developed two models to test associations between the microbiota, nutrition and growth: a categorical model with three successive microbiota phases (P1, P2, and P3) and a model with two periods (early and late PMA) defined by microbiota composition and PMA, respectively. The more significant associations with phase led us to use a phase-based framework for the majority of our analyses. Phase transitions were characterized by rapid shifts in the microbiota, with transition out of P1 occurring nearly simultaneously with the change from meconium to normal stool. The rate of phase progression was positively associated with gestational age at birth, and delayed transition to a P3 microbiota was associated with growth failure. We found distinct bacterial metabolic functions in P1-3 and significant associations between nutrition, microbiota phase, and infant growth. CONCLUSION The phase-dependent impact of nutrition on infant growth along with phase-specific metabolic functions suggests a pioneering potential for improving growth outcomes by tailoring nutrient intake to microbiota phase.
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MESH Headings
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Breast Feeding
- Cohort Studies
- DNA, Bacterial
- Feces/microbiology
- Female
- Gastrointestinal Microbiome
- Gestational Age
- Humans
- Infant
- Infant Health
- Infant, Newborn
- Infant, Premature/growth & development
- Infant, Premature/physiology
- Infant, Premature, Diseases/diet therapy
- Infant, Premature, Diseases/prevention & control
- Male
- Meconium/microbiology
- Nutritional Status
- RNA, Ribosomal, 16S
- Sequence Analysis, DNA
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Affiliation(s)
- Alex Grier
- Genomics Research Center, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Xing Qiu
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Sanjukta Bandyopadhyay
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Jeanne Holden-Wiltse
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Haeja A Kessler
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Ann L Gill
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Brooke Hamilton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Heidie Huyck
- Division of Neonatology, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Sara Misra
- Division of Neonatology, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Thomas J Mariani
- Division of Neonatology, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- Pediatric Molecular and Personalized Medicine Program, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Rita M Ryan
- Department of Pediatrics, Medical University of South Carolina, Charleston, SC, USA
| | - Lori Scholer
- Division of Neonatology, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Kristin M Scheible
- Division of Neonatology, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Yi-Horng Lee
- Division of Pediatric Surgery, Department of Surgery, Robert Wood Johnson University Hospital, New Brunswick, NJ, USA
| | - Mary T Caserta
- Division of Infectious Disease, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Gloria S Pryhuber
- Division of Neonatology, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Steven R Gill
- Genomics Research Center, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA.
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Bhattacharya S, Rosenberg AF, Peterson DR, Grzesik K, Baran AM, Ashton JM, Gill SR, Corbett AM, Holden-Wiltse J, Topham DJ, Walsh EE, Mariani TJ, Falsey AR. Transcriptomic Biomarkers to Discriminate Bacterial from Nonbacterial Infection in Adults Hospitalized with Respiratory Illness. Sci Rep 2017; 7:6548. [PMID: 28747714 PMCID: PMC5529430 DOI: 10.1038/s41598-017-06738-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [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: 12/09/2016] [Accepted: 06/16/2017] [Indexed: 02/02/2023] Open
Abstract
Lower respiratory tract infection (LRTI) commonly causes hospitalization in adults. Because bacterial diagnostic tests are not accurate, antibiotics are frequently prescribed. Peripheral blood gene expression to identify subjects with bacterial infection is a promising strategy. We evaluated whole blood profiling using RNASeq to discriminate infectious agents in adults with microbiologically defined LRTI. Hospitalized adults with LRTI symptoms were recruited. Clinical data and blood was collected, and comprehensive microbiologic testing performed. Gene expression was measured using RNASeq and qPCR. Genes discriminatory for bacterial infection were identified using the Bonferroni-corrected Wilcoxon test. Constrained logistic models to predict bacterial infection were fit using screened LASSO. We enrolled 94 subjects who were microbiologically classified; 53 as “non-bacterial” and 41 as “bacterial”. RNAseq and qPCR confirmed significant differences in mean expression for 10 genes previously identified as discriminatory for bacterial LRTI. A novel dimension reduction strategy selected three pathways (lymphocyte, α-linoleic acid metabolism, IGF regulation) including eleven genes as optimal markers for discriminating bacterial infection (naïve AUC = 0.94; nested CV-AUC = 0.86). Using these genes, we constructed a classifier for bacterial LRTI with 90% (79% CV) sensitivity and 83% (76% CV) specificity. This novel, pathway-based gene set displays promise as a method to distinguish bacterial from nonbacterial LRTI.
