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Samuelson DR, Smith DR, Cunningham KC, Haq S, Villageliú DN, Ellis CM, Chowdhury NB, Ramer-Tait AE, Price JD, Knoell DL. The Inherited Intestinal Microbiota from Myeloid-Specific ZIP8KO Mice Impairs Pulmonary Host Defense against Pneumococcal Pneumonia. Pathogens 2023; 12:639. [PMID: 37242309 PMCID: PMC10222741 DOI: 10.3390/pathogens12050639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Intestinal dysbiosis increases susceptibility to infection through the alteration of metabolic profiles, which increases morbidity. Zinc (Zn) homeostasis in mammals is tightly regulated by 24 Zn transporters. ZIP8 is unique in that it is required by myeloid cells to maintain proper host defense against bacterial pneumonia. In addition, a frequently occurring ZIP8 defective variant (SLC39A8 rs13107325) is strongly associated with inflammation-based disorders and bacterial infection. In this study, we developed a novel model to study the effects of ZIP8-mediated intestinal dysbiosis on pulmonary host defense independent of the genetic effects. Cecal microbial communities from a myeloid-specific Zip8 knockout mouse model were transplanted into germ-free mice. Conventionalized ZIP8KO-microbiota mice were then bred to produce F1 and F2 generations of ZIP8KO-microbiota mice. F1 ZIP8KO-microbiota mice were also infected with S. pneumoniae, and pulmonary host defense was assessed. Strikingly, the instillation of pneumococcus into the lung of F1 ZIP8KO-microbiota mice resulted in a significant increase in weight loss, inflammation, and mortality when compared to F1 wild-type (WT)-microbiota recipients. Similar defects in pulmonary host defense were observed in both genders, although consistently greater in females. From these results, we conclude that myeloid Zn homeostasis is not only critical for myeloid function but also plays a significant role in the maintenance and control of gut microbiota composition. Further, these data demonstrate that the intestinal microbiota, independent of host genetics, play a critical role in governing host defense in the lung against infection. Finally, these data strongly support future microbiome-based interventional studies, given the high incidence of zinc deficiency and the rs13107325 allele in humans.
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Affiliation(s)
- Derrick R. Samuelson
- Department of Internal Medicine-Pulmonary Division, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5910, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE 68508, USA
| | - Deandra R. Smith
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6120, USA
| | - Kelly C. Cunningham
- Department of Internal Medicine-Pulmonary Division, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5910, USA
| | - Sabah Haq
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6120, USA
| | - Daniel N. Villageliú
- Department of Internal Medicine-Pulmonary Division, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5910, USA
| | - Christi M. Ellis
- Department of Internal Medicine-Pulmonary Division, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5910, USA
| | - Niaz Bahar Chowdhury
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0643, USA
| | - Amanda E. Ramer-Tait
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE 68508, USA
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588-6205, USA
| | - Jeffrey D. Price
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE 68508, USA
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588-6205, USA
| | - Daren L. Knoell
- Department of Internal Medicine-Pulmonary Division, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5910, USA
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6120, USA
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2
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Samuelson DR, Haq S, Knoell DL. Divalent Metal Uptake and the Role of ZIP8 in Host Defense Against Pathogens. Front Cell Dev Biol 2022; 10:924820. [PMID: 35832795 PMCID: PMC9273032 DOI: 10.3389/fcell.2022.924820] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/26/2022] [Indexed: 01/13/2023] Open
Abstract
Manganese (Mn) and Zinc (Zn) are essential micronutrients whose concentration and location within cells are tightly regulated at the onset of infection. Two families of Zn transporters (ZIPs and ZnTs) are largely responsible for regulation of cytosolic Zn levels and to a certain extent, Mn levels, although much less is known regarding Mn. The capacity of pathogens to persevere also depends on access to micronutrients, yet a fundamental gap in knowledge remains regarding the importance of metal exchange at the host interface, often referred to as nutritional immunity. ZIP8, one of 14 ZIPs, is a pivotal importer of both Zn and Mn, yet much remains to be known. Dietary Zn deficiency is common and commonly occurring polymorphic variants of ZIP8 that decrease cellular metal uptake (Zn and Mn), are associated with increased susceptibility to infection. Strikingly, ZIP8 is the only Zn transporter that is highly induced following bacterial exposure in key immune cells involved with host defense against leading pathogens. We postulate that mobilization of Zn and Mn into key cells orchestrates the innate immune response through regulation of fundamental defense mechanisms that include phagocytosis, signal transduction, and production of soluble host defense factors including cytokines and chemokines. New evidence also suggests that host metal uptake may have long-term consequences by influencing the adaptive immune response. Given that activation of ZIP8 expression by pathogens has been shown to influence parenchymal, myeloid, and lymphoid cells, the impact applies to all mucosal surfaces and tissue compartments that are vulnerable to infection. We also predict that perturbations in metal homeostasis, either genetic- or dietary-induced, has the potential to impact bacterial communities in the host thereby adversely impacting microbiome composition. This review will focus on Zn and Mn transport via ZIP8, and how this vital metal transporter serves as a "go to" conductor of metal uptake that bolsters host defense against pathogens. We will also leverage past studies to underscore areas for future research to better understand the Zn-, Mn- and ZIP8-dependent host response to infection to foster new micronutrient-based intervention strategies to improve our ability to prevent or treat commonly occurring infectious disease.
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Affiliation(s)
- Derrick R. Samuelson
- Division of Pulmonary, Critical Care, and Sleep, Department of Internal Medicine, College of Medicine, University of Nebraska Medical Center, Omaha, NE, United States
| | - Sabah Haq
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Daren L. Knoell
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, United States,*Correspondence: Daren L. Knoell,
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Samuelson DR, Smith DR, Cunningham KC, Wyatt TA, Hall SC, Murry DJ, Chhonker YS, Knoell DL. ZIP8-Mediated Intestinal Dysbiosis Impairs Pulmonary Host Defense against Bacterial Pneumonia. Int J Mol Sci 2022; 23:1022. [PMID: 35162945 PMCID: PMC8834709 DOI: 10.3390/ijms23031022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 02/06/2023] Open
Abstract
Pneumococcal pneumonia is a leading cause of morbidity and mortality worldwide. An increased susceptibility is due, in part, to compromised immune function. Zinc is required for proper immune function, and an insufficient dietary intake increases the risk of pneumonia. Our group was the first to reveal that the Zn transporter, ZIP8, is required for host defense. Furthermore, the gut microbiota that is essential for lung immunity is adversely impacted by a commonly occurring defective ZIP8 allele in humans. Taken together, we hypothesized that loss of the ZIP8 function would lead to intestinal dysbiosis and impaired host defense against pneumonia. To test this, we utilized a novel myeloid-specific Zip8KO mouse model in our studies. The comparison of the cecal microbial composition of wild-type and Zip8KO mice revealed significant differences in microbial community structure. Most strikingly, upon a S. pneumoniae lung infection, mice recolonized with Zip8KO-derived microbiota exhibited an increase in weight loss, bacterial dissemination, and lung inflammation compared to mice recolonized with WT microbiota. For the first time, we reveal the critical role of myeloid-specific ZIP8 on the maintenance of the gut microbiome structure, and that loss of ZIP8 leads to intestinal dysbiosis and impaired host defense in the lung. Given the high incidence of dietary Zn deficiency and the ZIP8 variant allele in the human population, additional investigation is warranted to improve surveillance and treatment strategies.
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Affiliation(s)
- Derrick R. Samuelson
- Department of Internal Medicine-Pulmonary Division, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA; (K.C.C.); (T.A.W.)
| | - Deandra R. Smith
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198, USA; (D.R.S.); (S.C.H.); (D.J.M.); (Y.S.C.)
| | - Kelly C. Cunningham
- Department of Internal Medicine-Pulmonary Division, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA; (K.C.C.); (T.A.W.)
| | - Todd A. Wyatt
- Department of Internal Medicine-Pulmonary Division, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA; (K.C.C.); (T.A.W.)
