1
|
Uberoi A, McCready-Vangi A, Grice EA. The wound microbiota: microbial mechanisms of impaired wound healing and infection. Nat Rev Microbiol 2024; 22:507-521. [PMID: 38575708 DOI: 10.1038/s41579-024-01035-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2024] [Indexed: 04/06/2024]
Abstract
The skin barrier protects the human body from invasion by exogenous and pathogenic microorganisms. A breach in this barrier exposes the underlying tissue to microbial contamination, which can lead to infection, delayed healing, and further loss of tissue and organ integrity. Delayed wound healing and chronic wounds are associated with comorbidities, including diabetes, advanced age, immunosuppression and autoimmune disease. The wound microbiota can influence each stage of the multi-factorial repair process and influence the likelihood of an infection. Pathogens that commonly infect wounds, such as Staphylococcus aureus and Pseudomonas aeruginosa, express specialized virulence factors that facilitate adherence and invasion. Biofilm formation and other polymicrobial interactions contribute to host immunity evasion and resistance to antimicrobial therapies. Anaerobic organisms, fungal and viral pathogens, and emerging drug-resistant microorganisms present unique challenges for diagnosis and therapy. In this Review, we explore the current understanding of how microorganisms present in wounds impact the process of skin repair and lead to infection through their actions on the host and the other microbial wound inhabitants.
Collapse
Affiliation(s)
- Aayushi Uberoi
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amelia McCready-Vangi
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth A Grice
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
2
|
Norton AM, Buchmann G, Ashe A, Watson OT, Beekman M, Remnant EJ. Deformed wing virus genotypes A and B do not elicit immunologically different responses in naïve honey bee hosts. INSECT MOLECULAR BIOLOGY 2024. [PMID: 39072811 DOI: 10.1111/imb.12948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 07/11/2024] [Indexed: 07/30/2024]
Abstract
Iflavirus aladeformis (Picornavirales: Iflaviridae), commonly known as deformed wing virus(DWV), in association with Varroa destructor Anderson and Trueman (Mesostigmata: Varroidae), is a leading factor associated with honey bee (Apis mellifera L. [Hymenoptera: Apidae]) deaths. The virus and mite have a near global distribution, making it difficult to separate the effect of one from the other. The prevalence of two main DWV genotypes (DWV-A and DWV-B) has changed over time, leading to the possibility that the two strains elicit a different immune response by the host. Here, we use a honey bee population naïve to both the mite and the virus to investigate if honey bees show a different immunological response to DWV genotypes. We examined the expression of 19 immune genes by reverse transcription quantitative PCR (RT-qPCR) and analysed small RNA after experimental injection with DWV-A and DWV-B. We found no evidence that DWV-A and DWV-B elicit different immune responses in honey bees. RNA interference genes were up-regulated during DWV infection, and small interfering RNA (siRNA) responses were proportional to viral loads yet did not inhibit DWV accumulation. The siRNA response towards DWV was weaker than the response to another honey bee pathogen, Triatovirus nigereginacellulae (Picornavirales: Dicistroviridae; black queen cell virus), suggesting that DWV is comparatively better at evading host antiviral defences. There was no evidence for the production of virus-derived Piwi-interacting RNAs (piRNAs) in response to DWV. In contrast to previous studies, and in the absence of V. destructor, we found no evidence that DWV has an immunosuppressive effect. Overall, our results advance our understanding of the immunological effect that DWV in isolation elicits in honey bees.
Collapse
Affiliation(s)
- Amanda M Norton
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Gabriele Buchmann
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Alyson Ashe
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Owen T Watson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Madeleine Beekman
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Emily J Remnant
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| |
Collapse
|
3
|
Sela U, Corrêa da Rosa JM, Fischetti VA, Cohen JE. Quantifying how much host, pathogen, and other factors affect human protective adaptive immune responses. Front Immunol 2024; 15:1330253. [PMID: 38410519 PMCID: PMC10895049 DOI: 10.3389/fimmu.2024.1330253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/08/2024] [Indexed: 02/28/2024] Open
Abstract
Recognizing the "essential" factors that contribute to a clinical outcome is critical for designing appropriate therapies and prioritizing limited medical resources. Demonstrating a high correlation between a factor and an outcome does not necessarily imply an essential role of the factor to the outcome. Human protective adaptive immune responses to pathogens vary among (and perhaps within) pathogenic strains, human individual hosts, and in response to other factors. Which of these has an "essential" role? We offer three statistical approaches that predict the presence of newly contributing factor(s) and then quantify the influence of host, pathogen, and the new factors on immune responses. We illustrate these approaches using previous data from the protective adaptive immune response (cellular and humoral) by human hosts to various strains of the same pathogenic bacterial species. Taylor's law predicts the existence of other factors potentially contributing to the human protective adaptive immune response in addition to inter-individual host and intra-bacterial species inter-strain variability. A mixed linear model measures the relative contribution of the known variables, individual human hosts and bacterial strains, and estimates the summed contributions of the newly predicted but unknown factors to the combined adaptive immune response. A principal component analysis predicts the presence of sub-variables (currently not defined) within bacterial strains and individuals that may contribute to the combined immune response. These observations have statistical, biological, clinical, and therapeutic implications.
Collapse
Affiliation(s)
- Uri Sela
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, NY, United States
| | - Joel M. Corrêa da Rosa
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Vincent A. Fischetti
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, NY, United States
| | - Joel E. Cohen
- Laboratory of Populations, The Rockefeller University, New York, NY, United States
- Department of Statistics, Columbia University, New York, NY, United States
- Department of Statistics, University of Chicago, Chicago, IL, United States
| |
Collapse
|
4
|
Charron P, Gao R, Chmara J, Hoover E, Nadin-Davis S, Chauvin D, Hazelwood J, Makondo K, Duceppe MO, Kang M. Influence of genomic variations on glanders serodiagnostic antigens using integrative genomic and transcriptomic approaches. Front Vet Sci 2023; 10:1217135. [PMID: 38125681 PMCID: PMC10730941 DOI: 10.3389/fvets.2023.1217135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
Glanders is a highly contagious and life-threatening zoonotic disease caused by Burkholderia mallei (B. mallei). Without an effective vaccine or treatment, early diagnosis has been regarded as the most effective method to prevent glanders transmission. Currently, the diagnosis of glanders is heavily reliant on serological tests. However, given that markedly different host immune responses can be elicited by genetically different strains of the same bacterial species, infection by B. mallei, whose genome is unstable and plastic, may result in various immune responses. This variability can make the serodiagnosis of glanders challenging. Therefore, there is a need for a comprehensive understanding and assessment of how B. mallei genomic variations impact the appropriateness of specific target antigens for glanders serodiagnosis. In this study, we investigated how genomic variations in the B. mallei genome affect gene content (gene presence/absence) and expression, with a special focus on antigens used or potentially used in serodiagnosis. In all the genome sequences of B. mallei isolates available in NCBI's RefSeq database (accessed in July 2023) and in-house sequenced samples, extensive small and large variations were observed when compared to the type strain ATCC 23344. Further pan-genome analysis of those assemblies revealed variations of gene content among all available genomes of B. mallei. Specifically, differences in gene content ranging from 31 to 715 genes with an average of 334 gene presence-absence variations were found in strains with complete or chromosome-level genome assemblies, using the ATCC 23344 strain as a reference. The affected genes included some encoded proteins used as serodiagnostic antigens, which were lost due mainly to structural variations. Additionally, a transcriptomic analysis was performed using the type strain ATCC 23344 and strain Zagreb which has been widely utilized to produce glanders antigens. In total, 388 significant differentially expressed genes were identified between these two strains, including genes related to bacterial pathogenesis and virulence, some of which were associated with genomic variations, particularly structural variations. To our knowledge, this is the first comprehensive study to uncover the impacts of genetic variations of B. mallei on its gene content and expression. These differences would have significant impacts on host innate and adaptive immunity, including antibody production, during infection. This study provides novel insights into B. mallei genetic variants, knowledge which will help to improve glanders serodiagnosis.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Mingsong Kang
- Ottawa Laboratory-Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| |
Collapse
|
5
|
Holm JB, France MT, Gajer P, Ma B, Brotman RM, Shardell M, Forney L, Ravel J. Integrating compositional and functional content to describe vaginal microbiomes in health and disease. MICROBIOME 2023; 11:259. [PMID: 38031142 PMCID: PMC10688475 DOI: 10.1186/s40168-023-01692-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 10/07/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND A Lactobacillus-dominated vaginal microbiome provides the first line of defense against adverse genital tract health outcomes. However, there is limited understanding of the mechanisms by which the vaginal microbiome modulates protection, as prior work mostly described its composition through morphologic assessment and marker gene sequencing methods that do not capture functional information. To address this gap, we developed metagenomic community state types (mgCSTs) which use metagenomic sequences to describe and define vaginal microbiomes based on both composition and functional potential. RESULTS MgCSTs are categories of microbiomes classified using taxonomy and the functional potential encoded in their metagenomes. MgCSTs reflect unique combinations of metagenomic subspecies (mgSs), which are assemblages of bacterial strains of the same species, within a microbiome. We demonstrate that mgCSTs are associated with demographics such as age and race, as well as vaginal pH and Gram stain assessment of vaginal smears. Importantly, these associations varied between mgCSTs predominated by the same bacterial species. A subset of mgCSTs, including three of the six predominated by Gardnerella vaginalis mgSs, as well as mgSs of L. iners, were associated with a greater likelihood of bacterial vaginosis diagnosed by Amsel clinical criteria. This L. iners mgSs, among other functional features, encoded enhanced genetic capabilities for epithelial cell attachment that could facilitate cytotoxin-mediated cell lysis. Finally, we report a mgSs and mgCST classifier for which source code is provided and may be adapted for use by the microbiome research community. CONCLUSIONS MgCSTs are a novel and easily implemented approach to reduce the dimension of complex metagenomic datasets while maintaining their functional uniqueness. MgCSTs enable the investigation of multiple strains of the same species and the functional diversity in that species. Future investigations of functional diversity may be key to unraveling the pathways by which the vaginal microbiome modulates the protection of the genital tract. Importantly, our findings support the hypothesis that functional differences between vaginal microbiomes, including those that may look compositionally similar, are critical considerations in vaginal health. Ultimately, mgCSTs may lead to novel hypotheses concerning the role of the vaginal microbiome in promoting health and disease, and identify targets for novel prognostic, diagnostic, and therapeutic strategies to improve women's genital health. Video Abstract.