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Affiliation(s)
- Soumyaroop Bhattacharya
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, Department of Pediatrics, University of Rochester School Medicine, Rochester, NY, USA
| | - Alex F Rosenberg
- Division of Allergy Immunology & Rheumatology, Department of Medicine, University of Rochester School Medicine, Rochester, NY, USA
| | - Derick R Peterson
- Department of Biostatistics and Computational Biology, University of Rochester School Medicine, Rochester, NY, USA
| | - Katherine Grzesik
- Department of Biostatistics and Computational Biology, University of Rochester School Medicine, Rochester, NY, USA
| | - Andrea M Baran
- Department of Biostatistics and Computational Biology, University of Rochester School Medicine, Rochester, NY, USA
| | - John M Ashton
- Genomics Research Center, University of Rochester School Medicine, Rochester, NY, USA
| | - Steven R Gill
- Genomics Research Center, University of Rochester School Medicine, Rochester, NY, USA
| | - Anthony M Corbett
- Department of Biostatistics and Computational Biology, University of Rochester School Medicine, Rochester, NY, USA
| | - Jeanne Holden-Wiltse
- Department of Biostatistics and Computational Biology, University of Rochester School Medicine, Rochester, NY, USA
| | - David J Topham
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester School Medicine, Rochester, NY, USA.,Department of Microbiology and Immunology, University of Rochester School Medicine, Rochester, NY, USA
| | - Edward E Walsh
- Division of Infectious Diseases, Department of Medicine, University of Rochester School Medicine and Rochester General Hospital, Rochester, NY, USA
| | - Thomas J Mariani
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, Department of Pediatrics, University of Rochester School Medicine, Rochester, NY, USA
| | - Ann R Falsey
- Division of Infectious Diseases, Department of Medicine, University of Rochester School Medicine and Rochester General Hospital, Rochester, NY, USA.
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Caserta MT, Yang H, Gill SR, Holden-Wiltse J, Pryhuber G. Viral Respiratory Infections in Preterm Infants during and after Hospitalization. J Pediatr 2017; 182:53-58.e3. [PMID: 28041669 PMCID: PMC5328856 DOI: 10.1016/j.jpeds.2016.11.077] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/17/2016] [Accepted: 11/29/2016] [Indexed: 12/19/2022]
Abstract
OBJECTIVE To determine the burden of viral respiratory infections in preterm infants both during and subsequent to neonatal intensive care unit (NICU) hospitalization and to compare this with term infants living in the community. STUDY DESIGN From March 2013 through March 2015, we enrolled 189 newborns (96 term and 93 preterm) into a prospective, longitudinal study obtaining nose/throat swabs within 7 days of birth, weekly while hospitalized and then monthly to 4 months after hospital discharge. Taqman array cards were used to identify 16 viral respiratory pathogens by real-time polymerase chain reaction. Demographic, clinical, and laboratory data were gathered from electronic medical records, and parent interview while hospitalized with interval histories collected at monthly visits. The hospital course of all preterm infants who underwent late-onset sepsis evaluations was reviewed. RESULTS Over 119 weeks, we collected 618 nose/throat swabs from at risk preterm infants in our level IV regional NICU. Only 4 infants had viral respiratory infections, all less than 28 weeks gestation at birth. Two infants were symptomatic with the infections recognized by the clinical team. The daily risk of acquiring a respiratory viral infection in preterm infants in the NICU was significantly lower than in the full term cohort living in the community. Once discharged from the hospital, viral respiratory infections were common in all infants. CONCLUSIONS Viral respiratory infections are infrequent in a NICU with strict infection prevention strategies and do not appear to cause unrecognized illness. Both preterm and term infants living in the community quickly acquire respiratory viral infections.
