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Liu CM, Kohanski MA, Mendiola M, Soldanova K, Dwan MG, Lester R, Nordstrom L, Price LB, Lane AP. Impact of saline irrigation and topical corticosteroids on the postsurgical sinonasal microbiota. Int Forum Allergy Rhinol 2014; 5:185-90. [PMID: 25556553 DOI: 10.1002/alr.21467] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 11/01/2014] [Accepted: 11/07/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND Topical treatments with nasal saline irrigation, topical steroid sprays, or corticosteroid rinses can improve sinonasal symptoms in chronic rhinosinusitis (CRS). However, the impact of these therapies on commensals (Corynebacterium) and on biofilm pathogens associated with CRS (Staphylococcus aureus and Pseudomonas) is not well characterized. METHODS Paired nasal and sinus swabs were collected endoscopically from 28 controls and 14 CRS patients with nasal polyposis (CRSwNP) who had not received systemic antibiotics or corticosteroids in the previous 8 weeks. Total DNA from swab eluents were extracted and analyzed by 16S rRNA gene-based pyrosequencing. A total of 359,077 reads were obtained and classified taxonomically. The association of use of topical therapies with sinonasal microbiota composition was assessed by factor/vector-fitting. The proportional abundances of sinonasal bacteria between topical therapy users and nonusers were further compared by 2-tailed Kolmogorov-Smirnov test among controls and among CRSwNP participants. RESULTS Nasal saline irrigation, with or without added budesonide, was not associated with significantly distinct sinonasal microbiota composition or significantly decreased Pseudomonas or S. aureus abundances among either controls or CRSwNP participants. Corynebacterium was slightly lower in controls that reported using saline irrigation than those who did not. No significant association was found between nasal saline irrigation and the proportional abundances of Pseudomonas, S. aureus, and Corynebacterium in CRSwNP participants. However, male CRSwNP patients were noted to have significantly higher Corynebacterium proportional abundances than their female counterparts. The use of topical steroid sprays was associated with a distinct microbiota in control subjects, characterized by higher proportional abundances of Dolosigranulum and Simonsiella and a lower proportional abundance of Campylobacter. CONCLUSION Nasal saline irrigation is not associated with a distinct alteration in the proportional abundance of commensal bacteria or biofilm-forming pathogens in CRSwNP patients. However, use of topical intranasal corticosteroid sprays in control subjects is associated with a distinct sinonasal microbiota.
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Affiliation(s)
- Cindy M Liu
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD; Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ; Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ
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Liu CM, Osborne BJW, Hungate BA, Shahabi K, Huibner S, Lester R, Dwan MG, Kovacs C, Contente-Cuomo TL, Benko E, Aziz M, Price LB, Kaul R. The semen microbiome and its relationship with local immunology and viral load in HIV infection. PLoS Pathog 2014; 10:e1004262. [PMID: 25058515 PMCID: PMC4110035 DOI: 10.1371/journal.ppat.1004262] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [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: 01/14/2014] [Accepted: 06/06/2014] [Indexed: 12/02/2022] Open
Abstract
Semen is a major vector for HIV transmission, but the semen HIV RNA viral load (VL) only correlates moderately with the blood VL. Viral shedding can be enhanced by genital infections and associated inflammation, but it can also occur in the absence of classical pathogens. Thus, we hypothesized that a dysregulated semen microbiome correlates with local HIV shedding. We analyzed semen samples from 49 men who have sex with men (MSM), including 22 HIV-uninfected and 27 HIV-infected men, at baseline and after starting antiretroviral therapy (ART) using 16S rRNA gene-based pyrosequencing and quantitative PCR. We studied the relationship of semen bacteria with HIV infection, semen cytokine levels, and semen VL by linear regression, non-metric multidimensional scaling, and goodness-of-fit test. Streptococcus, Corynebacterium, and Staphylococcus were common semen bacteria, irrespective of HIV status. While Ureaplasma was the more abundant Mollicutes in HIV-uninfected men, Mycoplasma dominated after HIV infection. HIV infection was associated with decreased semen microbiome diversity and richness, which were restored after six months of ART. In HIV-infected men, semen bacterial load correlated with seven pro-inflammatory semen cytokines, including IL-6 (p = 0.024), TNF-α (p = 0.009), and IL-1b (p = 0.002). IL-1b in particular was associated with semen VL (r2 = 0.18, p = 0.02). Semen bacterial load was also directly linked to the semen HIV VL (r2 = 0.15, p = 0.02). HIV infection reshapes the relationship between semen bacteria and pro-inflammatory cytokines, and both are linked to semen VL, which supports a role of the semen microbiome in HIV sexual transmission. The classical paradigm of HIV infectivity centers on the blood HIV RNA viral load. However, while other fluid compartments such as semen and cerebrospinal fluid can have distinct viral loads from blood, the causes of localized HIV shedding are not fully understood. Since the semen viral load is an independent predictor of HIV transmission risk, it is critical to understand the local factors that trigger increased semen viral shedding in order to develop novel preventative strategies. Here, we evaluated the semen microbiome, bacterial load, and cytokine levels in 22 HIV-uninfected men who have sex with men (MSM) and in 27 HIV-infected MSM before and after initiation of antiretroviral therapy (ART). We found that HIV infection reduces semen microbiome biodiversity, which is restored with ART and immune reconstitution. We also found that semen bacterial load in untreated, HIV-infected men is associated with the levels of seven semen cytokines, relationships not seen in the uninfected controls. In particular, the cytokine IL-1b was uniquely correlated with both semen bacterial and viral load. Our findings support the interaction between semen microbiome and local immunology, and suggest that IL-1b could be a mechanism for semen microbiome to trigger semen viral shedding.