Collapse
Affiliation(s)
- Johanna B Holm
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michael T France
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Pawel Gajer
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Bing Ma
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Rebecca M Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michelle Shardell
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Larry Forney
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
6
|
Kulkarni RR, Gaghan C, Gorrell K, Fletcher OJ. Mucosal and systemic lymphoid immune responses against Clostridium perfringens strains with variable virulence in the production of necrotic enteritis in broiler chickens. Avian Pathol 2023; 52:108-118. [PMID: 36453684 DOI: 10.1080/03079457.2022.2154195] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Necrotic enteritis (NE), caused by Clostridium perfringens, is an economically important disease of chickens. Although NE pathogenesis is moderately well studied, the host immune responses against C. perfringens are poorly understood. The present study used an experimental NE model to characterize lymphoid immune responses in the caecal tonsils (CT), bursa of Fabricius, Harderian gland (HG) and spleen tissues of broiler chickens infected with four netB+ C. perfringens strains (CP1, CP5, CP18, and CP26), of which CP18 and CP26 strains also carried the tpeL gene. The gross and histopathological lesions in chickens revealed CP5 to be avirulent, while CP1, CP18, and CP26 strains were virulent with CP26 being "very virulent". Gene expression analysis showed that, while the virulent strains induced a significantly upregulated expression of pro-inflammatory IL-1β gene in CT, the CP26-infected birds had significantly higher CT transcription of IFNγ and IL-6 pro-inflammatory genes compared to CP5-infected or uninfected chickens. Furthermore, CP26 infection also led to significantly increased bursal and HG expression of the anti-inflammatory/regulatory genes, IL-10 or TGFβ, compared to control, CP5 and CP1 groups. Additionally, the splenic pro- and anti-inflammatory transcriptional changes were observed only in the CP26-infected chickens. An antibody-mediated response, as characterized by increased IL-4 and/or IL-13 transcription and elevated IgM levels in birds infected with virulent strains, particularly in the CP26-infected group compared to uninfected controls, was also evident. Collectively, our findings suggest that lymphoid immune responses during NE in chickens are spatially regulated such that the inflammatory responses against C. perfringens depend on the virulence of the strain.
Collapse
Affiliation(s)
- Raveendra R Kulkarni
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Carissa Gaghan
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Kaitlin Gorrell
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Oscar J Fletcher
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| |
Collapse
|
7
|
Holm JB, France MT, Gajer P, Ma B, Brotman RM, Shardell M, Forney L, Ravel J. High-resolution functional description of vaginal microbiomes in health and disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.533147. [PMID: 36993583 PMCID: PMC10055360 DOI: 10.1101/2023.03.24.533147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Background A Lactobacillus-dominated vaginal microbiome provides the first line of defense against numerous adverse genital tract health outcomes. However, there is limited understanding of the mechanisms by which the vaginal microbiome modulates protection, as prior work mostly described its composition through morphologic assessment and marker gene sequencing methods that do not capture functional information. To address this limitation, we developed metagenomic community state types (mgCSTs) which uses metagenomic sequences to describe and define vaginal microbiomes based on both composition and function. Results MgCSTs are categories of microbiomes classified using taxonomy and the functional potential encoded in their metagenomes. MgCSTs reflect unique combinations of metagenomic subspecies (mgSs), which are assemblages of bacterial strains of the same species, within a microbiome. We demonstrate that mgCSTs are associated with demographics such as age and race, as well as vaginal pH and Gram stain assessment of vaginal smears. Importantly, these associations varied between mgCSTs predominated by the same bacterial species. A subset of mgCSTs, including three of the six predominated by Gardnerella mgSs, as well as a mgSs of L. iners, were associated with a greater likelihood of Amsel bacterial vaginosis diagnosis. This L. iners mgSs, among other functional features, encoded enhanced genetic capabilities for epithelial cell attachment that could facilitate cytotoxin-mediated cell lysis. Finally, we report a mgSs and mgCST classifier as an easily applied, standardized method for use by the microbiome research community. Conclusions MgCSTs are a novel and easily implemented approach to reducing the dimension of complex metagenomic datasets, while maintaining their functional uniqueness. MgCSTs enable investigation of multiple strains of the same species and the functional diversity in that species. Future investigations of functional diversity may be key to unraveling the pathways by which the vaginal microbiome modulates protection to the genital tract. Importantly, our findings support the hypothesis that functional differences between vaginal microbiomes, including those that may look compositionally similar, are critical considerations in vaginal health. Ultimately, mgCSTs may lead to novel hypotheses concerning the role of the vaginal microbiome in promoting health and disease, and identify targets for novel prognostic, diagnostic, and therapeutic strategies to improve women's genital health.
Collapse
Affiliation(s)
- Johanna B. Holm
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michael T. France
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Pawel Gajer
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Bing Ma
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Rebecca M. Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michelle Shardell
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Larry Forney
- Department of Biological Sciences, University of Idaho, Moscow, ID
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| |
Collapse
|
8
|
Gaghan C, Gorrell K, Taha-Abdelaziz K, Sharif S, Kulkarni RR. Intracloacal Inoculation of Broiler Chickens with Clostridium perfringens Strains: Evaluation of Necrotic Enteritis Disease Development and Lymphoid Immune Responses. Microorganisms 2023; 11:microorganisms11030771. [PMID: 36985344 PMCID: PMC10054439 DOI: 10.3390/microorganisms11030771] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023] Open
Abstract
Necrotic enteritis (NE) is an economically important disease of chickens. We have recently shown that inflammatory responses in chickens inoculated orally with virulent Clostridium perfringens were spatially regulated. Here, we used previously virulence-characterized netB+ C. perfringens strains, avirulent CP5 and virulent CP18 and CP26, to assess the severity of NE and immune responses in broiler chickens when inoculated intracloacally. The results showed that CP18- and CP26-infected birds had a reduced weight gain and developed milder/less severe NE lesions, as determined by the gross lesions scores, suggesting a subclinical-grade infection. Gene expression analysis in infected birds revealed three statistically significant observations compared to uninfected-control: (1) Increased expression of anti-inflammatory/immunoregulatory interleukin (IL)-10/transforming growth factor (TGF)β in cecal tonsil (CT) and bursa of Fabricius in the CP18/CP26-infected groups. (2) Increased CT transcription of pro-inflammatory IL-1β, IL-6 and interferon (IFN)γ and decreased Harderian gland (HG) expression of IFNγ in the CP18/CP26-infected birds. (3) Increased HG or bursal expression of IL-4 and IL-13 in CP5-infected birds. Collectively, intracloacal C. perfringens inoculation seems to induce a highly regulated inflammatory response in the CT and other mucosal lymphoid organs and an intracloacal infection model may be useful in evaluating immune responses in chickens with subclinical NE.
Collapse
Affiliation(s)
- Carissa Gaghan
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Kaitlin Gorrell
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Khaled Taha-Abdelaziz
- Department of Animal and Veterinary Sciences, Clemson University, Clemson, SC 29634, USA
| | - Shayan Sharif
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Raveendra R. Kulkarni
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
- Correspondence: ; Tel.: +1-919-513-6277
| |
Collapse
|
9
|
vom Werth KL, Kemper B, Kampmeier S, Mellmann A. Application of Digital Holographic Microscopy to Analyze Changes in T-Cell Morphology in Response to Bacterial Challenge. Cells 2023; 12:cells12050762. [PMID: 36899897 PMCID: PMC10000559 DOI: 10.3390/cells12050762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/16/2023] [Accepted: 02/24/2023] [Indexed: 03/06/2023] Open
Abstract
Quantitative phase imaging (QPI) is a non-invasive, label-free technique used to detect aberrant cell morphologies caused by disease, thus providing a useful diagnostic approach. Here, we evaluated the potential of QPI to differentiate specific morphological changes in human primary T-cells exposed to various bacterial species and strains. Cells were challenged with sterile bacterial determinants, i.e., membrane vesicles or culture supernatants, derived from different Gram-positive and Gram-negative bacteria. Timelapse QPI by digital holographic microscopy (DHM) was applied to capture changes in T-cell morphology over time. After numerical reconstruction and image segmentation, we calculated single cell area, circularity and mean phase contrast. Upon bacterial challenge, T-cells underwent rapid morphological changes such as cell shrinkage, alterations of mean phase contrast and loss of cell integrity. Time course and intensity of this response varied between both different species and strains. The strongest effect was observed for treatment with S. aureus-derived culture supernatants that led to complete lysis of the cells. Furthermore, cell shrinkage and loss of circular shape was stronger in Gram-negative than in Gram-positive bacteria. Additionally, T-cell response to bacterial virulence factors was concentration-dependent, as decreases in cellular area and circularity were enhanced with increasing concentrations of bacterial determinants. Our findings clearly indicate that T-cell response to bacterial stress depends on the causative pathogen, and specific morphological alterations can be detected using DHM.