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Affiliation(s)
- Mary T Caserta
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY.
| | - Hongmei Yang
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY
| | - Steven R Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY
| | - Jeanne Holden-Wiltse
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY
| | - Gloria Pryhuber
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY; Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY
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Seppo AE, Fridy S, Varrone J, Gill SR, Grier A, Lomas JM, Martina C, Looney RJ, Jarvinen-Seppo KM. High Microbiome Diversity and IgA Responses in Breast Milk of Old Order Mennonites with a Low Prevalence of Allergic Diseases. J Allergy Clin Immunol 2017. [DOI: 10.1016/j.jaci.2016.12.893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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40
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Xiao J, Moon Y, Li L, Rustchenko E, Wakabayashi H, Zhao X, Feng C, Gill SR, McLaren S, Malmstrom H, Ren Y, Quivey R, Koo H, Kopycka-Kedzierawski DT. Candida albicans Carriage in Children with Severe Early Childhood Caries (S-ECC) and Maternal Relatedness. PLoS One 2016; 11:e0164242. [PMID: 27741258 PMCID: PMC5065202 DOI: 10.1371/journal.pone.0164242] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 08/26/2016] [Indexed: 11/23/2022] Open
Abstract
Introduction Candida albicans has been detected together with Streptococcus mutans in high numbers in plaque-biofilm from children with early childhood caries (ECC). The goal of this study was to examine the C. albicans carriage in children with severe early childhood caries (S-ECC) and the maternal relatedness. Methods Subjects in this pilot cross-sectional study were recruited based on a convenient sample. DMFT(S)/dmft(s) caries and plaque scores were assessed during a comprehensive oral exam. Social-demographic and related background information was collected through a questionnaire. Saliva and plaque sample from all children and mother subjects were collected. C. albicans were isolated by BBL™ CHROMagar™ and also identified using germ tube test. S. mutans was isolated using Mitis Salivarius with Bacitracin selective medium and identified by colony morphology. Genetic relatedness was examined using restriction endonuclease analysis of the C. albicans genome using BssHII (REAG-B). Multilocus sequence typing was used to examine the clustering information of isolated C. albicans. Spot assay was performed to examine the C. albicans Caspofungin susceptibility between S-ECC children and their mothers. All statistical analyses (power analysis for sample size, Spearman’s correlation coefficient and multiple regression analyses) were implemented with SAS 9.4 Results A total of 18 S-ECC child-mother pairs and 17 caries free child-mother pairs were enrolled in the study. Results indicated high C. albicans carriage rate in the oral cavity (saliva and plaque) of both S-ECC children and their mothers (>80%). Spearman’s correlation coefficient also indicated a significant correlation between salivary and plaque C. albicans and S. mutans carriage (p<0.01) and caries severity (p<0.05). The levels of C. albicans in the prepared saliva and plaque sample (1ml resuspension) of S-ECC children were 1.3 ± 4.5 x104 cfu/ml and 1.2 ± 3.5 x104 cfu/ml (~3-log higher vs. caries-free children). Among 18 child-mother pairs, >60% of them demonstrated identical C. albicans REAG-B pattern. C. albicans isolated from >65% of child-mother pairs demonstrated similar susceptibility to caspofungin in spot assay, while no caspofungin resistant strains were seen when compared with C. albicans wild-type strain SC5314. Interestingly, the regression analysis showed that factors such as antibiotic usage, birth weight, inhaler use, brushing frequency, and daycare attendance had no significant effect on the oral carriage of C. albicans in the S-ECC children. Conclusions Our results reveal that both the child with S-ECC and the mother were highly infected with C. albicans, while most of the strains were genetically related, suggesting that the mother might be a source for C. albicans acquisition in the oral cavity of children affected by the disease.