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Affiliation(s)
- Cindy M. Liu
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | | | - Bruce A. Hungate
- Department of Biology, Northern Arizona University, Flagstaff, Arizona, United States of America
| | | | - Sanja Huibner
- Department of Medicine, University of Toronto, Toronto, Canada
| | - Richard Lester
- Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Michael G. Dwan
- Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Colin Kovacs
- Department of Medicine, University of Toronto, Toronto, Canada
- Maple Leaf Medical Centre, Toronto, Canada
| | - Tania L. Contente-Cuomo
- Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | | | - Maliha Aziz
- Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- Department of Environmental and Occupational Health, George Washington University School of Public Health, Washington, D.C., United States of America
| | - Lance B. Price
- Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- Department of Environmental and Occupational Health, George Washington University School of Public Health, Washington, D.C., United States of America
- * E-mail: (LBP); (RK)
| | - Rupert Kaul
- Department of Medicine, University of Toronto, Toronto, Canada
- Department of Medicine, University Health Network, Toronto, Canada
- * E-mail: (LBP); (RK)
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Liu CM, Soldanova K, Nordstrom L, Dwan MG, Moss OL, Contente-Cuomo TL, Keim P, Price LB, Lane AP. Medical therapy reduces microbiota diversity and evenness in surgically recalcitrant chronic rhinosinusitis. Int Forum Allergy Rhinol 2013; 3:775-81. [PMID: 23843343 DOI: 10.1002/alr.21195] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/27/2013] [Accepted: 05/21/2013] [Indexed: 01/07/2023]
Abstract
BACKGROUND Chronic rhinosinusitis (CRS) is a highly prevalent and heterogeneous condition frequently treated with antibiotics and corticosteroid therapy. However, the effect of medical therapy on sinus microbiota remains unknown. METHODS We enrolled CRS patients (n = 6) with patent maxillary antrostomies and active mucosal inflammation, who had not received antibiotics or corticosteroids in the previous 8 weeks. A pretreatment and posttreatment maxillary sinus swab was collected, from which DNA was extracted, pyrosequenced, and analyzed using a naïve Bayesian classifier and ecological analyses. RESULTS Four patients showed significant improvement in endoscopic appearance. The shifts in microbiota in response to therapy were highly individualized. There was no single common microbiota profile among patients with similar clinical outcomes, but overall there was significant decrease in microbiota diversity (t(5) = 2.05, p = 0.10) and evenness (t(5) = 2.28, p = 0.07) after treatment. CONCLUSION Our findings strongly correlate with earlier studies that examined the impact of antibiotics on human microbiota. We observed that posttreatment, patients frequently became colonized by taxa that are less susceptible to the prescribed antibiotics. Our findings highlight the challenge in seeking generalizable diagnostic and therapeutic options in CRS, particularly regarding microbiological response and outcomes.
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Affiliation(s)
- Cindy M Liu
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ; Center for Microbiomics and Human Health, Translational Genomics Research Institute, Flagstaff, AZ; Department of Pathology, The Johns Hopkins School of Medicine, Baltimore, MD
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Liu CM, Kachur S, Dwan MG, Abraham AG, Aziz M, Hsueh PR, Huang YT, Busch JD, Lamit LJ, Gehring CA, Keim P, Price LB. FungiQuant: a broad-coverage fungal quantitative real-time PCR assay. BMC Microbiol 2012; 12:255. [PMID: 23136846 PMCID: PMC3565980 DOI: 10.1186/1471-2180-12-255] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 10/24/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fungal load quantification is a critical component of fungal community analyses. Limitation of current approaches for quantifying the fungal component in the human microbiome suggests the need for new broad-coverage techniques. METHODS We analyzed 2,085 18S rRNA gene sequences from the SILVA database for assay design. We generated and quantified plasmid standards using a qPCR-based approach. We evaluated assay coverage against 4,968 sequences and performed assay validation following the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines. RESULTS We designed FungiQuant, a TaqMan® qPCR assay targeting a 351 bp region in the fungal 18S rRNA gene. Our in silico analysis showed that FungiQuant is a perfect sequence match to 90.0% of the 2,617 fungal species analyzed. We showed that FungiQuant's is 100% sensitive and its amplification efficiencies ranged from 76.3% to 114.5%, with r(2)-values of >0.99 against the 69 fungal species tested. Additionally, FungiQuant inter- and intra-run coefficients of variance ranged from <10% and <20%, respectively. We further showed that FungiQuant has a limit of quantification 25 copies and a limit of detection at 5 copies. Lastly, by comparing results from human-only background DNA with low-level fungal DNA, we showed that amplification in two or three of a FungiQuant performed in triplicate is statistically significant for true positive fungal detection. CONCLUSIONS FungiQuant has comprehensive coverage against diverse fungi and is a robust quantification and detection tool for delineating between true fungal detection and non-target human DNA.
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Affiliation(s)
- Cindy M Liu
- Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ, 86011, USA
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Sergey Kachur
- Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ, 86011, USA
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Current address: Ross University School of Medicine, Roseau, Dominica
| | - Michael G Dwan
- Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ, 86011, USA
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Alison G Abraham
- Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21201, USA
| | - Maliha Aziz
- Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ, 86011, USA
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yu-Tsung Huang
- Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan
| | - Joseph D Busch
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Louis J Lamit
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Catherine A Gehring
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Paul Keim
- Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ, 86011, USA
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Lance B Price
- Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ, 86011, USA
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