- Department of Environmental, Agricultural and Occupational Health, College of Public Health, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Veterans Affairs Nebraska-Western Iowa Health Care System, Omaha, NE 68105, USA
| | - Sannette C. Hall
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198, USA; (D.R.S.); (S.C.H.); (D.J.M.); (Y.S.C.)
| | - Daryl J. Murry
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198, USA; (D.R.S.); (S.C.H.); (D.J.M.); (Y.S.C.)
| | - Yashpal S. Chhonker
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198, USA; (D.R.S.); (S.C.H.); (D.J.M.); (Y.S.C.)
| | - Daren L. Knoell
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198, USA; (D.R.S.); (S.C.H.); (D.J.M.); (Y.S.C.)
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4
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Hall SC, Smith DR, Dyavar SR, Wyatt TA, Samuelson DR, Bailey KL, Knoell DL. Critical Role of Zinc Transporter (ZIP8) in Myeloid Innate Immune Cell Function and the Host Response against Bacterial Pneumonia. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:1357-1370. [PMID: 34380651 PMCID: PMC10575710 DOI: 10.4049/jimmunol.2001395] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 06/29/2021] [Indexed: 11/19/2022]
Abstract
Zinc (Zn) is required for proper immune function and host defense. Zn homeostasis is tightly regulated by Zn transporters that coordinate biological processes through Zn mobilization. Zn deficiency is associated with increased susceptibility to bacterial infections, including Streptococcus pneumoniae, the most commonly identified cause of community-acquired pneumonia. Myeloid cells, including macrophages and dendritic cells (DCs), are at the front line of host defense against invading bacterial pathogens in the lung and play a critical role early on in shaping the immune response. Expression of the Zn transporter ZIP8 is rapidly induced following bacterial infection and regulates myeloid cell function in a Zn-dependent manner. To what extent ZIP8 is instrumental in myeloid cell function requires further study. Using a novel, myeloid-specific, Zip8 knockout model, we identified vital roles of ZIP8 in macrophage and DC function upon pneumococcal infection. Administration of S. pneumoniae into the lung resulted in increased inflammation, morbidity, and mortality in Zip8 knockout mice compared with wild-type counterparts. This was associated with increased numbers of myeloid cells, cytokine production, and cell death. In vitro analysis of macrophage and DC function revealed deficits in phagocytosis and increased cytokine production upon bacterial stimulation that was, in part, due to increased NF-κB signaling. Strikingly, alteration of myeloid cell function resulted in an imbalance of Th17/Th2 responses, which is potentially detrimental to host defense. These results (for the first time, to our knowledge) reveal a vital ZIP8- and Zn-mediated axis that alters the lung myeloid cell landscape and the host response against pneumococcus.
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Affiliation(s)
- Sannette C Hall
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE
| | - Deandra R Smith
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE
| | - Shetty Ravi Dyavar
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE
| | - Todd A Wyatt
- Department of Environmental, Agricultural and Occupational Health, College of Public Health, University of Nebraska Medical Center, Omaha, NE
- Pulmonary Division, Department of Internal Medicine, College of Medicine, University of Nebraska Medical Center, Omaha, NE; and
- Department of Veterans Affairs Nebraska, University of Nebraska Medical Center, Western Iowa Health Care System, Omaha, NE
| | - Derrick R Samuelson
- Pulmonary Division, Department of Internal Medicine, College of Medicine, University of Nebraska Medical Center, Omaha, NE; and
| | - Kristina L Bailey
- Pulmonary Division, Department of Internal Medicine, College of Medicine, University of Nebraska Medical Center, Omaha, NE; and
- Department of Veterans Affairs Nebraska, University of Nebraska Medical Center, Western Iowa Health Care System, Omaha, NE
| | - Daren L Knoell
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE;
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5
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Van Belkum A, Gros MF, Ferry T, Lustig S, Laurent F, Durand G, Jay C, Rochas O, Ginocchio CC. Novel strategies to diagnose prosthetic or native bone and joint infections. Expert Rev Anti Infect Ther 2021; 20:391-405. [PMID: 34384319 DOI: 10.1080/14787210.2021.1967745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Bone and Joint Infections (BJI) are medically important, costly and occur in native and prosthetic joints. Arthroplasties will increase significantly in absolute numbers over time as well as the incidence of Prosthetic Joint Infections (PJI). Diagnosis of BJI and PJI is sub-optimal. The available diagnostic tests have variable effectiveness, are often below standard in sensitivity and/or specificity, and carry significant contamination risks during the collection of clinical samples. Improvement of diagnostics is urgently needed. AREAS COVERED We provide a narrative review on current and future diagnostic microbiology technologies. Pathogen identification, antibiotic resistance detection, and assessment of the epidemiology of infections via bacterial typing are considered useful for improved patient management. We confirm the continuing importance of culture methods and successful introduction of molecular, mass spectrometry-mediated and next-generation genome sequencing technologies. The diagnostic algorithms for BJI must be better defined, especially in the context of diversity of both disease phenotypes and clinical specimens rendered available. EXPERT OPINION Whether interventions in BJI or PJI are surgical or chemo-therapeutic (antibiotics and bacteriophages included), prior sensitive and specific pathogen detection remains a therapy-substantiating necessity. Innovative tests for earlier and more sensitive and specific detection of bacterial pathogens in BJI are urgently needed.
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Affiliation(s)
- Alex Van Belkum
- bioMérieux, Open Innovation and Partnerships, 3 Route De Port Michaud, La Balme Les Grottes, France
| | | | - Tristan Ferry
- Service Des Maladies Infectieuses Et Tropicales, Hospices Civils De Lyon, Hôpital De La Croix-Rousse, Lyon, France.,Maladies Infectieuses, Université Claude Bernard Lyon 1, Villeurbanne, France.,Centre Interrégional De Référence Pour La Prise En Charge Des Infections Ostéo-articulaires Complexes (Crioac Lyon), Hôpital De La Croix-Rousse, Lyon, France.,Ciri - Centre International De Recherche En Infectiologie, Inserm, U1111, Université́ Claude Bernard Lyon 1CNRS, UMR5308, Ecole Normale Supérieure De Lyon, Univ Lyon, Lyon, France
| | - Sebastien Lustig
- Maladies Infectieuses, Université Claude Bernard Lyon 1, Villeurbanne, France.,Service De Chirurgie Orthopédique, Hôpital De La Croix-Rousse, Lyon, France
| | - Frédéric Laurent
- Service Des Maladies Infectieuses Et Tropicales, Hospices Civils De Lyon, Hôpital De La Croix-Rousse, Lyon, France.,Ciri - Centre International De Recherche En Infectiologie, Inserm, U1111, Université́ Claude Bernard Lyon 1CNRS, UMR5308, Ecole Normale Supérieure De Lyon, Univ Lyon, Lyon, France
| | | | - Corinne Jay
- bioMérieux, BioFire Development Emea, Grenoble, France
| | - Olivier Rochas
- Corporate Business Development, bioMérieux, Marcy-l'Étoile, France
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6
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Maurya R, Kanakan A, Vasudevan JS, Chattopadhyay P, Pandey R. Infection outcome needs two to tango: human host and the pathogen. Brief Funct Genomics 2021; 21:90-102. [PMID: 34402498 PMCID: PMC8385967 DOI: 10.1093/bfgp/elab037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/15/2021] [Accepted: 07/21/2021] [Indexed: 12/15/2022] Open
Abstract
Infectious diseases are potential drivers for human evolution, through a complex, continuous and dynamic interaction between the host and the pathogen/s. It is this dynamic interaction that contributes toward the clinical outcome of a pathogenic disease. These are modulated by contributions from the human genetic variants, transcriptional response (including noncoding RNA) and the pathogen’s genome architecture. Modern genomic tools and techniques have been crucial for the detection and genomic characterization of pathogens with respect to the emerging infectious diseases. Aided by next-generation sequencing (NGS), risk stratification of host population/s allows for the identification of susceptible subgroups and better disease management. Nevertheless, many challenges to a general understanding of host–pathogen interactions remain. In this review, we elucidate how a better understanding of the human host-pathogen interplay can substantially enhance, and in turn benefit from, current and future applications of multi-omics based approaches in infectious and rare diseases. This includes the RNA-level response, which modulates the disease severity and outcome. The need to understand the role of human genetic variants in disease severity and clinical outcome has been further highlighted during the Coronavirus disease 2019 (COVID-19) pandemic. This would enhance and contribute toward our future pandemic preparedness.