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Affiliation(s)
- Jin Xiao
- Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY, United States of America
- * E-mail:
| | - Yonghwi Moon
- Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Lihua Li
- Department of Dentistry, North Sichuan Medical University, Sichuan, China
| | - Elena Rustchenko
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Hironao Wakabayashi
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Xiaoyi Zhao
- School of Dentistry, Peking University, Beijing, China
| | - Changyong Feng
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Steven R. Gill
- Genomics Research Center, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Sean McLaren
- Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Hans Malmstrom
- Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Yanfang Ren
- Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Robert Quivey
- Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Hyun Koo
- Department of Orthodontics and Pediatric Dentistry & Community Oral Health Divisions, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
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41
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Chu CY, Qiu X, Wang L, Bhattacharya S, Lofthus G, Corbett A, Holden-Wiltse J, Grier A, Tesini B, Gill SR, Falsey AR, Caserta MT, Walsh EE, Mariani TJ. The Healthy Infant Nasal Transcriptome: A Benchmark Study. Sci Rep 2016; 6:33994. [PMID: 27658638 PMCID: PMC5034274 DOI: 10.1038/srep33994] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 09/06/2016] [Indexed: 01/21/2023] Open
Abstract
Responses by resident cells are likely to play a key role in determining the severity of respiratory disease. However, sampling of the airways poses a significant challenge, particularly in infants and children. Here, we report a reliable method for obtaining nasal epithelial cell RNA from infants for genome-wide transcriptomic analysis, and describe baseline expression characteristics in an asymptomatic cohort. Nasal epithelial cells were collected by brushing of the inferior turbinates, and gene expression was interrogated by RNA-seq analysis. Reliable recovery of RNA occurred in the absence of adverse events. We observed high expression of epithelial cell markers and similarity to the transcriptome for intrapulmonary airway epithelial cells. We identified genes displaying low and high expression variability, both inherently, and in response to environmental exposures. The greatest gene expression differences in this asymptomatic cohort were associated with the presence of known pathogenic viruses and/or bacteria. Robust bacteria-associated gene expression patterns were significantly associated with the presence of Moraxella. In summary, we have developed a reliable method for interrogating the infant airway transcriptome by sampling the nasal epithelium. Our data demonstrates both the fidelity and feasibility of our methodology, and describes normal gene expression and variation within a healthy infant cohort.
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Affiliation(s)
- Chin-Yi Chu
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, University of Rochester Medical Center, Rochester NY, USA
| | - Xing Qiu
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester NY, USA
| | - Lu Wang
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester NY, USA
| | - Soumyaroop Bhattacharya
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, University of Rochester Medical Center, Rochester NY, USA
| | - Gerry Lofthus
- Department of Medicine, University of Rochester Medical Center, Rochester NY, USA
| | - Anthony Corbett
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester NY, USA
| | - Jeanne Holden-Wiltse
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester NY, USA
| | - Alex Grier
- Department of Microbiology and Immunology and University of Rochester Medical Center, Rochester NY, USA
| | - Brenda Tesini
- Division of Pediatric Infectious Diseases, University of Rochester Medical Center, Rochester NY, USA
| | - Steven R. Gill
- Department of Microbiology and Immunology and University of Rochester Medical Center, Rochester NY, USA
| | - Ann R. Falsey