Collapse
Affiliation(s)
| | - Björn Kemper
- Biomedical Technology Center of the Medical Faculty, University of Münster, 48149 Münster, Germany
| | - Stefanie Kampmeier
- Institute of Hygiene, University Hospital Münster, 48149 Münster, Germany
| | - Alexander Mellmann
- Institute of Hygiene, University Hospital Münster, 48149 Münster, Germany
- Correspondence: ; Tel.: +49-251-83-55361
| |
Collapse
|
10
|
Mattoo SUS, Aganja RP, Kim SC, Jeong CG, Nazki S, Khatun A, Kim WI, Lee SM. A standardized method to study immune responses using porcine whole blood. J Vet Sci 2023; 24:e11. [PMID: 36726276 PMCID: PMC9899947 DOI: 10.4142/jvs.22210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Peripheral blood mononuclear cells (PBMCs) are commonly used to assess in vitro immune responses. However, PBMC isolation is a time-consuming procedure, introduces technical variability, and requires a relatively large volume of blood. By contrast, whole blood assay (WBA) is faster, cheaper, maintains more physiological conditions, and requires less sample volume, laboratory training, and equipment. OBJECTIVES Herein, this study aimed to develop a porcine WBA for in vitro evaluation of immune responses. METHODS Heparinized whole blood (WB) was diluted (non-diluted, 1/2, 1/8, and 1/16) in RPMI-1640 media, followed by phorbol myristate acetate and ionomycin. After 24 h, cells were stained for interferon (IFN)-γ secreting T-cells followed by flow cytometry, and the supernatant was analyzed for tumor necrosis factor (TNF)-α. In addition, diluted WB was stimulated by lipopolysaccharide (LPS) and polyinosinic:polycytidylic acid (poly I:C), reference strain KCTC3557 (RS), field isolate (FI), of heat-killed (HK) Streptococcus suis, and porcine reproductive and respiratory syndrome virus (PRRSV). RESULTS The frequency of IFN-γ+CD3+ T-cells and concentration of TNF-α in the supernatant of WB increased with increasing dilution factor and were optimal at 1/8. WB TNF-α and interleukin (IL)-10 cytokine levels increased significantly following stimulation with LPS or poly I:C. Further, FI and RS induced IL-10 production in WB. Additionally, PRRSV strains increased the frequency of IFN-γ+CD4-CD8+ cells, and IFN-γ was non-significantly induced in the supernatant of re-stimulated samples. CONCLUSIONS We propose that the WBA is a rapid, reliable, and simple method to evaluate immune responses and WB should be diluted to trigger immune cells.
Collapse
Affiliation(s)
| | - Ram Prasad Aganja
- College of Veterinary Medicine, Jeonbuk National University, Iksan 54596, Korea
| | - Seung-Chai Kim
- College of Veterinary Medicine, Jeonbuk National University, Iksan 54596, Korea
| | - Chang-Gi Jeong
- College of Veterinary Medicine, Jeonbuk National University, Iksan 54596, Korea
| | - Salik Nazki
- The Pirbright Institute, Pirbright, GU24 0NF, United Kingdom
| | - Amina Khatun
- Department of Veterinary Pathology, Faculty of Animal Science and Veterinary Medicine, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh
| | - Won-Il Kim
- College of Veterinary Medicine, Jeonbuk National University, Iksan 54596, Korea.
| | - Sang-Myeong Lee
- College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea.
| |
Collapse
|
11
|
Zhao B, Yin Q, Fei Y, Zhu J, Qiu Y, Fang W, Li Y. Research progress of mechanisms for tight junction damage on blood-brain barrier inflammation. Arch Physiol Biochem 2022; 128:1579-1590. [PMID: 32608276 DOI: 10.1080/13813455.2020.1784952] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Inflammation in the central nervous system (CNS) contributes to disease pathologies by disrupting the integrity of the blood-brain barrier (BBB). Tight junctions (TJ) are a key component of the BBB. Following hypoxic-ischaemic or mechanical injury to the brain, inflammatory mediators are released such as cytokines, chemokines, and growth factors. Simultaneously, matrix metalloproteinases (MMPs) are released which can degrade TJ proteins. Subsequently, the function and morphology of the BBB are disrupted, which allows immune cells an opportunity to enter into the brain parenchyma. This review summarises the information on the role of TJ protein families in the BBB and provides a comprehensive summary of the mechanisms whereby inflammation breaks down the BBB by increasing degradation of TJ proteins.
Collapse
Affiliation(s)
- Bo Zhao
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Qiyang Yin
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Yuxiang Fei
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Jianping Zhu
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Yanying Qiu
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Weirong Fang
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Yunman Li
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| |
Collapse
|
12
|
Bulman ZP, Wicha SG, Nielsen EI, Lenhard JR, Nation RL, Theuretzbacher U, Derendorf H, Tängdén T, Zeitlinger M, Landersdorfer CB, Bulitta JB, Friberg LE, Li J, Tsuji BT. Research priorities towards precision antibiotic therapy to improve patient care. THE LANCET. MICROBE 2022; 3:e795-e802. [PMID: 35777386 DOI: 10.1016/s2666-5247(22)00121-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 04/04/2022] [Accepted: 04/28/2022] [Indexed: 12/24/2022]
Abstract
Antibiotic resistance presents an incessant threat to our drug armamentarium that necessitates novel approaches to therapy. Over the past several decades, investigation of pharmacokinetic and pharmacodynamic (PKPD) principles has substantially improved our understanding of the relationships between the antibiotic, pathogen, and infected patient. However, crucial gaps in our understanding of the pharmacology of antibacterials and their optimal use in the care of patients continue to exist; simply attaining antibiotic exposures that are considered adequate based on traditional targets can still result in treatment being unsuccessful and resistance proliferation for some infections. It is this salient paradox that points to key future directions for research in antibiotic therapeutics. This Personal View discusses six priority areas for antibiotic pharmacology research: (1) antibiotic-pathogen interactions, (2) antibiotic targets for combination therapy, (3) mechanistic models that describe the time-course of treatment response, (4) understanding and modelling of host response to infection, (5) personalised medicine through therapeutic drug management, and (6) application of these principles to support development of novel therapies. Innovative approaches that enhance our understanding of antibiotic pharmacology and facilitate more accurate predictions of treatment success, coupled with traditional pharmacology research, can be applied at the population level and to individual patients to improve outcomes.
Collapse
Affiliation(s)
- Zackery P Bulman
- Department of Pharmacy Practice, University of Illinois Chicago, Chicago, IL, USA.
| | - Sebastian G Wicha
- Department of Clinical Pharmacy, Institute of Pharmacy, University of Hamburg, Hamburg, Germany
| | | | - Justin R Lenhard
- Department of Clinical and Administrative Sciences, California Northstate University College of Pharmacy, Elk Grove, CA, USA
| | - Roger L Nation
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
| | | | - Hartmut Derendorf
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Thomas Tängdén
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Markus Zeitlinger
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Cornelia B Landersdorfer
- Centre for Medicine Use and Safety, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
| | - Jürgen B Bulitta
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Orlando, FL, USA
| | - Lena E Friberg
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Jian Li
- Monash Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Brian T Tsuji
- Department of Pharmacy Practice, University at Buffalo, Buffalo, NY, USA
| |
Collapse
|
13
|
Lee CJ, Qiu TA, Hong Z, Zhang Z, Min Y, Zhang L, Dai L, Zhao H, Si T, Sweedler JV. Profiling of d-alanine production by the microbial isolates of rat gut microbiota. FASEB J 2022; 36:e22446. [PMID: 35816159 DOI: 10.1096/fj.202101595r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 06/07/2022] [Accepted: 06/27/2022] [Indexed: 11/11/2022]
Abstract
d-alanine (d-Ala) and several other d-amino acids (d-AAs) act as hormones and neuromodulators in nervous and endocrine systems. Unlike the endogenously synthesized d-serine in animals, d-Ala may be from exogenous sources, e.g., diet and intestinal microorganisms. However, it is unclear if the capability to produce d-Ala and other d-AAs varies among different microbial strains in the gut. We isolated individual microorganisms of rat gut microbiota and profiled their d-AA production in vitro, focusing on d-Ala. Serial dilutions of intestinal contents from adult male rats were plated on agar to obtain clonal cultures. Using MALDI-TOF MS for rapid strain typing, we identified 38 unique isolates, grouped into 11 species based on 16S rRNA gene sequences. We then used two-tier screening to profile bacterial d-AA production, combining a d-amino acid oxidase-based enzymatic assay for rapid assessment of non-acidic d-AA amount and chiral LC-MS/MS to quantify individual d-AAs, revealing 19 out of the 38 isolated strains as d-AA producers. LC-MS/MS analysis of the eight top d-AA producers showed high levels of d-Ala in all strains tested, with substantial inter- and intra-species variations. Though results from the enzymatic assay and LC-MS/MS analysis aligned well, LC-MS/MS further revealed the existence of d-glutamate and d-aspartate, which are poor substrates for this enzymatic assay. We observed large inter- and intra-species variation of d-AA production profiles from rat gut microbiome species, demonstrating the importance of chemical profiling of gut microbiota in addition to sequencing, furthering the idea that microbial metabolites modulate host physiology.