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Affiliation(s)
- Ranjeet Maurya
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Akshay Kanakan
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
| | - Janani Srinivasa Vasudevan
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
| | - Partha Chattopadhyay
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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7
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Knoell DL, Wyatt TA. The adverse impact of cadmium on immune function and lung host defense. Semin Cell Dev Biol 2021; 115:70-76. [PMID: 33158728 PMCID: PMC10603789 DOI: 10.1016/j.semcdb.2020.10.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/09/2020] [Accepted: 10/16/2020] [Indexed: 01/08/2023]
Abstract
Cadmium (Cd) is a transition metal, also referred to as a heavy metal, that is naturally abundant in the earth's crust. It has no known benefit to humans. It is primarily released into our environment through mining and smelting in industrial processes and enters the food chain through uptake by plants from contaminated soil and water. In humans, Cd primarily enters the body through ingestion of foods and cigarette smoke and has an extremely long resident half-life in the body compared to other transition metals. Environmental workplace exposure is also a source through inhalation, although much less common. The principal organs adversely affected by Cd following acute and chronic exposure are the kidneys, bone, vasculature and lung. Cd adversely impacts cell function through changes in gene expression and signal transduction and is recognized as a carcinogen. Despite a substantial body of mechanistic studies in cells and animal models, the overall impact of Cd on innate immune function in humans remains poorly understood. The best evidence is perhaps alteration of reactive oxygen species balance and signaling in cells that regulate innate immunity causing alteration of the inflammatory response that is postulated to contribute to chronic diseases. Epidemiologic studies support this possibility since increased tissue levels in humans are strongly associated with leading chronic diseases including chronic obstructive pulmonary disease (COPD), which will be discussed in depth. Additional studies are required to understand how chronic exposure and accumulation of this leading environmental toxicant in vital organs negatively impact innate immune function and host defense leading to chronic disease in humans.
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Affiliation(s)
- Daren L Knoell
- The University of Nebraska Medical Center College of Pharmacy, Omaha, NE 68198, USA.
| | - Todd A Wyatt
- The University of Nebraska Medical Center College of Public Health, Omaha NE 68198, USA; VA Nebraska-Western Iowa Health Care System, Omaha, NE 68105, USA.
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8
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Bourgeois JS, Smith CM, Ko DC. These Are the Genes You're Looking For: Finding Host Resistance Genes. Trends Microbiol 2021; 29:346-362. [PMID: 33004258 PMCID: PMC7969353 DOI: 10.1016/j.tim.2020.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/05/2020] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
Humanity's ongoing struggle with new, re-emerging and endemic infectious diseases serves as a frequent reminder of the need to understand host-pathogen interactions. Recent advances in genomics have dramatically advanced our understanding of how genetics contributes to host resistance or susceptibility to bacterial infection. Here we discuss current trends in defining host-bacterial interactions at the genome-wide level, including screens that harness CRISPR/Cas9 genome editing, natural genetic variation, proteomics, and transcriptomics. We report on the merits, limitations, and findings of these innovative screens and discuss their complementary nature. Finally, we speculate on future innovation as we continue to progress through the postgenomic era and towards deeper mechanistic insight and clinical applications.
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Affiliation(s)
- Jeffrey S Bourgeois
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | - Clare M Smith
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA; Duke Human Vaccine Institute, School of Medicine, Duke University Durham, NC, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA; Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC, USA.
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9
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Miller LS, Fowler VG, Shukla SK, Rose WE, Proctor RA. Development of a vaccine against Staphylococcus aureus invasive infections: Evidence based on human immunity, genetics and bacterial evasion mechanisms. FEMS Microbiol Rev 2020; 44:123-153. [PMID: 31841134 PMCID: PMC7053580 DOI: 10.1093/femsre/fuz030] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022] Open
Abstract
Invasive Staphylococcus aureus infections are a leading cause of morbidity and mortality in both hospital and community settings, especially with the widespread emergence of virulent and multi-drug resistant methicillin-resistant S. aureus strains. There is an urgent and unmet clinical need for non-antibiotic immune-based approaches to treat these infections as the increasing antibiotic resistance is creating a serious threat to public health. However, all vaccination attempts aimed at preventing S. aureus invasive infections have failed in human trials, especially all vaccines aimed at generating high titers of opsonic antibodies against S. aureus surface antigens to facilitate antibody-mediated bacterial clearance. In this review, we summarize the data from humans regarding the immune responses that protect against invasive S. aureus infections as well as host genetic factors and bacterial evasion mechanisms, which are important to consider for the future development of effective and successful vaccines and immunotherapies against invasive S. aureus infections in humans. The evidence presented form the basis for a hypothesis that staphylococcal toxins (including superantigens and pore-forming toxins) are important virulence factors, and targeting the neutralization of these toxins are more likely to provide a therapeutic benefit in contrast to prior vaccine attempts to generate antibodies to facilitate opsonophagocytosis.
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Affiliation(s)
- Lloyd S Miller
- Immunology, Janssen Research and Development, 1400 McKean Road, Spring House, PA, 19477, USA.,Department of Dermatology, Johns Hopkins University School of Medicine, 1550 Orleans Street, Cancer Research Building 2, Suite 209, Baltimore, MD, 21231, USA.,Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, 1830 East Monument Street, Baltimore, MD, 21287, USA.,Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, 601 North Caroline Street, Baltimore, MD, 21287, USA.,Department of Materials Science and Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Vance G Fowler
- Department of Medicine, Division of Infectious Diseases, Duke University Medical Center, 315 Trent Drive, Hanes House, Durham, NC, 27710, USA.,Duke Clinical Research Institute, Duke University Medical Center, 40 Duke Medicine Circle, Durham, NC, 27710, USA
| | - Sanjay K Shukla
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, 1000 North Oak Avenue, Marshfield, WI, 54449, USA.,Computation and Informatics in Biology and Medicine, University of Wisconsin, 425 Henry Mall, Room 3445, Madison, WI, 53706, USA
| | - Warren E Rose
- Department of Medicine, University of Wisconsin-Madison School of Medicine and Public Health, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI, 53705, USA.,Pharmacy Practice Division, University of Wisconsin-Madison, 777 Highland Avenue, 4123 Rennebohm Hall, Madison, WI, 53705 USA
| | - Richard A Proctor
- Department of Medicine, University of Wisconsin-Madison School of Medicine and Public Health, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI, 53705, USA.,Department of Medical Microbiology and Immunology, University of Wisconsin-Madison School of Medicine and Public Health, 1550 Linden Drive, Microbial Sciences Building, Room 1334, Madison, WI, 53705, USA
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10
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Israelsson E, Chaussabel D, Fischer RSB, Moore HC, Robinson DA, Dunkle JW, Essigmann HT, Record S, Brown EL. Characterization of peripheral blood mononuclear cells gene expression profiles of pediatric Staphylococcus aureus persistent and non-carriers using a targeted assay. Microbes Infect 2020; 22:540-549. [PMID: 32758644 DOI: 10.1016/j.micinf.2020.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 06/26/2020] [Accepted: 07/25/2020] [Indexed: 11/28/2022]
Abstract
Defects in innate immunity affect many different physiologic systems and several studies of patients with primary immunodeficiency disorders demonstrated the importance of innate immune system components in disease prevention or colonization of bacterial pathogens. To assess the role of the innate immune system on nasal colonization with Staphylococcus aureus, innate immune responses in pediatric S. aureus nasal persistent carriers (n = 14) and non-carriers (n = 15) were profiled by analyzing co-clustered gene sets (modules). We stimulated previously frozen peripheral blood mononuclear cells (PBMCs) from these subjects with i) a panel of TLR ligands, ii) live S. aureus (either a mixture of strains or stimulation with respective carriage isolates), or iii) heat-killed S. aureus. We found no difference in responses between carriers and non-carriers when PBMCs were stimulated with a panel of TLR ligands. However, PBMC gene expression profiles differed between persistent and non-S. aureus carriers following stimulation with either live or dead S. aureus. These observations suggest that individuals susceptible to persistent carriage with S. aureus may possess differences in their live/dead bacteria recognition pathway and that innate pathway signaling is different between persistent and non-carriers of S. aureus.