- Department of Medicine, Rochester General Hospital University of Rochester Medical Center, Rochester NY, USA
| | - Mary T. Caserta
- Division of Pediatric Infectious Diseases, University of Rochester Medical Center, Rochester NY, USA
| | - Edward E. Walsh
- Department of Medicine, Rochester General Hospital University of Rochester Medical Center, Rochester NY, USA
| | - Thomas J. Mariani
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, University of Rochester Medical Center, Rochester NY, USA
- Department of Medicine, University of Rochester Medical Center, Rochester NY, USA
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Yoshida T, Myers JR, Ashton JM, De Benedetto A, Gill SR, Philpot C, David G, Leung DY, Beck LA. Novel Gene Signatures Observed in the Nonlesional Skin from European American Atopic Dermatitis Subjects Who Are Colonized with Staphyloccoccus Aureus. J Allergy Clin Immunol 2016. [DOI: 10.1016/j.jaci.2015.12.730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Merkley MA, Bice TC, Grier A, Strohl AM, Man LX, Gill SR. The effect of antibiotics on the microbiome in acute exacerbations of chronic rhinosinusitis. Int Forum Allergy Rhinol 2015. [DOI: 10.1002/alr.21591] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mark A. Merkley
- Department of Otolaryngology Head and Neck Surgery, University of Rochester Medical Center; Rochester NY
| | - Tristan C. Bice
- School of Medicine and Dentistry, University of Rochester; Rochester NY
| | - Alex Grier
- Genomics Research Center, University of Rochester Medical Center; Rochester NY
| | - Alexis M. Strohl
- Department of Otolaryngology Head and Neck Surgery, University of Rochester Medical Center; Rochester NY
| | - Li-Xing Man
- Department of Otolaryngology Head and Neck Surgery, University of Rochester Medical Center; Rochester NY
| | - Steven R. Gill
- Genomics Research Center, University of Rochester Medical Center; Rochester NY
- Department of Microbiology and Immunology, University of Rochester Medical Center; Rochester NY
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Sharma-Kuinkel BK, Mongodin EF, Myers JR, Vore KL, Canfield GS, Fraser CM, Rude TH, Fowler VG, Gill SR. Potential Influence of Staphylococcus aureus Clonal Complex 30 Genotype and Transcriptome on Hematogenous Infections. Open Forum Infect Dis 2015. [PMID: 26213692 PMCID: PMC4512144 DOI: 10.1093/ofid/ofv093] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background. The contemporary Staphylococcus aureus clonal complex (CC) 30 lineage is associated with complicated infections, including endocarditis and osteomyelitis. This lineage diverged from the phage-type 80/81 S aureus clone responsible for a major bacterial epidemic of the 20th century. The genome and transcriptome features that contribute to complicated infections of the CC30 lineage are unknown. Methods. Twenty-nine clinical methicillin-resistant S aureus (MRSA) strains (8 from CC30 and 21 from other major CCs were evaluated for virulence using murine and Galleria mellonella sepsis models. Genomic features of CC30 were identified by comparative genome sequencing and RNA-Seq transcriptome analysis of the 29 strains and 31 previously sequenced S aureus genomes. Results. The CC30 isolates displayed lower virulence in the sepsis models compared with other CCs [P < .0001]. Comparisons of orthologous proteins and transcriptome analysis identified genes (eg, nitric oxide reductase) and changes in metabolic pathways (eg, pyrimidine metabolism) that contribute to the distinct CC30 phenotype. Previously reported nonsynonymous single-nucleotide polymorphisms (SNPs) were found in accessory gene regulator C (agrC) and α-hemolysin (hla), molecules important for virulence. Additional nonsynonymous SNPs conserved across clinical CC30 isolates when compared with the first sequenced contemporary CC30 clone, MRSA-16, were identified in multiple genes, suggesting continuing evolutionary divergence in this lineage. Conclusions. Genomic and transcriptional analyses suggest that the CC30 lineage has acquired metabolic features that contribute to persistent and complicated infections. Absence of sepsis-induced mortality in animal models may be due in part to its unique genomic profile and suggests that specific genotypes of S aureus elicit distinct types of infection types.