Collapse
Affiliation(s)
- Cindy J Lee
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Tian A Qiu
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Zhilai Hong
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zhenkun Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yuhao Min
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Linzixuan Zhang
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Huimin Zhao
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Tong Si
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jonathan V Sweedler
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| |
Collapse
|
14
|
Luzala MM, Muanga CK, Kyana J, Safari JB, Zola EN, Mbusa GV, Nuapia YB, Liesse JMI, Nkanga CI, Krause RWM, Balčiūnaitienė A, Memvanga PB. A Critical Review of the Antimicrobial and Antibiofilm Activities of Green-Synthesized Plant-Based Metallic Nanoparticles. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:1841. [PMID: 35683697 PMCID: PMC9182092 DOI: 10.3390/nano12111841] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/03/2022] [Accepted: 04/05/2022] [Indexed: 02/01/2023]
Abstract
Metallic nanoparticles (MNPs) produced by green synthesis using plant extracts have attracted huge interest in the scientific community due to their excellent antibacterial, antifungal and antibiofilm activities. To evaluate these pharmacological properties, several methods or protocols have been successfully developed and implemented. Although these protocols were mostly inspired by the guidelines from national and international regulatory bodies, they suffer from a glaring absence of standardization of the experimental conditions. This situation leads to a lack of reproducibility and comparability of data from different study settings. To minimize these problems, guidelines for the antimicrobial and antibiofilm evaluation of MNPs should be developed by specialists in the field. Being aware of the immensity of the workload and the efforts required to achieve this, we set out to undertake a meticulous literature review of different experimental protocols and laboratory conditions used for the antimicrobial and antibiofilm evaluation of MNPs that could be used as a basis for future guidelines. This review also brings together all the discrepancies resulting from the different experimental designs and emphasizes their impact on the biological activities as well as their interpretation. Finally, the paper proposes a general overview that requires extensive experimental investigations to set the stage for the future development of effective antimicrobial MNPs using green synthesis.
Collapse
Affiliation(s)
- Miryam M. Luzala
- Laboratory of Pharmaceutics and Phytopharmaceutical Drug Development, Faculty of Pharmaceutical Sciences, University of Kinshasa, Kinshasa XI B.P. 212, Democratic Republic of the Congo; (M.M.L.); (C.K.M.); (E.N.Z.); (C.I.N.)
| | - Claude K. Muanga
- Laboratory of Pharmaceutics and Phytopharmaceutical Drug Development, Faculty of Pharmaceutical Sciences, University of Kinshasa, Kinshasa XI B.P. 212, Democratic Republic of the Congo; (M.M.L.); (C.K.M.); (E.N.Z.); (C.I.N.)
| | - Joseph Kyana
- Department of Pharmacy, Faculty of Medecine and Pharmacy, University of Kisangani, Kisangani XI B.P. 2012, Democratic Republic of the Congo;
| | - Justin B. Safari
- Department of Pharmacy, Faculty of Pharmaceutical Sciences and Public Health, Official University of Bukavu, Bukavu B.P. 570, Democratic Republic of the Congo;
- Department of Chemistry, Faculty of Science, Rhodes University, P.O. Box 94, Makhana 6140, South Africa
| | - Eunice N. Zola
- Laboratory of Pharmaceutics and Phytopharmaceutical Drug Development, Faculty of Pharmaceutical Sciences, University of Kinshasa, Kinshasa XI B.P. 212, Democratic Republic of the Congo; (M.M.L.); (C.K.M.); (E.N.Z.); (C.I.N.)
| | - Grégoire V. Mbusa
- Centre Universitaire de Référence de Surveillance de la Résistance aux Antimicrobiens (CURS-RAM), Faculty of Pharmaceutical Sciences, University of Kinshasa, Kinshasa XI B.P. 212, Democratic Republic of the Congo; (G.V.M.); (J.-M.I.L.)
- Laboratory of Experimental and Pharmaceutical Microbiology, Faculty of Pharmaceutical Sciences, University of Kinshasa, Kinshasa XI B.P. 212, Democratic Republic of the Congo
| | - Yannick B. Nuapia
- Laboratory of Toxicology, Faculty of Pharmaceutical Sciences, University of Kinshasa, Kinshasa XI B.P. 212, Democratic Republic of the Congo;
| | - Jean-Marie I. Liesse
- Centre Universitaire de Référence de Surveillance de la Résistance aux Antimicrobiens (CURS-RAM), Faculty of Pharmaceutical Sciences, University of Kinshasa, Kinshasa XI B.P. 212, Democratic Republic of the Congo; (G.V.M.); (J.-M.I.L.)
- Laboratory of Experimental and Pharmaceutical Microbiology, Faculty of Pharmaceutical Sciences, University of Kinshasa, Kinshasa XI B.P. 212, Democratic Republic of the Congo
| | - Christian I. Nkanga
- Laboratory of Pharmaceutics and Phytopharmaceutical Drug Development, Faculty of Pharmaceutical Sciences, University of Kinshasa, Kinshasa XI B.P. 212, Democratic Republic of the Congo; (M.M.L.); (C.K.M.); (E.N.Z.); (C.I.N.)
| | - Rui W. M. Krause
- Department of Chemistry, Faculty of Science, Rhodes University, P.O. Box 94, Makhana 6140, South Africa
- Center for Chemico- and Bio-Medicinal Research (CCBR), Faculty of Science, Rhodes University, P.O. Box 94, Makhana 6140, South Africa
| | - Aistė Balčiūnaitienė
- Lithuanian Research Centre for Agriculture and Forestry, Institute of Horticulture, 54333 Babtai, Lithuania;
| | - Patrick B. Memvanga
- Laboratory of Pharmaceutics and Phytopharmaceutical Drug Development, Faculty of Pharmaceutical Sciences, University of Kinshasa, Kinshasa XI B.P. 212, Democratic Republic of the Congo; (M.M.L.); (C.K.M.); (E.N.Z.); (C.I.N.)
- Department of Pharmacy, Faculty of Medecine and Pharmacy, University of Kisangani, Kisangani XI B.P. 2012, Democratic Republic of the Congo;
- Department of Pharmacy, Faculty of Pharmaceutical Sciences and Public Health, Official University of Bukavu, Bukavu B.P. 570, Democratic Republic of the Congo;
- Centre de Recherche et d’Innovation Technologique en Environnement et en Sciences de la Santé (CRITESS), University of Kinshasa, Kinshasa XI B.P. 212, Democratic Republic of the Congo
| |
Collapse
|
15
|
Clarkson KA, Porter CK, Talaat KR, Kapulu MC, Chen WH, Frenck RW, Bourgeois AL, Kaminski RW, Martin LB. Shigella-Controlled Human Infection Models: Current and Future Perspectives. Curr Top Microbiol Immunol 2022. [PMID: 35616717 DOI: 10.1007/82_2021_248] [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] [Indexed: 10/18/2022]
Abstract
Shigella-controlled human infection models (CHIMs) are an invaluable tool utilized by the vaccine community to combat one of the leading global causes of infectious diarrhea, which affects infants, children and adults regardless of socioeconomic status. The impact of shigellosis disproportionately affects children in low- and middle-income countries (LMICs) resulting in cognitive and physical stunting, perpetuating a cycle that must be halted. Shigella-CHIMs not only facilitate the early evaluation of enteric countermeasures and up-selection of the most promising products but also provide insight into mechanisms of infection and immunity that are not possible utilizing animal models or in vitro systems. The greater understanding of shigellosis obtained in CHIMs builds and empowers the development of new generation solutions to global health issues which are unattainable in the conventional laboratory and clinical settings. Therefore, refining, mining and expansion of safe and reproducible infection models hold the potential to create effective means to end diarrheal disease and associated co-morbidities associated with Shigella infection.
Collapse
Affiliation(s)
- Kristen A Clarkson
- Department of Diarrheal Disease Research, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
| | - Chad K Porter
- Enteric Disease Department, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
| | - Kawsar R Talaat
- Center for Immunization Research, Johns Hopkins Bloomberg School of Public Health, 624 North Broadway Street Hampton House, Baltimore, MD, 21205, USA
| | - Melissa C Kapulu
- Department of Biosciences, KEMRI-Wellcome Trust Research Programme, Kilifi County Hospital, Off Bofa Road, Kilifi, 80108, Kenya
| | - Wilbur H Chen
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, 685 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Robert W Frenck
- Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - A Louis Bourgeois
- PATH Center for Vaccine Innovation and Access, 455 Massachusetts Avenue NW, Washington, DC, 20001, USA
| | - Robert W Kaminski
- Department of Diarrheal Disease Research, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA
| | - Laura B Martin
- GSK Vaccines Institute for Global Health, Via Fiorentina 1, 53100, Siena, Italy.
| |
Collapse
|
16
|
Luo X, Kang X, Schönhuth A. Enhancing Long-Read-Based Strain-Aware Metagenome Assembly. Front Genet 2022; 13:868280. [PMID: 35646097 PMCID: PMC9136235 DOI: 10.3389/fgene.2022.868280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/01/2022] [Indexed: 11/18/2022] Open
Abstract
Microbial communities are usually highly diverse and often involve multiple strains from the participating species due to the rapid evolution of microorganisms. In such a complex microecosystem, different strains may show different biological functions. While reconstruction of individual genomes at the strain level is vital for accurately deciphering the composition of microbial communities, the problem has largely remained unresolved so far. Next-generation sequencing has been routinely used in metagenome assembly but there have been struggles to generate strain-specific genome sequences due to the short-read length. This explains why long-read sequencing technologies have recently provided unprecedented opportunities to carry out haplotype- or strain-resolved genome assembly. Here, we propose MetaBooster and MetaBooster-HiFi, as two pipelines for strain-aware metagenome assembly from PacBio CLR and Oxford Nanopore long-read sequencing data. Benchmarking experiments on both simulated and real sequencing data demonstrate that either the MetaBooster or the MetaBooster-HiFi pipeline drastically outperforms the state-of-the-art de novo metagenome assemblers, in terms of all relevant metagenome assembly criteria, involving genome fraction, contig length, and error rates.