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Affiliation(s)
- Elisabeth Israelsson
- Department of Systems Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Damien Chaussabel
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
| | - Rebecca S B Fischer
- Texas A&M Health Science Center School of Public Health, Department of Epidemiology and Biostatistics, College Station, TX, USA
| | - Heather C Moore
- Baylor College of Medicine, Complex Care Clinic, Texas Children's Hospital, Houston, TX, USA
| | - D Ashley Robinson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jesse W Dunkle
- Icahn School of Medicine, Mount Sinai Hospital, Institute for Advanced Medicine, New York, NY, USA
| | - Heather T Essigmann
- Division of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas Health Science Center, Houston, TX, USA
| | - Sharron Record
- Texas Children's Hospital, Department of Pediatrics, TX, USA
| | - Eric L Brown
- Division of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas Health Science Center, Houston, TX, USA.
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11
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Roe C, Stegger M, Lilje B, Johannesen TB, Ng KL, Sieber RN, Driebe E, Engelthaler DM, Andersen PS. Genomic analyses of Staphylococcus aureus clonal complex 45 isolates does not distinguish nasal carriage from bacteraemia. Microb Genom 2020; 6:mgen000403. [PMID: 32667872 PMCID: PMC7641415 DOI: 10.1099/mgen.0.000403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 06/16/2020] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus is a colonizing opportunistic pathogen and a leading cause of bloodstream infection with high morbidity and mortality. S. aureus carriage frequency is reportedly between 20 and 40 % among healthy adults, with S. aureus colonization considered to be a risk factor for S. aureus bacteraemia. It is unknown whether a genetic component of the bacterium is associated with S. aureus bacteraemia in comparison to nasal carriage strains. Previous association studies primarily focusing on the clinical outcome of an S. aureus infection have produced conflicting results, often limited by study design challenged by sample collections and the clonal diversity of S. aureus. To date, no study has investigated whether genomic features separate nasal carriage isolates from S. aureus bacteraemia isolates within a single clonal lineage. Here we have investigated whether genomic features, including single-nucleotide polymorphisms (SNPs), genes, or kmers, distinguish S. aureus nasal carriage isolates from bacteraemia isolates that all belong to the same clonal lineage [clonal complex 45 (CC45)] using whole-genome sequencing (WGS) and a genome-wide association (GWA) approach. From CC45, 100 isolates (50 bacteraemia and 50 nasal carriage, geographically and temporally matched) from Denmark were whole-genome sequenced and subjected to GWA analyses involving gene copy number variation, SNPs, gene content, kmers and gene combinations, while correcting for lineage effects. No statistically significant association involving SNPs, specific genes, gene variants, gene copy number variation, or a combination of genes was identified that could distinguish bacteraemia isolates from nasal carriage isolates. The presented results suggest that all S. aureus nasal CC45 isolates carry the potential to cause invasive disease, as no core or accessory genome content or variations were statistically associated with invasiveness.
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Affiliation(s)
- Chandler Roe
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- Northern Arizona University, Flagstaff, AZ, USA
| | - Marc Stegger
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Berit Lilje
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | - Kim Lee Ng
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Raphael N. Sieber
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | | | - Paal Skytt Andersen
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
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12
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Association of variants in selected genes mediating host immune response with duration of Staphylococcus aureus bacteremia. Genes Immun 2020; 21:240-248. [PMID: 32507857 DOI: 10.1038/s41435-020-0101-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 05/12/2020] [Accepted: 05/18/2020] [Indexed: 12/26/2022]
Abstract
Host genetic variation may be a contributing factor to variability in Staphylococcus aureus bacteremia duration. We assessed whether 28 single nucleotide polymorphisms (SNPs) in seven genes (TLR2, TLR4, TIRAP, IRAK4, TRAF6, NOD2, and CISH) that mediate host immune response were associated with S. aureus bacteremia duration. Subjects included 158 patients with short-term (≤4 days) and 44 with persistent (>4 days) S. aureus bacteremia from an academic medical center. In single SNP analyses, the minor allele frequencies of three TIRAP SNPs (rs655540, rs563011, and rs8177376) were higher in persistent bacteremia (P < 0.05). A haplotype with all three minor alleles was also associated with persistent bacteremia (P = 0.037). The minor allele frequencies of four other TIRAP SNPs (rs8177342, rs4937114, rs3802813, and rs4937115) were higher in short-term bacteremia (P < 0.05), and a haplotype containing the four minor alleles was associated with short-term bacteremia (P = 0.045). All seven SNPs are located in binding sites for proteins or noncoding RNAs that regulate transcription. None of the associations remained statistically significant after adjustment for multiple comparisons. Further investigation is needed to understand how genetic variation in TIRAP and other host immune genes may influence the duration of S. aureus bacteremia.
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13
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Single nucleotide polymorphisms in piRNA-pathway genes: an insight into genetic determinants of human diseases. Mol Genet Genomics 2019; 295:1-12. [DOI: 10.1007/s00438-019-01612-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/22/2019] [Indexed: 12/23/2022]
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14
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Abstract
Mastitis is an inflammatory disease of the mammary gland, which has a significant economic impact and is an animal welfare concern. This work examined the association between single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) with the incidence of clinical mastitis (CM). Using information from 16 half-sib pairs of Holstein-Friesian cows (32 animals in total) we searched for genomic regions that differed between a healthy (no incidence of CM) and a mastitis-prone (multiple incidences of CM) half-sib. Three cows with average sequence depth of coverage below 10 were excluded, which left 13 half-sib pairs available for comparisons. In total, 191 CNV regions were identified, which were deleted in a mastitis-prone cow, but present in its healthy half-sib and overlapped in at least nine half-sib pairs. These regions overlapped with exons of 46 genes, among which APP (BTA1), FOXL2 (BTA1), SSFA2 (BTA2), OTUD3 (BTA2), ADORA2A (BTA17), TXNRD2 (BTA17) and NDUFS6 (BTA20) have been reported to influence CM. Moreover, two duplicated CNV regions present in nine healthy individuals and absent in their mastitis-affected half-sibs overlapped with exons of a cholinergic receptor nicotinic α 10 subunit on BTA15 and a novel gene (ENSBTAG00000008519) on BTA27. One CNV region deleted in nine mastitis-affected sibs overlapped with two neighbouring long non-coding RNA sequences located on BTA12. Single nucleotide polymorphisms with differential genotypes between a healthy and a mastitis-affected sib included 17 polymorphisms with alternate alleles in eight affected and healthy half-sib families. Three of these SNPs were located introns of genes: MET (BTA04), RNF122 (BTA27) and WRN (BTA27). In summary, structural polymorphisms in form of CNVs, putatively play a role in susceptibility to CM. Specifically, sequence deletions have a greater effect on reducing resistance against mastitis, than sequence duplications have on increasing resistance against the disease.
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15
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A gene-based recessive diplotype exome scan discovers FGF6, a novel hepcidin-regulating iron-metabolism gene. Blood 2019; 133:1888-1898. [PMID: 30814063 DOI: 10.1182/blood-2018-10-879585] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/20/2019] [Indexed: 12/14/2022] Open
Abstract
Standard analyses applied to genome-wide association data are well designed to detect additive effects of moderate strength. However, the power for standard genome-wide association study (GWAS) analyses to identify effects from recessive diplotypes is not typically high. We proposed and conducted a gene-based compound heterozygosity test to reveal additional genes underlying complex diseases. With this approach applied to iron overload, a strong association signal was identified between the fibroblast growth factor-encoding gene, FGF6, and hemochromatosis in the central Wisconsin population. Functional validation showed that fibroblast growth factor 6 protein (FGF-6) regulates iron homeostasis and induces transcriptional regulation of hepcidin. Moreover, specific identified FGF6 variants differentially impact iron metabolism. In addition, FGF6 downregulation correlated with iron-metabolism dysfunction in systemic sclerosis and cancer cells. Using the recessive diplotype approach revealed a novel susceptibility hemochromatosis gene and has extended our understanding of the mechanisms involved in iron metabolism.