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Affiliation(s)
| | - Emmanuel F Mongodin
- Institute for Genome Sciences , University of Maryland School of Medicine , Baltimore
| | - Jason R Myers
- Department of Microbiology and Immunology , University of Rochester , New York ; University of Rochester Genomics Research Center , University of Rochester , New York
| | - Kelly L Vore
- Department of Microbiology and Immunology , University of Rochester , New York
| | - Greg S Canfield
- Department of Microbiology and Immunology , University of Rochester , New York
| | - Claire M Fraser
- Institute for Genome Sciences , University of Maryland School of Medicine , Baltimore
| | - Thomas H Rude
- Department of Medicine , Duke University Medical Center , Durham, North Carolina
| | - Vance G Fowler
- Department of Medicine , Duke University Medical Center , Durham, North Carolina ; Duke Clinical Research Institute , Durham, North Carolina
| | - Steven R Gill
- Department of Microbiology and Immunology , University of Rochester , New York ; University of Rochester Genomics Research Center , University of Rochester , New York
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Dardas M, Gill SR, Grier A, Pryhuber GS, Gill AL, Lee YH, Guillet R. The impact of postnatal antibiotics on the preterm intestinal microbiome. Pediatr Res 2014; 76:150-8. [PMID: 24819377 DOI: 10.1038/pr.2014.69] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 02/07/2014] [Indexed: 01/27/2023]
Abstract
BACKGROUND Development of the intestinal microbiome in preterm infants has significant impact on infant health. Our objective was to determine if duration of antibiotics within the first 10 and 30 d after birth affects the intestinal microbiome. METHODS Subjects were 24 0/7-31 6/7 wk of gestational age who received ≥ 50% breast milk and a total of ≥ 100 ml/kg of feeds by 10 d. Rectal (fecal) swabs were collected at 10 and 30 d and analyzed by 16S rRNA pyrosequencing. At both time points, we examined the rectal microbiome from infants who received only 2 d of antibiotics and those who received at least 7 d of antibiotics. RESULTS In the 29 infants enrolled in our study, we found a decrease in diversity index from 10 d samples in those who received more antibiotics. Such difference in diversity and richness was not as pronounced in 30 d samples. Firmicutes and Bacteroidetes were most abundant in the 10 d samples. While these two phyla remained dominant in 30 d samples, there was an increase in Proteobacteria and Actinobacteria. CONCLUSION Despite antibiotic therapy, neonates continued to acquire bacteria in the gastrointestinal tract. The process of bacterial acquisition is perturbed with the use of antibiotics.
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Affiliation(s)
- Majd Dardas
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
| | - Steven R Gill
- 1] Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York [2] Genomics Research Center, University of Rochester Medical Center, Rochester, New York
| | - Alex Grier
- Genomics Research Center, University of Rochester Medical Center, Rochester, New York
| | - Gloria S Pryhuber
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
| | - Ann L Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York
| | - Yi-Horng Lee
- Division of Pediatric Surgery, Department of Surgery, University of Rochester Medical Center, Rochester, New York
| | - Ronnie Guillet
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
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Zhu L, Baker SS, Gill C, Liu W, Alkhouri R, Baker RD, Gill SR. Characterization of gut microbiomes in nonalcoholic steatohepatitis (NASH) patients: a connection between endogenous alcohol and NASH. Hepatology 2013; 57:601-9. [PMID: 23055155 DOI: 10.1002/hep.26093] [Citation(s) in RCA: 1108] [Impact Index Per Article: 100.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Accepted: 09/24/2012] [Indexed: 02/06/2023]
Abstract
UNLABELLED Nonalcoholic steatohepatitis (NASH) is a serious liver disease associated with obesity. Characterized by metabolic syndrome, hepatic steatosis, and liver inflammation, NASH is believed to be under the influence of the gut microflora. Here, the composition of gut bacterial communities of NASH, obese, and healthy children was determined by 16S ribosomal RNA pyrosequencing. In addition, peripheral blood ethanol was analyzed to monitor endogenous ethanol production of patients and healthy controls. UniFrac-based principle coordinates analysis indicated that most of the microbiome samples clustered by disease status. Each group was associated with a unique pattern of enterotypes. Differences were abundant at phylum, family, and genus levels between healthy subjects and obese patients (with or without NASH), and relatively fewer differences were observed between obese and the NASH microbiomes. Among those taxa with greater than 1% representation in any of the disease groups, Proteobacteria, Enterobacteriaceae, and Escherichia were the only phylum, family and genus types exhibiting significant difference between obese and NASH microbiomes. Similar blood-ethanol concentrations were observed between healthy subjects and obese non-NASH patients, but NASH patients exhibited significantly elevated blood ethanol levels. CONCLUSIONS The increased abundance of alcohol-producing bacteria in NASH microbiomes, elevated blood-ethanol concentration in NASH patients, and the well-established role of alcohol metabolism in oxidative stress and, consequently, liver inflammation suggest a role for alcohol-producing microbiota in the pathogenesis of NASH. We postulate that the distinct composition of the gut microbiome among NASH, obese, and healthy controls could offer a target for intervention or a marker for disease.