Collapse
Affiliation(s)
- Xiao Luo
- Genome Data Science, Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Life Science and Health, Centrum Wiskunde and Informatica, Amsterdam, Netherlands
| | - Xiongbin Kang
- Genome Data Science, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Alexander Schönhuth
- Genome Data Science, Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Life Science and Health, Centrum Wiskunde and Informatica, Amsterdam, Netherlands
| |
Collapse
|
17
|
Jin S, Wetzel D, Schirmer M. Deciphering mechanisms and implications of bacterial translocation in human health and disease. Curr Opin Microbiol 2022; 67:102147. [PMID: 35461008 DOI: 10.1016/j.mib.2022.102147] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 12/12/2022]
Abstract
Significant increases in potential microbial translocation, especially along the oral-gut axis, have been identified in many immune-related and inflammatory diseases, such as inflammatory bowel disease, colorectal cancer, rheumatoid arthritis, and liver cirrhosis, for which we currently have no cure or long-term treatment options. Recent advances in computational and experimental omics approaches now enable strain tracking, functional profiling, and strain isolation in unprecedented detail, which has the potential to elucidate the causes and consequences of microbial translocation. In this review, we discuss current evidence for the detection of bacterial translocation, examine different translocation axes with a primary focus on the oral-gut axis, and outline currently known translocation mechanisms and how they adversely affect the host in disease. Finally, we conclude with an overview of state-of-the-art computational and experimental tools for strain tracking and highlight the required next steps to elucidate the role of bacterial translocation in human health.
Collapse
Affiliation(s)
- Shen Jin
- ZIEL - Institute for Food and Health, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany
| | - Daniela Wetzel
- ZIEL - Institute for Food and Health, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany
| | - Melanie Schirmer
- ZIEL - Institute for Food and Health, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany.
| |
Collapse
|
18
|
Pawar K, Aranha C. Lactobacilli metabolites restore E-cadherin and suppress MMP9 in cervical cancer cells. Curr Res Toxicol 2022; 3:100088. [PMID: 36176311 PMCID: PMC9513734 DOI: 10.1016/j.crtox.2022.100088] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 08/18/2022] [Accepted: 09/20/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
| | - Clara Aranha
- Corresponding author at: Department of Molecular Immunology and Microbiology, ICMR-National Institute for Research in Reproductive and Child Health, Parel, Mumbai 400102, India
| |
Collapse
|
19
|
Fang X, Li FJ, Hong DJ. Potential Role of Akkermansia muciniphila in Parkinson's Disease and Other Neurological/Autoimmune Diseases. Curr Med Sci 2021; 41:1172-1177. [PMID: 34893951 DOI: 10.1007/s11596-021-2464-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 06/22/2021] [Indexed: 10/19/2022]
Abstract
The composition of the gut microbiota, including Akkermansia muciniphila (A. muciniphila), is altered in many neurological diseases and may be involved in the pathophysiological processes of Parkinson's disease (PD). A. muciniphila, a mucin-degrading bacterium, is a potential next-generation microbe that has anti-inflammatory properties and is responsible for keeping the body healthy. As the role of A. muciniphila in PD has become increasingly apparent, we discuss the potential link between A. muciniphila and various neurological diseases (including PD) in the current review.
Collapse
Affiliation(s)
- Xin Fang
- Department of Neurology, the First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Fang-Jun Li
- Department of Neurology, the First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Dao-Jun Hong
- Department of Neurology, the First Affiliated Hospital of Nanchang University, Nanchang, 330006, China.
| |
Collapse
|
20
|
Thomassen GMB, Krych L, Knøchel S, Mehli L. ON-rep-seq as a rapid and cost-effective alternative to whole-genome sequencing for species-level identification and strain-level discrimination of Listeria monocytogenes contamination in a salmon processing plant. Microbiologyopen 2021; 10:e1246. [PMID: 34964295 PMCID: PMC8591450 DOI: 10.1002/mbo3.1246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/19/2021] [Indexed: 12/28/2022] Open
Abstract
Identification, source tracking, and surveillance of food pathogens are crucial factors for the food-producing industry. Over the last decade, the techniques used for this have moved from conventional enrichment methods, through species-specific detection by PCR to sequencing-based methods, whole-genome sequencing (WGS) being the ultimate method. However, using WGS requires the right infrastructure, high computational power, and bioinformatics expertise. Therefore, there is a need for faster, more cost-effective, and more user-friendly methods. A newly developed method, ON-rep-seq, combines the classical rep-PCR method with nanopore sequencing, resulting in a highly discriminating set of sequences that can be used for species identification and also strain discrimination. This study is essentially a real industry case from a salmon processing plant. Twenty Listeria monocytogenes isolates were analyzed both by ON-rep-seq and WGS to identify and differentiate putative L. monocytogenes from a routine sampling of processing equipment and products, and finally, compare the strain-level discriminatory power of ON-rep-seq to different analyzing levels delivered from the WGS data. The analyses revealed that among the isolates tested there were three different strains. The isolates of the most frequently detected strain (n = 15) were all detected in the problematic area in the processing plant. The strain level discrimination done by ON-rep-seq was in full accordance with the interpretation of WGS data. Our findings also demonstrate that ON-rep-seq may serve as a primary screening method alternative to WGS for identification and strain-level differentiation for surveillance of potential pathogens in a food-producing environment.
Collapse
Affiliation(s)
| | - Lukasz Krych
- Department of Food ScienceUniversity of CopenhagenFrederiksbergDenmark
| | - Susanne Knøchel
- Department of Food ScienceUniversity of CopenhagenFrederiksbergDenmark
| | - Lisbeth Mehli
- Department of Biotechnology and Food ScienceNorwegian University of Science and Technology (NTNU)TrondheimNorway
| |
Collapse
|
21
|
Pace RM, Chu DM, Prince AL, Ma J, Seferovic MD, Aagaard KM. Complex species and strain ecology of the vaginal microbiome from pregnancy to postpartum and association with preterm birth. MED 2021; 2:1027-1049. [PMID: 34617072 DOI: 10.1016/j.medj.2021.06.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background Lactobacillus was described as a keystone bacterial taxon in the human vagina over 100 years ago. Using metagenomics, we and others have characterized lactobacilli and other vaginal taxa across health and disease states, including pregnancy. While shifts in community membership have been resolved at the genus/species level, strain dynamics remain poorly characterized. Methods We performed a metagenomic analysis of the complex ecology of the vaginal econiche during and after pregnancy in a large U.S. based longitudinal cohort of women who were initially sampled in the third trimester of pregnancy, then validated key findings in a second cohort of women initially sampled in the second trimester of pregnancy. Findings First, we resolved microbial species and strains, interrogated their co-occurrence patterns, and probed the relationship between keystone species and preterm birth outcomes. Second, to determine the role of human heredity in shaping vaginal microbial ecology in relation to preterm birth, we performed a mtDNA-bacterial species association analysis. Finally, we explored the clinical utility of metagenomics in detection and co-occurrence patterns for the pathobiont Group B Streptococcus (causative bacterium of invasive neonatal sepsis). Conclusions Our highly refined resolutions of the vaginal ecology during and post-pregnancy provide insights into not only structural and functional community dynamics, but highlight the capacity of metagenomics to reveal finer aspects of the vaginal microbial ecologic framework. Funding NIH-NINR R01NR014792, NIH-NICHD R01HD091731, NIH National Children's Study Formative Research, Burroughs Wellcome Fund Preterm Birth Initiative, March of Dimes Preterm Birth Research Initiative, NIH-NIGMS (K12GM084897, T32GM007330, T32GM088129).
Collapse
Affiliation(s)
- Ryan M Pace
- Department of Obstetrics & Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Derrick M Chu
- Department of Obstetrics & Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine, Houston, TX, United States.,Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, United States.,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, United States
| | - Amanda L Prince
- Department of Obstetrics & Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Jun Ma
- Department of Obstetrics & Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Maxim D Seferovic
- Department of Obstetrics & Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Kjersti M Aagaard
- Department of Obstetrics & Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine, Houston, TX, United States.,Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, United States.,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, United States.,Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, United States.,Department of Molecular & Cell Biology, Baylor College of Medicine, Houston, TX, United States
| |
Collapse
|
22
|
Podlacha M, Grabowski Ł, Kosznik-Kawśnicka K, Zdrojewska K, Stasiłojć M, Węgrzyn G, Węgrzyn A. Interactions of Bacteriophages with Animal and Human Organisms-Safety Issues in the Light of Phage Therapy. Int J Mol Sci 2021; 22:8937. [PMID: 34445641 PMCID: PMC8396182 DOI: 10.3390/ijms22168937] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 12/13/2022] Open
Abstract
Bacteriophages are viruses infecting bacterial cells. Since there is a lack of specific receptors for bacteriophages on eukaryotic cells, these viruses were for a long time considered to be neutral to animals and humans. However, studies of recent years provided clear evidence that bacteriophages can interact with eukaryotic cells, significantly influencing the functions of tissues, organs, and systems of mammals, including humans. In this review article, we summarize and discuss recent discoveries in the field of interactions of phages with animal and human organisms. Possibilities of penetration of bacteriophages into eukaryotic cells, tissues, and organs are discussed, and evidence of the effects of phages on functions of the immune system, respiratory system, central nervous system, gastrointestinal system, urinary tract, and reproductive system are presented and discussed. Modulations of cancer cells by bacteriophages are indicated. Direct and indirect effects of virulent and temperate phages are discussed. We conclude that interactions of bacteriophages with animal and human organisms are robust, and they must be taken under consideration when using these viruses in medicine, especially in phage therapy, and in biotechnological applications.
Collapse
Affiliation(s)
- Magdalena Podlacha
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.P.); (K.Z.); (M.S.); (G.W.)
| | - Łukasz Grabowski
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland; (Ł.G.); (K.K.-K.)
| | - Katarzyna Kosznik-Kawśnicka
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland; (Ł.G.); (K.K.-K.)
| | - Karolina Zdrojewska
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.P.); (K.Z.); (M.S.); (G.W.)
| | - Małgorzata Stasiłojć
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.P.); (K.Z.); (M.S.); (G.W.)