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16
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Abstract
ABSTRACT
Fulminant staphylococcal infection indicates an explosive, intense, and severe infection occurring in a patient whose previous condition and antecedent would never have caused any anticipation of life-threatening development. This includes necrotizing pneumonia, necrotizing fasciitis, and to some extent toxic shock syndrome and infective endocarditis. In the three former diseases, toxin production plays a major role whereas in the latter (fulminant presentation of infective endocarditis), association with any particular toxinic profile has never been demonstrated. This article reviews the clinical, pathophysiological, and therapeutic aspects of these diseases.
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17
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Moreau K, Clemenceau A, Le Moing V, Messika-Zeitoun D, Andersen PS, Bruun NE, Skov RL, Couzon F, Bouchiat C, Erpelding ML, van Belkum A, Bossé Y, Duval X, Vandenesch F. Human Genetic Susceptibility to Native Valve Staphylococcus aureus Endocarditis in Patients With S. aureus Bacteremia: Genome-Wide Association Study. Front Microbiol 2018; 9:640. [PMID: 29670602 PMCID: PMC5893849 DOI: 10.3389/fmicb.2018.00640] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 03/19/2018] [Indexed: 01/26/2023] Open
Abstract
Staphylococcus aureus infective endocarditis (SaIE) is a severe complication of S. aureus bacteremia (SAB) occurring in up to 22% of patients. Bacterial genetic factors and host conditions for SaIE have been intensely studied before; however, to date no study has focused on predisposing host genetic factors to SaIE. The present study aimed to identify genetic polymorphisms associated with SaIE by a Genome-Wide Association Study (GWAS) of 67 patients with definite native valve SaIE (cases) and 72 matched native valve patients with SAB but without IE (controls). All patients were enrolled in the VIRSTA cohort (Le Moing et al., 2015) study. Four single nucleotide polymorphisms (SNPs) located on chromosome 3 were associated with SaIE (P < 1 × 10-5) without reaching conventional genome-wide significance. For all, the frequency of the minor allele was lower in cases than in controls, suggesting a protective effect of the minor allele against SaIE. The same association was observed using an independent Danish verification cohort of SAB with (n = 57) and without (n = 123) IE. Ex vivo analysis of aortic valve tissues revealed that SaIE associated SNPs mentioned above were associated with significantly higher mRNA expression levels of SLC7A14, a predicted cationic amino acid transporter protein. Taken together, our results suggest an IE-protective effect of SNPs on chromosome 3 during the course of SAB. The effects of protective minor alleles may be mediated by increasing expression levels of SLC7A14 in valve tissues. We conclude that occurrence of SaIE may be the combination of a well-adapted bacterial genotype to a susceptible host.
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Affiliation(s)
- Karen Moreau
- International Center for Infectiology Research, CNRS UMR5308, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, Lyon, France
| | - Alisson Clemenceau
- Institut Universitaire de Cardiologie et de Pneumologie de Québec - Université Laval, Quebec City, QC, Canada
| | - Vincent Le Moing
- Department for Infectious Diseases and Tropical Medicine, Centre Hospitalier, Universitaire de Montpellier, Montpellier, France
| | - David Messika-Zeitoun
- Department of Cardiology, AP-HP, Bichat Hospital, Paris, France.,INSERM U698 and University Paris 7, Paris, France
| | | | - Niels E Bruun
- Statens Serum Institut, Copenhagen, Denmark.,Clinical Institute, Aalborg University, Aalborg, Denmark
| | | | - Florence Couzon
- International Center for Infectiology Research, CNRS UMR5308, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, Lyon, France
| | - Coralie Bouchiat
- International Center for Infectiology Research, CNRS UMR5308, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, Lyon, France.,Centre National de Référence des Staphylocoques, Centre de Biologie Est, Hospices Civils de Lyon, Lyon, France
| | - Marie L Erpelding
- INSERM, CIC-1433 Clinical Epidemiology, CHRU Nancy, University of Lorraine, Nancy, France
| | - Alex van Belkum
- Data Analytics Unit, bioMerieux, La Balme-les-Grottes, France
| | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec - Université Laval, Quebec City, QC, Canada.,Département de Médecine Moléculaire, Université Laval, Quebec City, QC, Canada
| | - Xavier Duval
- INSERM, UMR1138 IAME, CIC 1425, Université Paris Diderot, Paris, France.,AP-HP, Hôpital Bichat-Claude Bernard, Paris, France
| | - Francois Vandenesch
- International Center for Infectiology Research, CNRS UMR5308, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, Lyon, France.,Centre National de Référence des Staphylocoques, Centre de Biologie Est, Hospices Civils de Lyon, Lyon, France
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18
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Costas J. The highly pleiotropic gene SLC39A8 as an opportunity to gain insight into the molecular pathogenesis of schizophrenia. Am J Med Genet B Neuropsychiatr Genet 2018; 177:274-283. [PMID: 28557351 DOI: 10.1002/ajmg.b.32545] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 03/28/2017] [Indexed: 12/19/2022]
Abstract
There is a long way from the initial discovery of a genome-wide significant signal to mechanistic understanding of the association. Identification of the gene and causal polymorphism usually requires an extensive additional effort. The schizophrenia genome-wide significant locus at 4q24 may be a rare exception to this pattern. As discussed in this review, the association at this locus is most probably driven by a functional missense variant at the metal cations transporter SLC39A8. The variant, rs13107325, is almost exclusive of European populations and is one of the most pleiotropic variants of the genome, being associated at genome-wide significant level with several additional traits, such as body mass index, Crohn's disease, blood pressure related-traits, and serum levels of manganese, N-terminal pro-B-type natriuretic peptide and HDL-cholesterol. SLC39A8 seems to be subject to recent natural selection in Europeans. It is almost ubiquitously expressed and its physiological role is beginning to be elucidated, mainly in relation to immunity. This manuscript presents arguments in favor of the rs13107325 variant as the functional variant responsible for the association of this locus with schizophrenia, reviews the genetic associations with this gene, the evidences of natural selection on the gene, and the known aspects about its structure and physiological functions. Finally, some hypotheses about putative mechanisms for its association with schizophrenia are presented based on this knowledge, including impaired immunity/inflammation, interference with glutamatergic neurotransmission, homeostasis of essential metals in brain, such as iron, zinc or manganese, or neurotoxicity by heavy metals, such as cadmium or lead.