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Affiliation(s)
- Lixin Zhu
- Digestive Diseases and Nutrition Center, Department of Pediatrics, State University of New York at Buffalo, Buffalo, NY 14214, USA
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Gill SR, McIntyre LM, Nelson CL, Remortel B, Rude T, Reller LB, Fowler VG. Potential associations between severity of infection and the presence of virulence-associated genes in clinical strains of Staphylococcus aureus. PLoS One 2011; 6:e18673. [PMID: 21541311 PMCID: PMC3082525 DOI: 10.1371/journal.pone.0018673] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [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: 10/07/2010] [Accepted: 03/15/2011] [Indexed: 01/31/2023] Open
Abstract
Background The clinical spectrum of Staphylococcus aureus infection ranges from asymptomatic nasal carriage to osteomyelitis, infective endocarditis (IE) and death. In this study, we evaluate potential association between the presence of specific genes in a collection of prospectively characterized S. aureus clinical isolates and clinical outcome. Methodology/Principal Findings Two hundred thirty-nine S. aureus isolates (121 methicillin-resistant S. aureus [MRSA] and 118 methicillin-susceptible S. aureus [MSSA]) were screened by array comparative genomic hybridization (aCGH) to identify genes implicated in complicated infections. After adjustment for multiple tests, 226 genes were significantly associated with severity of infection. Of these 226 genes, 185 were not in the SCCmec element. Within the 185 non-SCCmec genes, 171 were less common and 14 more common in the complicated infection group. Among the 41 genes in the SCCmec element, 37 were more common and 4 were less common in the complicated group. A total of 51 of the 2014 sequences evaluated, 14 non-SCCmec and 37 SCCmec, were identified as genes of interest. Conclusions/Significance Of the 171 genes less common in complicated infections, 152 are of unknown function and may contribute to attenuation of virulence. The 14 non-SCCmec genes more common in complicated infections include bacteriophage-encoded genes such as regulatory factors and autolysins with potential roles in tissue adhesion or biofilm formation.
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Affiliation(s)
- Steven R Gill
- Department of Oral Biology, University at Buffalo, Buffalo, New York, United States of America.
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Madhusoodanan J, Seo KS, Remortel B, Park JY, Hwang SY, Fox LK, Park YH, Deobald CF, Wang D, Liu S, Daugherty SC, Gill AL, Bohach GA, Gill SR. An Enterotoxin-Bearing Pathogenicity Island in Staphylococcus epidermidis. J Bacteriol 2011; 193:1854-62. [PMID: 21317317 PMCID: PMC3133018 DOI: 10.1128/jb.00162-10] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [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] [Received: 02/15/2010] [Accepted: 02/01/2011] [Indexed: 11/20/2022] Open
Abstract
Cocolonization of human mucosal surfaces causes frequent encounters between various staphylococcal species, creating opportunities for the horizontal acquisition of mobile genetic elements. The majority of Staphylococcus aureus toxins and virulence factors are encoded on S. aureus pathogenicity islands (SaPIs). Horizontal movement of SaPIs between S. aureus strains plays a role in the evolution of virulent clinical isolates. Although there have been reports of the production of toxic shock syndrome toxin 1 (TSST-1), enterotoxin, and other superantigens by coagulase-negative staphylococci, no associated pathogenicity islands have been found in the genome of Staphylococcus epidermidis, a generally less virulent relative of S. aureus. We show here the first evidence of a composite S. epidermidis pathogenicity island (SePI), the product of multiple insertions in the genome of a clinical isolate. The taxonomic placement of S. epidermidis strain FRI909 was confirmed by a number of biochemical tests and multilocus sequence typing. The genome sequence of this strain was analyzed for other unique gene clusters and their locations. This pathogenicity island encodes and expresses staphylococcal enterotoxin C3 (SEC3) and staphylococcal enterotoxin-like toxin L (SElL), as confirmed by quantitative reverse transcription-PCR (qRT-PCR) and immunoblotting. We present here an initial characterization of this novel pathogenicity island, and we establish that it is stable, expresses enterotoxins, and is not obviously transmissible by phage transduction. We also describe the genome sequence, excision, replication, and packaging of a novel bacteriophage in S. epidermidis FRI909, as well as attempts to mobilize the SePI element by this phage.