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.P.); (K.Z.); (M.S.); (G.W.)
| | - Alicja Węgrzyn
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland; (Ł.G.); (K.K.-K.)
| |
Collapse
|
23
|
Elmaleh DR, Downey MA, Kundakovic L, Wilkinson JE, Neeman Z, Segal E. New Approaches to Profile the Microbiome for Treatment of Neurodegenerative Disease. J Alzheimers Dis 2021; 82:1373-1401. [PMID: 34219718 DOI: 10.3233/jad-210198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Progressive neurodegenerative diseases represent some of the largest growing treatment challenges for public health in modern society. These diseases mainly progress due to aging and are driven by microglial surveillance and activation in response to changes occurring in the aging brain. The lack of efficacious treatment options for Alzheimer's disease (AD), as the focus of this review, and other neurodegenerative disorders has encouraged new approaches to address neuroinflammation for potential treatments. Here we will focus on the increasing evidence that dysbiosis of the gut microbiome is characterized by inflammation that may carry over to the central nervous system and into the brain. Neuroinflammation is the common thread associated with neurodegenerative diseases, but it is yet unknown at what point and how innate immune function turns pathogenic for an individual. This review will address extensive efforts to identify constituents of the gut microbiome and their neuroactive metabolites as a peripheral path to treatment. This approach is still in its infancy in substantive clinical trials and requires thorough human studies to elucidate the metabolic microbiome profile to design appropriate treatment strategies for early stages of neurodegenerative disease. We view that in order to address neurodegenerative mechanisms of the gut, microbiome and metabolite profiles must be determined to pre-screen AD subjects prior to the design of specific, chronic titrations of gut microbiota with low-dose antibiotics. This represents an exciting treatment strategy designed to balance inflammatory microglial involvement in disease progression with an individual's manifestation of AD as influenced by a coercive inflammatory gut.
Collapse
Affiliation(s)
- David R Elmaleh
- Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,AZTherapies, Inc., Boston, MA, USA
| | | | | | - Jeremy E Wilkinson
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Ziv Neeman
- Department of Radiology, Emek Medical Center, Afula, Israel.,Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
24
|
Shigella-Specific Immune Profiles Induced after Parenteral Immunization or Oral Challenge with Either Shigella flexneri 2a or Shigella sonnei. mSphere 2021; 6:e0012221. [PMID: 34259559 PMCID: PMC8386581 DOI: 10.1128/msphere.00122-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shigella spp. are a leading cause of diarrhea-associated global morbidity and mortality. Development and widespread implementation of an efficacious vaccine remain the best option to reduce Shigella-specific morbidity. Unfortunately, the lack of a well-defined correlate of protection for shigellosis continues to hinder vaccine development efforts. Shigella controlled human infection models (CHIM) are often used in the early stages of vaccine development to provide preliminary estimates of vaccine efficacy; however, CHIMs also provide the opportunity to conduct in-depth immune response characterizations pre- and postvaccination or pre- and postinfection. In the current study, principal-component analyses were used to examine immune response data from two recent Shigella CHIMs in order to characterize immune response profiles associated with parenteral immunization, oral challenge with Shigella flexneri 2a, or oral challenge with Shigella sonnei. Although parenteral immunization induced an immune profile characterized by robust systemic antibody responses, it also included mucosal responses. Interestingly, oral challenge with S. flexneri 2a induced a distinctively different profile compared to S. sonnei, characterized by a relatively balanced systemic and mucosal response. In contrast, S. sonnei induced robust increases in mucosal antibodies with no differences in systemic responses across shigellosis outcomes postchallenge. Furthermore, S. flexneri 2a challenge induced significantly higher levels of intestinal inflammation compared to S. sonnei, suggesting that both serotypes may also differ in how they trigger induction and activation of innate immunity. These findings could have important implications for Shigella vaccine development as protective immune mechanisms may differ across Shigella serotypes. IMPORTANCE Although immune correlates of protection have yet to be defined for shigellosis, prior studies have demonstrated that Shigella infection provides protection against reinfection in a serotype-specific manner. Therefore, it is likely that subjects with moderate to severe disease post-oral challenge would be protected from a homologous rechallenge, and investigating immune responses in these subjects may help identify immune markers associated with the development of protective immunity. This is the first study to describe distinct innate and adaptive immune profiles post-oral challenge with two different Shigella serotypes. Analyses conducted here provide essential insights into the potential of different immune mechanisms required to elicit protective immunity, depending on the Shigella serotype. Such differences could have significant impacts on vaccine design and development within the Shigella field and should be further investigated across multiple Shigella serotypes.
Collapse
|
25
|
Hussen J. Bacterial species-specific modulatory effects on phenotype and function of camel blood leukocytes. BMC Vet Res 2021; 17:241. [PMID: 34247606 PMCID: PMC8274054 DOI: 10.1186/s12917-021-02939-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 06/17/2021] [Indexed: 11/21/2022] Open
Abstract
Background Recent studies have reported pathogen-species-specific modulating effects on the innate immune system. Escherichia coli, Staphylococcus aureus, and Streptococcus agalactiae are important pathogenic bacteria responsible for different infectious diseases in several animal species. In the present study, a whole blood culture with S. aureus, E. coli, or S. agalactiae and flow cytometry were used to investigate, whether stimulation with different bacterial species induces different immunomodulation patterns in camel leukocytes. The expression of different cell surface myeloid markers and cell adhesion molecules on monocytes and neutrophils was investigated. In addition, the capacity of monocytes and neutrophils to produce reactive oxygen species (ROS) was analyzed. Results Stimulation with either of the bacterial species resulted in the expansion of the camel CD14highMHCIIhigh monocyte subset with a reduced fraction of CD14highMHCIIlow monocytes. For the CD14lowMHCIIhigh monocytes, however, only stimulation with S. aureus or S. agalactiae increased their fractions in blood. Although all bacterial species elicited the upregulation of cell surface MHC class II molecules on granulocytes, the increase was, however, highest on cells stimulated with S. aureus. The expression levels of the two adhesion molecules, CD11a and CD18, on neutrophils and monocytes were differently affected by bacterial stimulation. Functionally, E. coli failed to stimulate ROS production in monocytes, while induced a strong ROS production response in granulocytes. S. agalactiae elicited a week ROS production in granulocytes when compared to the other two pathogens. Conclusions The different responsiveness of monocytes and granulocytes toward different bacterial species indicates different host-pathogen interaction mechanisms for the two cell populations. In addition, the phenotypic and functional differences between cells stimulated with E. coli, S. aureus, or S. agalactiae suggests pathogen-species-specific modulating effects of the bacterial pathogens on the camel innate myeloid cells.
Collapse
Affiliation(s)
- Jamal Hussen
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia.
| |
Collapse
|
26
|
Allen JP, Snitkin E, Pincus NB, Hauser AR. Forest and Trees: Exploring Bacterial Virulence with Genome-wide Association Studies and Machine Learning. Trends Microbiol 2021; 29:621-633. [PMID: 33455849 PMCID: PMC8187264 DOI: 10.1016/j.tim.2020.12.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022]
Abstract
The advent of inexpensive and rapid sequencing technologies has allowed bacterial whole-genome sequences to be generated at an unprecedented pace. This wealth of information has revealed an unanticipated degree of strain-to-strain genetic diversity within many bacterial species. Awareness of this genetic heterogeneity has corresponded with a greater appreciation of intraspecies variation in virulence. A number of comparative genomic strategies have been developed to link these genotypic and pathogenic differences with the aim of discovering novel virulence factors. Here, we review recent advances in comparative genomic approaches to identify bacterial virulence determinants, with a focus on genome-wide association studies and machine learning.
Collapse
Affiliation(s)
- Jonathan P Allen
- Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 60153, USA.
| | - Evan Snitkin
- Department of Microbiology and Immunology, Department of Internal Medicine/Division of Infectious Diseases, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nathan B Pincus
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Alan R Hauser
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Medicine/Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| |
Collapse
|
27
|
Cieślik M, Bagińska N, Jończyk-Matysiak E, Węgrzyn A, Węgrzyn G, Górski A. Temperate Bacteriophages-The Powerful Indirect Modulators of Eukaryotic Cells and Immune Functions. Viruses 2021; 13:v13061013. [PMID: 34071422 PMCID: PMC8228536 DOI: 10.3390/v13061013] [Citation(s) in RCA: 3] [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: 04/28/2021] [Revised: 05/22/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022] Open
Abstract
Bacteriophages are natural biological entities that limit the growth and amplification of bacteria. They are important stimulators of evolutionary variability in bacteria, and currently are considered a weapon against antibiotic resistance of bacteria. Nevertheless, apart from their antibacterial activity, phages may act as modulators of mammalian immune responses. In this paper, we focus on temperate phages able to execute the lysogenic development, which may shape animal or human immune response by influencing various processes, including phagocytosis of bacterial invaders and immune modulation of mammalian host cells.
Collapse
Affiliation(s)
- Martyna Cieślik
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (N.B.); (E.J.-M.)
| | - Natalia Bagińska
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (N.B.); (E.J.-M.)
| | - Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (N.B.); (E.J.-M.)
| | - Alicja Węgrzyn
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdańsk, Poland;
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland;
| | - Andrzej Górski
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (N.B.); (E.J.-M.)