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Affiliation(s)
- Javier Costas
- Grupo de Xenética Psiquiátrica, Hospital Clínico Universitario de Santiago de Compostela, Instituto de Investigación Sanitaria de Santiago (IDIS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
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19
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Hayden LP, Cho MH, McDonald MLN, Crapo JD, Beaty TH, Silverman EK, Hersh CP. Susceptibility to Childhood Pneumonia: A Genome-Wide Analysis. Am J Respir Cell Mol Biol 2017; 56:20-28. [PMID: 27508494 DOI: 10.1165/rcmb.2016-0101oc] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Previous studies have indicated that in adult smokers, a history of childhood pneumonia is associated with reduced lung function and chronic obstructive pulmonary disease. There have been few previous investigations using genome-wide association studies to investigate genetic predisposition to pneumonia. This study aims to identify the genetic variants associated with the development of pneumonia during childhood and over the course of the lifetime. Study subjects included current and former smokers with and without chronic obstructive pulmonary disease participating in the COPDGene Study. Pneumonia was defined by subject self-report, with childhood pneumonia categorized as having the first episode at <16 years. Genome-wide association studies for childhood pneumonia (843 cases, 9,091 control subjects) and lifetime pneumonia (3,766 cases, 5,659 control subjects) were performed separately in non-Hispanic whites and African Americans. Non-Hispanic white and African American populations were combined in the meta-analysis. Top genetic variants from childhood pneumonia were assessed in network analysis. No single-nucleotide polymorphisms reached genome-wide significance, although we identified potential regions of interest. In the childhood pneumonia analysis, this included variants in NGR1 (P = 6.3 × 10-8), PAK6 (P = 3.3 × 10-7), and near MATN1 (P = 2.8 × 10-7). In the lifetime pneumonia analysis, this included variants in LOC339862 (P = 8.7 × 10-7), RAPGEF2 (P = 8.4 × 10-7), PHACTR1 (P = 6.1 × 10-7), near PRR27 (P = 4.3 × 10-7), and near MCPH1 (P = 2.7 × 10-7). Network analysis of the genes associated with childhood pneumonia included top networks related to development, blood vessel morphogenesis, muscle contraction, WNT signaling, DNA damage, apoptosis, inflammation, and immune response (P ≤ 0.05). We have identified genes potentially associated with the risk of pneumonia. Further research will be required to confirm these associations and to determine biological mechanisms. CLINICAL TRIAL REGISTRATION NCT00608764.
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Affiliation(s)
- Lystra P Hayden
- 1 Division of Respiratory Diseases, Boston Children's Hospital, Boston, Massachusetts.,2 Channing Division of Network Medicine and
| | - Michael H Cho
- 2 Channing Division of Network Medicine and.,3 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | | | - Terri H Beaty
- 5 Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland
| | - Edwin K Silverman
- 2 Channing Division of Network Medicine and.,3 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Craig P Hersh
- 2 Channing Division of Network Medicine and.,3 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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20
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Yan Q, Ahn SH, Medie FM, Sharma-Kuinkel BK, Park LP, Scott WK, Deshmukh H, Tsalik EL, Cyr DD, Woods CW, Yu CHA, Adams C, Qi R, Hansen B, Fowler VG. Candidate genes on murine chromosome 8 are associated with susceptibility to Staphylococcus aureus infection in mice and are involved with Staphylococcus aureus septicemia in humans. PLoS One 2017; 12:e0179033. [PMID: 28594911 PMCID: PMC5464679 DOI: 10.1371/journal.pone.0179033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 05/23/2017] [Indexed: 02/06/2023] Open
Abstract
We previously showed that chromosome 8 of A/J mice was associated with susceptibility to S. aureus infection. However, the specific genes responsible for this susceptibility are unknown. Chromosome substitution strain 8 (CSS8) mice, which have chromosome 8 from A/J but an otherwise C57BL/6J genome, were used to identify the genetic determinants of susceptibility to S. aureus on chromosome 8. Quantitative trait loci (QTL) mapping of S. aureus-infected N2 backcross mice (F1 [C8A] × C57BL/6J) identified a locus 83180780–88103009 (GRCm38/mm10) on A/J chromosome 8 that was linked to S. aureus susceptibility. All genes on the QTL (n~ 102) were further analyzed by three different strategies: 1) different expression in susceptible (A/J) and resistant (C57BL/6J) mice only in response to S. aureus, 2) consistently different expression in both uninfected and infected states between the two strains, and 3) damaging non-synonymous SNPs in either strain. Eleven candidate genes from the QTL region were significantly differently expressed in patients with S. aureus infection vs healthy human subjects. Four of these 11 genes also exhibited significantly different expression in S. aureus-challenged human neutrophils: Ier2, Crif1, Cd97 and Lyl1. CD97 ligand binding was evaluated within peritoneal neutrophils from A/J and C57BL/6J. CD97 from A/J had stronger CD55 but weaker integrin α5β1 ligand binding as compared with C57BL/6J. Because CD55/CD97 binding regulates immune cell activation and cytokine production, and integrin α5β1 is a membrane receptor for fibronectin, which is also bound by S. aureus, strain-specific differences could contribute to susceptibility to S. aureus. Down-regulation of Crif1 with siRNA was associated with increased host cell apoptosis among both naïve and S. aureus-infected bone marrow-derived macrophages. Specific genes in A/J chromosome 8, including Cd97 and Crif1, may play important roles in host defense against S. aureus.
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Affiliation(s)
- Qin Yan
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Sun Hee Ahn
- Department of Biochemistry School of Dentistry, Chonnam National University, Bukgu, Gwangju, Korea
| | - Felix Mba Medie
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Batu K. Sharma-Kuinkel
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Lawrence P. Park
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
| | - William K. Scott
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, United States of America
| | - Hitesh Deshmukh
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Ephraim L. Tsalik
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
- Emergency Medicine Service, Durham Veteran’s Affairs Medical Center, Durham, North Carolina, United States of America
- Duke Clinical Research Institute, Durham, North Carolina, United States of America
| | - Derek D. Cyr
- Duke Clinical Research Institute, Durham, North Carolina, United States of America
| | - Christopher W. Woods
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Clinical Research Institute, Durham, North Carolina, United States of America
- Section on Infectious Diseases, Durham Veteran’s Affairs Medical Center, Durham, North Carolina, United States of America
| | - Chen-Hsin Albert Yu
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Carlton Adams
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Robert Qi
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Brenda Hansen
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Vance G. Fowler
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Clinical Research Institute, Durham, North Carolina, United States of America
- * E-mail:
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21
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Cyr DD, Allen AS, Du GJ, Ruffin F, Adams C, Thaden JT, Maskarinec SA, Souli M, Guo S, Dykxhoorn DM, Scott WK, Fowler VG. Evaluating genetic susceptibility to Staphylococcus aureus bacteremia in African Americans using admixture mapping. Genes Immun 2017; 18:95-99. [PMID: 28332560 PMCID: PMC5435963 DOI: 10.1038/gene.2017.6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 02/14/2017] [Accepted: 02/16/2017] [Indexed: 12/12/2022]
Abstract
The incidence of Staphylococcus aureus bacteremia (SAB) is significantly higher in African American (AA) than in European-descended populations. We used admixture mapping (AM) to test the hypothesis that genomic variations with different frequencies in European and African ancestral genomes influence susceptibility to SAB in AAs. A total of 565 adult AAs (390 cases with SAB; 175 age-matched controls) were genotyped for AM analysis. A case-only admixture score and a mixed χ2(1df) score (MIX) to jointly evaluate both single-nucleotide polymorphism (SNP) and admixture association (P<5.00e-08) were computed using MIXSCORE. In addition, a permutation scheme was implemented to derive multiplicity adjusted P-values (genome-wide 0.05 significance threshold: P<9.46e-05). After empirical multiplicity adjustment, one region on chromosome 6 (52 SNPs, P=4.56e-05) in the HLA class II region was found to exhibit a genome-wide statistically significant increase in European ancestry. This region encodes genes involved in HLA-mediated immune response and these results provide additional evidence for genetic variation influencing HLA-mediated immunity, modulating susceptibility to SAB.