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Affiliation(s)
| | - Keun Seok Seo
- Department of Microbiology, Molecular Biology and Biochemistry, University of Idaho, Moscow, Idaho
| | | | - Joo Youn Park
- Department of Veterinary Medicine, Washington State University, Pullman, Washington
| | - Sun Young Hwang
- Department of Microbiology, Molecular Biology and Biochemistry, University of Idaho, Moscow, Idaho
- Department of Microbiology, College of Veterinary Medicine and School of Agricultural Biotechnology, Seoul National University, Seoul 151-742, South Korea
| | - Lawrence K. Fox
- Department of Veterinary Medicine, Washington State University, Pullman, Washington
| | - Yong Ho Park
- Department of Microbiology, College of Veterinary Medicine and School of Agricultural Biotechnology, Seoul National University, Seoul 151-742, South Korea
| | - Claudia F. Deobald
- Department of Microbiology, Molecular Biology and Biochemistry, University of Idaho, Moscow, Idaho
| | - Dan Wang
- Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, New York
| | - Song Liu
- Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, New York
| | - Sean C. Daugherty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland
| | - Ann Lindley Gill
- Departments of Oral Biology
- Infectious Disease and Genomics, NYS Center of Excellence in Bioinformatics and Life Sciences, The State University of New York
| | - Gregory A. Bohach
- Department of Microbiology, Molecular Biology and Biochemistry, University of Idaho, Moscow, Idaho
| | - Steven R. Gill
- Departments of Oral Biology
- Microbiology and Immunology
- Infectious Disease and Genomics, NYS Center of Excellence in Bioinformatics and Life Sciences, The State University of New York
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Gerrish RS, Gill SR. Tailed pooled suppression subtractive hybridization (PSSH) adaptors do not alter efficiency. Antonie Van Leeuwenhoek 2010; 98:573-9. [DOI: 10.1007/s10482-010-9465-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Accepted: 05/26/2010] [Indexed: 11/28/2022]
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50
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Christie GE, Matthews AM, King DG, Lane KD, Olivarez NP, Tallent SM, Gill SR, Novick RP. The complete genomes of Staphylococcus aureus bacteriophages 80 and 80α--implications for the specificity of SaPI mobilization. Virology 2010; 407:381-90. [PMID: 20869739 DOI: 10.1016/j.virol.2010.08.036] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [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: 07/22/2010] [Revised: 08/22/2010] [Accepted: 08/31/2010] [Indexed: 11/19/2022]
Abstract
Staphylococcus aureus pathogenicity islands (SaPIs) are mobile elements that are induced by a helper bacteriophage to excise and replicate and to be encapsidated in phage-like particles smaller than those of the helper, leading to high-frequency transfer. SaPI mobilization is helper phage specific; only certain SaPIs can be mobilized by a particular helper phage. Staphylococcal phage 80α can mobilize every SaPI tested thus far, including SaPI1, SaPI2 and SaPIbov1. Phage 80, on the other hand, cannot mobilize SaPI1, and ϕ11 mobilizes only SaPIbov1. In order to better understand the relationship between SaPIs and their helper phages, the genomes of phages 80 and 80α were sequenced, compared with other staphylococcal phage genomes, and analyzed for unique features that may be involved in SaPI mobilization.
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Affiliation(s)
- G E Christie
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, 1101 E Marshall Street; PO Box 980678, Richmond, VA 23298-0678, USA.
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