- Phage Therapy Unit, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland
- Infant Jesus Hospital, The Medical University of Warsaw, 02-006 Warsaw, Poland
- Correspondence:
| |
Collapse
|
28
|
Maity S, Ambatipudi K. Mammary microbial dysbiosis leads to the zoonosis of bovine mastitis: a One-Health perspective. FEMS Microbiol Ecol 2021; 97:6006870. [PMID: 33242081 DOI: 10.1093/femsec/fiaa241] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/24/2020] [Indexed: 12/21/2022] Open
Abstract
Bovine mastitis is a prototypic emerging and reemerging bacterial disease that results in cut-by-cut torture to animals, public health and the global economy. Pathogenic microbes causing mastitis have overcome a series of hierarchical barriers resulting in the zoonotic transmission from bovines to humans either by proximity or remotely through milk and meat. The disease control is challenging and has been attributed to faulty surveillance systems to monitor their emergence at the human-animal interface. The complex interaction between the pathogens, the hidden pathobionts and commensals of the bovine mammary gland that create a menace during mastitis remains unexplored. Here, we review the zoonotic potential of these pathogens with a primary focus on understanding the interplay between the host immunity, mammary ecology and the shift from symbiosis to dysbiosis. We also address the pros and cons of the current management strategies and the extent of the success in implementing the One-Health approach to keep these pathogens at bay.
Collapse
Affiliation(s)
- Sudipa Maity
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, , India
| | - Kiran Ambatipudi
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, , India
| |
Collapse
|
29
|
Gates DE, Staley M, Tardy L, Giraudeau M, Hill GE, McGraw KJ, Bonneaud C. Levels of pathogen virulence and host resistance both shape the antibody response to an emerging bacterial disease. Sci Rep 2021; 11:8209. [PMID: 33859241 PMCID: PMC8050079 DOI: 10.1038/s41598-021-87464-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/24/2021] [Indexed: 11/09/2022] Open
Abstract
Quantifying variation in the ability to fight infection among free-living hosts is challenging and often constrained to one or a few measures of immune activity. While such measures are typically taken to reflect host resistance, they can also be shaped by pathogen effects, for example, if more virulent strains trigger more robust immune responses. Here, we test the extent to which pathogen-specific antibody levels, a commonly used measure of immunocompetence, reflect variation in host resistance versus pathogen virulence, and whether these antibodies effectively clear infection. House finches (Haemorhous mexicanus) from resistant and susceptible populations were inoculated with > 50 isolates of their novel Mycoplasma gallisepticum pathogen collected over a 20-year period during which virulence increased. Serum antibody levels were higher in finches from resistant populations and increased with year of pathogen sampling. Higher antibody levels, however, did not subsequently give rise to greater reductions in pathogen load. Our results show that antibody responses can be shaped by levels of host resistance and pathogen virulence, and do not necessarily signal immune clearance ability. While the generality of this novel finding remains unclear, particularly outside of mycoplasmas, it cautions against using antibody levels as implicit proxies for immunocompetence and/or host resistance.
Collapse
Affiliation(s)
- Daisy E Gates
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Molly Staley
- Department Biological Science, Auburn University, Auburn, Alabama, 36849-5414, USA.,Biology Department, Loyola University Chicago, Chicago, IL, 60660-1537, USA
| | - Luc Tardy
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Mathieu Giraudeau
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall, TR10 9FE, UK.,School of Life Sciences, Arizona State University, Tempe, AZ, 85287-4501, USA.,Centre for Ecological and Evolutionary Research On Cancer, UMR CNRS/IRD/UM 5290 MIVEGEC, 34394, Montpellier, France
| | - Geoffrey E Hill
- Department Biological Science, Auburn University, Auburn, Alabama, 36849-5414, USA
| | - Kevin J McGraw
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-4501, USA
| | - Camille Bonneaud
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall, TR10 9FE, UK.
| |
Collapse
|
30
|
Monowar T, Rahman MS, Bhore SJ, Sathasivam KV. Endophytic Bacteria Enterobacter hormaechei Fabricated Silver Nanoparticles and Their Antimicrobial Activity. Pharmaceutics 2021; 13:511. [PMID: 33917798 PMCID: PMC8068190 DOI: 10.3390/pharmaceutics13040511] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/04/2021] [Accepted: 04/06/2021] [Indexed: 11/17/2022] Open
Abstract
Antimicrobial resistance (AMR), one of the greatest issues for humankind, draws special attention to the scientists formulating new drugs to prevent it. Great emphasis on the biological synthesis of silver nanoparticles (AgNPs) for utilization in single or combinatorial therapy will open up new avenues to the discovery of new antimicrobial drugs. The purpose of this study was to synthesize AgNPs following a green approach by using an endophytic bacterial strain, Enterobacter hormaechei, and to assess their antimicrobial potential against five pathogenic and four multidrug-resistant (MDR) microbes. UV-Vis spectroscopy, fourier-transform infrared spectroscopy (FTIR), transmission electron microscopy (TEM), scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDX), and zeta potential (ζ) were used to characterize the synthesized AgNPs. Endophytic E. hormaechei-mediated AgNPs (Eh-AgNPs) were represented by a strong UV-Vis absorbance peak at 418 nm within 5 min, forming spherical and polydispersed nanoparticles in the size range of 9.91 nm to 92.54 nm. The Eh-AgNPs were moderately stable with a mean ζ value of -19.73 ± 3.94 mV. The presence of amine, amide, and hydroxyl functional groups was observed from FTIR analysis. In comparison to conventional antibiotics, the Eh-AgNPs were more effective against Bacillus cereus (ATCC 10876) and Candida albicans (ATCC 10231), exhibiting 9.14 ± 0.05 mm and 8.24 ± 0.05 mm zones of inhibition (ZOIs), respectively, while displaying effective inhibitory activity with ZOIs ranging from 10.98 ± 0.08 to 13.20 ± 0.07 mm against the MDR bacteria. Eh-AgNP synthesis was rapid and eco-friendly. The results showed that Eh-AgNPs are promising antimicrobial agents that can be used in the development and formulation of new drugs to curb the menace of antimicrobial resistance in pathogenic and MDR microbes.
Collapse
Affiliation(s)
- Tahmina Monowar
- Unit of Microbiology, Faculty of Medicine, AIMST University, Bedong 08100, Kedah, Malaysia
| | - Md. Sayedur Rahman
- Government of the People’s Republic of Bangladesh, Ministry of Information, Bangladesh Betar, Mymensingh 2202, Bangladesh;
| | - Subhash J. Bhore
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong 08100, Kedah, Malaysia; (S.J.B.); (K.V.S.)
| | - Kathiresan V. Sathasivam
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong 08100, Kedah, Malaysia; (S.J.B.); (K.V.S.)
| |
Collapse
|
31
|
Liao J, Cai Y, Wang X, Shang C, Zhang Q, Shi H, Wang S, Zhang D, Zhou Y. Effects of a Potential Host Gut-Derived Probiotic, Bacillus subtilis 6-3-1, on the Growth, Non-specific Immune Response and Disease Resistance of Hybrid Grouper (Epinephelus fuscoguttatus♀ × Epinephelus lanceolatus♂). Probiotics Antimicrob Proteins 2021; 13:1119-1137. [PMID: 33715082 DOI: 10.1007/s12602-021-09768-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2021] [Indexed: 11/26/2022]
Abstract
A potential host-derived probiotic, Bacillus subtilis 6-3-1, was successfully screened from 768 isolates from the intestines of healthy hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) based on multiple probiotic characteristics in vitro assays, such as, non-hemolytic activity, extracellular enzyme activity, inhibitory activity against pathogens, tolerance to gastrointestinal stress, cell surface hydrophobicity, autoaggregation, and antibiotic susceptibility. Eight weeks of feeding trial revealed that dietary supplementation of B. subtilis 6-3-1 at all three concentrations (1 × 106 CFU g-1 as BS6; 1 × 107 CFU g-1 as BS7; 1 × 108 CFU g-1 as BS8) could promote the growth performance of hybrid groupers to a certain extent at different time points. At the end of 8th week, BS6 and BS8 significantly promoted the weight gain rate (WGR), specific growth rate (SGR) of hybrid groupers. The digestive enzyme activities were also increased in BS6 and BS8 groups comparing with those in control group, except that the increase of amylase activities in BS6 was not significant (P > 0.05). However, BS7 showed the best non-specific immunity stimulating effects among the three concentration groups. While BS7 significantly boosted serum total protein contents, lysozyme (LZM), total antioxidant capacity (T-AOC), superoxide dismutase (SOD), catalase (CAT), and acid phosphatase (ACP) levels, BS6 significantly enhanced serum total protein, LZM activity, and BS8 significantly improved LZM, respiratory bursts activity. B. subtilis 6-3-1 up-regulated the expression of MyD88 in head kidney and intestine and increased villi length (VL) in intestine of BS7 group. It also up-regulated the expression of IgM in head kidney in BS6 group and IgM and TLR1 in intestine of BS8 group. Though all B. subtilis 6-3-1 supplemented groups reduced the cumulative mortality rate post-Vibro harveyi-challenge, BS7 showed the best protection effects among the three concentration groups. In conclusion, with its immune promoting, intestine health enhancing, and V. harveyi resisting effects, BS7 show great potential to be used as a probiotic in hybrid grouper culture.
Collapse
Affiliation(s)
- Jingqiu Liao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, People's Republic of China
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Haikou, Hainan, 570228, People's Republic of China
| | - Yan Cai
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, People's Republic of China
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Haikou, Hainan, 570228, People's Republic of China
| | - Xinrui Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, People's Republic of China
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Haikou, Hainan, 570228, People's Republic of China
| | - Chenxu Shang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, People's Republic of China
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Haikou, Hainan, 570228, People's Republic of China
| | - Qian Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, People's Republic of China
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Haikou, Hainan, 570228, People's Republic of China
| | - Huizhong Shi
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, People's Republic of China
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Haikou, Hainan, 570228, People's Republic of China
| | - Shifeng Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, People's Republic of China.