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Affiliation(s)
- D D Cyr
- Duke Clinical Research Institute, Duke University Medical Center, Durham, NC, USA
| | - A S Allen
- Duke Clinical Research Institute, Duke University Medical Center, Durham, NC, USA.,Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - G-J Du
- Duke Center for Genomic and Computational Biology, Durham, NC, USA
| | - F Ruffin
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - C Adams
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - J T Thaden
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - S A Maskarinec
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - M Souli
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA.,School of Medicine, National and Kapodistrian University of Athens, Chaidari, Greece
| | - S Guo
- Dr John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - D M Dykxhoorn
- Dr John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - W K Scott
- Dr John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - V G Fowler
- Duke Clinical Research Institute, Duke University Medical Center, Durham, NC, USA.,Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
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22
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Jackson KL, Mbagwu M, Pacheco JA, Baldridge AS, Viox DJ, Linneman JG, Shukla SK, Peissig PL, Borthwick KM, Carrell DA, Bielinski SJ, Kirby JC, Denny JC, Mentch FD, Vazquez LM, Rasmussen-Torvik LJ, Kho AN. Performance of an electronic health record-based phenotype algorithm to identify community associated methicillin-resistant Staphylococcus aureus cases and controls for genetic association studies. BMC Infect Dis 2016; 16:684. [PMID: 27855652 PMCID: PMC5114817 DOI: 10.1186/s12879-016-2020-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 11/11/2016] [Indexed: 12/25/2022] Open
Abstract
Background Community associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is one of the most common causes of skin and soft tissue infections in the United States, and a variety of genetic host factors are suspected to be risk factors for recurrent infection. Based on the CDC definition, we have developed and validated an electronic health record (EHR) based CA-MRSA phenotype algorithm utilizing both structured and unstructured data. Methods The algorithm was validated at three eMERGE consortium sites, and positive predictive value, negative predictive value and sensitivity, were calculated. The algorithm was then run and data collected across seven total sites. The resulting data was used in GWAS analysis. Results Across seven sites, the CA-MRSA phenotype algorithm identified a total of 349 cases and 7761 controls among the genotyped European and African American biobank populations. PPV ranged from 68 to 100% for cases and 96 to 100% for controls; sensitivity ranged from 94 to 100% for cases and 75 to 100% for controls. Frequency of cases in the populations varied widely by site. There were no plausible GWAS-significant (p < 5 E −8) findings. Conclusions Differences in EHR data representation and screening patterns across sites may have affected identification of cases and controls and accounted for varying frequencies across sites. Future work identifying these patterns is necessary. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-2020-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kathryn L Jackson
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Michael Mbagwu
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | | | - Daniel J Viox
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,Emory University School of Medicine, Atlanta, GA, USA
| | - James G Linneman
- Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, WI, USA
| | | | - Peggy L Peissig
- Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, WI, USA
| | | | - David A Carrell
- Group Health Research Institute, Group Health Cooperative, Seattle, WA, USA
| | | | - Jacqueline C Kirby
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | - Frank D Mentch
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lyam M Vazquez
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Abel N Kho
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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Omics Approaches for the Study of Adaptive Immunity to Staphylococcus aureus and the Selection of Vaccine Candidates. Proteomes 2016; 4:proteomes4010011. [PMID: 28248221 PMCID: PMC5217363 DOI: 10.3390/proteomes4010011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 02/05/2016] [Accepted: 03/01/2016] [Indexed: 01/20/2023] Open
Abstract
Staphylococcus aureus is a dangerous pathogen both in hospitals and in the community. Due to the crisis of antibiotic resistance, there is an urgent need for new strategies to combat S. aureus infections, such as vaccination. Increasing our knowledge about the mechanisms of protection will be key for the successful prevention or treatment of S. aureus invasion. Omics technologies generate a comprehensive picture of the physiological and pathophysiological processes within cells, tissues, organs, organisms and even populations. This review provides an overview of the contribution of genomics, transcriptomics, proteomics, metabolomics and immunoproteomics to the current understanding of S. aureus‑host interaction, with a focus on the adaptive immune response to the microorganism. While antibody responses during colonization and infection have been analyzed in detail using immunoproteomics, the full potential of omics technologies has not been tapped yet in terms of T-cells. Omics technologies promise to speed up vaccine development by enabling reverse vaccinology approaches. In consequence, omics technologies are powerful tools for deepening our understanding of the “superbug” S. aureus and for improving its control.
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DeLorenze GN, Nelson CL, Scott WK, Allen AS, Ray GT, Tsai AL, Quesenberry CP, Fowler VG. Polymorphisms in HLA Class II Genes Are Associated With Susceptibility to Staphylococcus aureus Infection in a White Population. J Infect Dis 2016; 213:816-23. [PMID: 26450422 PMCID: PMC4747615 DOI: 10.1093/infdis/jiv483] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 09/30/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Staphylococcus aureus can cause life-threatening infections. Human susceptibility to S. aureus infection may be influenced by host genetic variation. METHODS A genome-wide association study (GWAS) in a large health plan-based cohort included biologic specimens from 4701 culture-confirmed S. aureus cases and 45 344 matched controls; 584 535 single-nucleotide polymorphisms (SNPs) were genotyped on an array specific to individuals of European ancestry. Coverage was increased by imputation of >25 million common SNPs, using the 1000 Genomes Reference panel. In addition, human leukocyte antigen (HLA) serotypes were also imputed. RESULTS Logistic regression analysis, performed under the assumption of an additive genetic model, revealed several imputed SNPs (eg, rs115231074: odds ratio [OR], 1.22 [P = 1.3 × 10(-10)]; rs35079132: OR, 1.24 [P = 3.8 × 10(-8)]) achieving genome-wide significance on chromosome 6 in the HLA class II region. One adjacent genotyped SNP was nearly genome-wide significant (rs4321864: OR, 1.13; P = 8.8 × 10(-8)). These polymorphisms are located near the genes encoding HLA-DRA and HLA-DRB1. Results of further logistic regression analysis, in which the most significant GWAS SNPs were conditioned on HLA-DRB1*04 serotype, showed additional support for the strength of association between HLA class II genetic variants and S. aureus infection. CONCLUSIONS Our study results are the first reported evidence of human genetic susceptibility to S. aureus infection.
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Affiliation(s)
| | | | - William K Scott
- John P. Hussman Institute for Human Genomics Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Florida
| | - Andrew S Allen
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina
| | - G Thomas Ray
- Division of Research, Kaiser Permanente Northern California, Oakland
| | - Ai-Lin Tsai
- Division of Research, Kaiser Permanente Northern California, Oakland
| | | | - Vance G Fowler
- Duke Clinical Research Institute Division of Infectious Diseases, Duke University Medical Center
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25
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Messina JA, Thaden JT, Sharma-Kuinkel BK, Fowler VG. Impact of Bacterial and Human Genetic Variation on Staphylococcus aureus Infections. PLoS Pathog 2016; 12:e1005330. [PMID: 26766507 PMCID: PMC4713168 DOI: 10.1371/journal.ppat.1005330] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Julia A. Messina
- Division of Infectious Diseases, Department of Medicine, Duke University, Durham, North Carolina, United States of America
- Duke Clinical Research Institute, Duke University, Durham, North Carolina, United States of America
| | - Joshua T. Thaden
- Division of Infectious Diseases, Department of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Batu K. Sharma-Kuinkel
- Division of Infectious Diseases, Department of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Vance G. Fowler
- Division of Infectious Diseases, Department of Medicine, Duke University, Durham, North Carolina, United States of America
- Duke Clinical Research Institute, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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26
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Conjunctival fibrosis and the innate barriers to Chlamydia trachomatis intracellular infection: a genome wide association study. Sci Rep 2015; 5:17447. [PMID: 26616738 PMCID: PMC4663496 DOI: 10.1038/srep17447] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/29/2015] [Indexed: 01/26/2023] Open
Abstract
Chlamydia trachomatis causes both trachoma and sexually transmitted
infections. These diseases have similar pathology and potentially similar genetic
predisposing factors. We aimed to identify polymorphisms and pathways associated
with pathological sequelae of ocular Chlamydia trachomatis infections in The
Gambia. We report a discovery phase genome-wide association study (GWAS) of scarring
trachoma (1090 cases, 1531 controls) that identified 27 SNPs with strong, but not
genome-wide significant, association with disease
(5 × 10−6 > P > 5 × 10−8).
The most strongly associated SNP (rs111513399,
P = 5.38 × 10−7)
fell within a gene (PREX2) with homology to factors known to facilitate
chlamydial entry to the host cell. Pathway analysis of GWAS data was significantly
enriched for mitotic cell cycle processes (P = 0.001), the
immune response (P = 0.00001) and for multiple cell surface
receptor signalling pathways. New analyses of published transcriptome data sets from
Gambia, Tanzania and Ethiopia also revealed that the same cell cycle and immune
response pathways were enriched at the transcriptional level in various disease
states. Although unconfirmed, the data suggest that genetic associations with
chlamydial scarring disease may be focussed on processes relating to the immune
response, the host cell cycle and cell surface receptor signalling.
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27
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Skallerup P, Espinosa-Gongora C, Jørgensen CB, Guardabassi L, Fredholm M. Genome-wide association study reveals a locus for nasal carriage of Staphylococcus aureus in Danish crossbred pigs. BMC Vet Res 2015; 11:290. [PMID: 26612358 PMCID: PMC4662016 DOI: 10.1186/s12917-015-0599-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/18/2015] [Indexed: 11/25/2022] Open
Abstract
Background Staphylococcus aureus is an important human opportunistic pathogen residing on skin and mucosae of healthy people. Pigs have been identified as a source of human colonization and infection with methicillin-resistant Staphylococcus aureus (MRSA) and novel measures are needed to control zoonotic transmission. A recent longitudinal study indicated that a minority of pigs characterized by high nasal load and stable carriage may be responsible for the maintenance of S. aureus within farms. The primary objective of the present study was to detect genetic loci associated with nasal carriage of S. aureus in Danish crossbred pigs (Danish Landrace/Yorkshire/Duroc). Results Fifty-six persistent carriers and 65 non-carriers selected from 15 farms surveyed in the previous longitudinal study were genotyped using Illumina’s Porcine SNP60 beadchip. In addition, spa typing was performed on 126 S. aureus isolates from 37 pigs to investigate possible relationships between host and S. aureus genotypes. A single SNP (MARC0099960) on chromosome 12 was found to be associated with nasal carriage of S. aureus at a genome-wide level after permutation testing (p = 0.0497) whereas the association of a neighboring SNP was found to be borderline (p = 0.114). Typing of S. aureus isolates led to detection of 11 spa types belonging to the three main S. aureus clonal complexes (CC) previously described in pigs (CC9, CC30 and CC398). Individual carriers often harbored multiple S. aureus genotypes and the host-pathogen interaction seems to be independent of S. aureus genotype. Conclusion Our results suggest it may be possible to select pigs genetically resistant to S. aureus nasal colonization as a tool to control transmission of livestock-associated MRSA to humans. Electronic supplementary material The online version of this article (doi:10.1186/s12917-015-0599-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Per Skallerup
- Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.
| | | | - Claus B Jørgensen
- Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.
| | - Luca Guardabassi
- Department of Veterinary Disease Biology, University of Copenhagen, Frederiksberg, Denmark.
| | - Merete Fredholm
- Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.
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28
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Genome-Wide Association Study of Staphylococcus aureus Carriage in a Community-Based Sample of Mexican-Americans in Starr County, Texas. PLoS One 2015; 10:e0142130. [PMID: 26569114 PMCID: PMC4646511 DOI: 10.1371/journal.pone.0142130] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/16/2015] [Indexed: 02/07/2023] Open
Abstract
Staphylococcus aureus is the number one cause of hospital-acquired infections. Understanding host pathogen interactions is paramount to the development of more effective treatment and prevention strategies. Therefore, whole exome sequence and chip-based genotype data were used to conduct rare variant and genome-wide association analyses in a Mexican-American cohort from Starr County, Texas to identify genes and variants associated with S. aureus nasal carriage. Unlike most studies of S. aureus that are based on hospitalized populations, this study used a representative community sample. Two nasal swabs were collected from participants (n = 858) 11–17 days apart between October 2009 and December 2013, screened for the presence of S. aureus, and then classified as either persistent, intermittent, or non-carriers. The chip-based and exome sequence-based single variant association analyses identified 1 genome-wide significant region (KAT2B) for intermittent and 11 regions suggestively associated with persistent or intermittent S. aureus carriage. We also report top findings from gene-based burden analyses of rare functional variation. Notably, we observed marked differences between signals associated with persistent and intermittent carriage. In single variant analyses of persistent carriage, 7 of 9 genes in suggestively associated regions and all 5 top gene-based findings are associated with cell growth or tight junction integrity or are structural constituents of the cytoskeleton, suggesting that variation in genes associated with persistent carriage impact cellular integrity and morphology.
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29
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Shukla SK, Rose W, Schrodi SJ. Complex host genetic susceptibility to Staphylococcus aureus infections. Trends Microbiol 2015; 23:529-36. [PMID: 26112911 DOI: 10.1016/j.tim.2015.05.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/11/2015] [Accepted: 05/22/2015] [Indexed: 12/20/2022]
Abstract
Understanding of the host genetic susceptibility to carriage of, and infections, due to Staphylococcus aureus, a nosocomial pathogen, is still in its nascent stages. Mouse models show variable susceptibility to S. aureus infections across mouse strains and disease models with roles for signaling pathways involving Toll-like receptors (TLR-1, TLR-2, and TLR-6), interleukins (IL-4, IL-6, IL-10, and IL-13), chemokines [CXC ligand (CXCL)-1 and CXCL-2], and T helper (Th)1/Th2 responses. Genome-wide association studies (GWASs) for carriage in humans identified SNPs in IL4, DEFB1, CRP, and VDR for persistent nasal carriage. NR3C1 haplotypes may either enhance risk or provide protection from colonization. GWASs for all S. aureus diseases have suggested roles for DAPK3, a kinase, and XRN1, a nuclease, while CDON could have a role in complicated bacteremia. More studies are needed to identify host susceptibility genes along with confirmation from functional assays.
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Affiliation(s)
- Sanjay K Shukla
- Center for Human Genetics, Marshfield Clinic Research Foundation, 1000 North Oak Avenue-MLR, Marshfield, WI, USA.
| | - Warren Rose
- Pharmacy Practice Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Steven J Schrodi
- Center for Human Genetics, Marshfield Clinic Research Foundation, 1000 North Oak Avenue-MLR, Marshfield, WI, USA
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30
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Selenium and chronic diseases: a nutritional genomics perspective. Nutrients 2015; 7:3621-51. [PMID: 25988760 PMCID: PMC4446770 DOI: 10.3390/nu7053621] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 04/28/2015] [Accepted: 05/06/2015] [Indexed: 01/10/2023] Open
Abstract
Mechanistic data have revealed a key role for selenium (Se) and selenoproteins in biological pathways known to be altered in multifactorial diseases, such as cellular maintenance, response to oxidative stress and correct protein folding. Although epidemiological studies indicate that low Se intake is linked to increased risk for various chronic diseases, supplementation trials have given confusing outcomes, suggesting that additional genetic factors could affect the relationship between Se and health. Genetic data support this hypothesis, as risk for several chronic diseases, in particular cancer, was linked to a number of single nucleotide polymorphisms (SNP) altering Se metabolism, selenoprotein synthesis or activity. Interactions between SNPs in selenoprotein genes, SNPs in related molecular pathways and biomarkers of Se status were found to further modulate the genetic risk carried by the SNPs. Taken together, nutritional genomics approaches uncovered the potential implication of some selenoproteins as well as the influence of complex interactions between genetic variants and Se status in the aetiology of several chronic diseases. This review discusses the results from these genetic associations in the context of selenoprotein functions and epidemiological investigations and emphasises the need to assess in future studies the combined contribution of Se status, environmental stress, and multiple or individual SNPs to disease risk.
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31
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Ritchie MD, de Andrade M, Kuivaniemi H. The foundation of precision medicine: integration of electronic health records with genomics through basic, clinical, and translational research. Front Genet 2015; 6:104. [PMID: 25852745 PMCID: PMC4362332 DOI: 10.3389/fgene.2015.00104] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 02/27/2015] [Indexed: 12/30/2022] Open
Affiliation(s)
- Marylyn D Ritchie
- Biochemistry and Molecular Biology, Center for Systems Genomics, The Pennsylvania State University University Park, PA, USA ; Institute of Biomedical and Translational Informatics, Geisinger Health System Danville, PA, USA
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Department of Health Science Research, Mayo Clinic Rochester, MN, USA
| | - Helena Kuivaniemi
- The Sigfried and Janet Weis Center for Research, Geisinger Health System Danville, PA, USA ; Department of Surgery, Temple University School of Medicine Philadelphia, PA, USA
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