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Haikou, Hainan, 570228, People's Republic of China.
| | - Dongdong Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, People's Republic of China
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Haikou, Hainan, 570228, People's Republic of China
| | - Yongcan Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, People's Republic of China.
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Haikou, Hainan, 570228, People's Republic of China.
| |
Collapse
|
32
|
Constantinou A, Kanti V, Polak-Witka K, Blume-Peytavi U, Spyrou GM, Vogt A. The Potential Relevance of the Microbiome to Hair Physiology and Regeneration: The Emerging Role of Metagenomics. Biomedicines 2021; 9:biomedicines9030236. [PMID: 33652789 PMCID: PMC7996884 DOI: 10.3390/biomedicines9030236] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 12/18/2022] Open
Abstract
Human skin and hair follicles are recognized sites of microbial colonization. These microbiota help regulate host immune mechanisms via an interplay between microbes and immune cells, influencing homeostasis and inflammation. Bacteria affect immune responses by controlling the local inflammatory milieu, the breakdown of which can result in chronic inflammatory disorders. Follicular microbiome shifts described in some inflammatory cutaneous diseases suggest a link between their development or perpetuation and dysbiosis. Though the hair follicle infundibulum is an area of intense immunological interactions, bulb and bulge regions represent immune-privileged niches. Immune privilege maintenance seems essential for hair growth and regeneration, as collapse and inflammation characterize inflammatory hair disorders like alopecia areata and primary cicatricial alopecia. Current research largely focuses on immunological aberrations. However, studies suggest that external stimuli and interactions across the follicular epithelium can have profound effects on the local immune system, homeostasis, and cycling. Herein, we review hair follicle bacterial colonization, its possible effects on the underlying tissue, and links to the pathogenesis of alopecia, beyond the pure investigation of specific species abundance. As skin microbiology enters the metagenomics era, multi-dimensional approaches will enable a new level of investigations on the effects of microorganisms and metabolism on host tissue.
Collapse
Affiliation(s)
- Andria Constantinou
- Charité-Universitatsmedizin Berlin, Corporate Member of Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, Clinical Research Center for Hair and Skin Science, Department of Dermatology, Venereology and Allergy, Charitéplatz 1, 10117 Berlin, Germany; (A.C.); (V.K.); (K.P.-W.); (U.B.-P.)
| | - Varvara Kanti
- Charité-Universitatsmedizin Berlin, Corporate Member of Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, Clinical Research Center for Hair and Skin Science, Department of Dermatology, Venereology and Allergy, Charitéplatz 1, 10117 Berlin, Germany; (A.C.); (V.K.); (K.P.-W.); (U.B.-P.)
| | - Katarzyna Polak-Witka
- Charité-Universitatsmedizin Berlin, Corporate Member of Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, Clinical Research Center for Hair and Skin Science, Department of Dermatology, Venereology and Allergy, Charitéplatz 1, 10117 Berlin, Germany; (A.C.); (V.K.); (K.P.-W.); (U.B.-P.)
| | - Ulrike Blume-Peytavi
- Charité-Universitatsmedizin Berlin, Corporate Member of Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, Clinical Research Center for Hair and Skin Science, Department of Dermatology, Venereology and Allergy, Charitéplatz 1, 10117 Berlin, Germany; (A.C.); (V.K.); (K.P.-W.); (U.B.-P.)
| | - George M. Spyrou
- Bioinformatics ERA Chair, The Cyprus Institute of Neurology and Genetics, 6 Iroon Avenue, 2371 Ayios Dometios, Nicosia, Cyprus;
| | - Annika Vogt
- Charité-Universitatsmedizin Berlin, Corporate Member of Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, Clinical Research Center for Hair and Skin Science, Department of Dermatology, Venereology and Allergy, Charitéplatz 1, 10117 Berlin, Germany; (A.C.); (V.K.); (K.P.-W.); (U.B.-P.)
- Correspondence:
| |
Collapse
|
33
|
Fu X, Norbäck D, Yuan Q, Li Y, Zhu X, Hashim JH, Hashim Z, Ali F, Hu Q, Deng Y, Sun Y. Association between indoor microbiome exposure and sick building syndrome (SBS) in junior high schools of Johor Bahru, Malaysia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 753:141904. [PMID: 32890872 DOI: 10.1016/j.scitotenv.2020.141904] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 06/11/2023]
Abstract
Sick building syndrome (SBS) is a collection of nonspecific syndromes linked with the built environment. The occurrence of SBS is associated with humidity, ventilation, moulds and microbial compounds exposure. However, no study has reported the association between indoor microbiome and SBS. In this study, 308 students were surveyed for SBS symptoms from 21 classrooms of 7 junior high schools from Johor Bahru, Malaysia, and vacuum dust from floor, desks and chairs was collected. High throughput amplicon sequencing (16S rRNA gene and ITS region) and quantitative PCR were conducted to characterize the absolute concentration of bacteria and fungi taxa. In total, 326 bacterial and 255 fungal genera were detected in dust with large compositional variation among classrooms. Also, half of these samples showed low compositional similarity to microbiome data deposited in the public database. The number of observed OTUs in Gammaproteobacteria was positively associated with SBS (p = 0.004). Eight microbial genera were associated with SBS (p < 0.01). Bacterial genera, Rhodomicrobium, Scytonema and Microcoleus, were protectively (negatively) associated with ocular and throat symptoms and tiredness, and Izhakiella and an unclassified genus from Euzebyaceae were positively associated with the throat and ocular symptoms. Three fungal genera, Polychaeton, Gympopus and an unclassified genus from Microbotryaceae, were mainly positively associated with tiredness. The associations differed with our previous study in microbial compounds (endotoxin and ergosterol) and SBS in the same population, in which nasal and dermal symptoms were affected. A higher indoor relative humidity and visible dampness or mould in classrooms were associated with a higher concentration of potential risk bacteria and a lower concentration of potential protective bacteria (p < 0.01). This is the first study to characterize the SBS-associated microorganisms in the indoor environment, revealing complex interactions between microbiome, SBS symptoms and environmental characteristics.
Collapse
Affiliation(s)
- Xi Fu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China; Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, PR China
| | - Dan Norbäck
- Occupational and Environmental Medicine, Dept. of Medical Science, University Hospital, Uppsala University, 75237 Uppsala, Sweden
| | - Qianqian Yuan
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Yanling Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Xunhua Zhu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | | | - Zailina Hashim
- Department of Environmental and Occupational Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, Serdang, Selangor, Malaysia
| | - Faridah Ali
- Primary Care Unit, Johor State Health Department, Johor Bahru, Malaysia
| | - Qiansheng Hu
- Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, PR China
| | - Yiqun Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Yu Sun
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China.
| |
Collapse
|
34
|
Deshpande RP, Sharma S, Watabe K. The Confounders of Cancer Immunotherapy: Roles of Lifestyle, Metabolic Disorders and Sociological Factors. Cancers (Basel) 2020; 12:E2983. [PMID: 33076303 PMCID: PMC7602474 DOI: 10.3390/cancers12102983] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/06/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023] Open
Abstract
Checkpoint blockade immunotherapy (CPI) is an effective treatment option for many types of cancers. Irrespective of its wide clinical implications, the overall efficacy remains unpredictable and even poor in certain pathologies such as breast cancer. Thus, it is imperative to understand the role of factors affecting its responsiveness. In this review, we provide an overview on the involvement of sociological factors, lifestyles and metabolic disorders in modulating the CPI response in patients from multiple malignancies. Lifestyle habits including exercise, and diet promoted therapeutic responsiveness while alcohol consumption mitigated the CPI effect by decreasing mutational burden and hampering antigen presentation by dendritic cells. Metabolic disorder such as obesity was recognized to enhance the PD-1 expression while diabetes and hypertension were consequences of CPI therapy rather than causes. Among the sociologic factors, sex and race positively influenced the CPI effectiveness on account of increased effector T cell activity and increased PD-1 expression while ageing impaired CPI responsiveness by decreasing functional T cell and increased toxicity. The combined effect of these factors was observed for obesity and gender, in which obese males had the most significant effect of CPI. Therefore these variables should be carefully considered before treating patients with CPI for optimal treatment outcome.
Collapse
Affiliation(s)
| | | | - Kounosuke Watabe
- Department of Cancer Biology, Wake Forest Baptist Medical Center, Winston-Salem, NC 27157, USA; (R.P.D.); (S.S.)
| |
Collapse
|
35
|
Comparative Analysis of Infection by Rickettsia rickettsii Sheila Smith and Taiaçu Strains in a Murine Model. Pathogens 2020; 9:pathogens9090744. [PMID: 32927666 PMCID: PMC7557639 DOI: 10.3390/pathogens9090744] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/28/2020] [Accepted: 09/07/2020] [Indexed: 11/22/2022] Open
Abstract
Rocky Mountain spotted fever (RMSF) is a life-threatening tick-borne disease caused by Rickettsia rickettsii, which is widely distributed throughout the Americas. Over 4000 cases of RMSF are recorded annually in the United States, while only around 100 cases are reported in Brazil. Conversely, while case fatality rates in the United States oscillate around 5%, in Brazil they can surpass 70%, suggesting that differences in tick vectoring capacity, population sensitivity, and/or variability in virulence of the rickettsial strains may exist. In this study, we compared the susceptibility of C3H/HeN mice to two highly virulent strains of R. rickettsii, one from the United States (Sheila Smith) and the other from Brazil (Taiaçu). Animals inoculated with the Taiaçu strain succumbed to infection earlier and exhibited severe histological lesions in both liver and spleen sooner than mice infected with the Sheila Smith strain. These differences in survival and signs of the disease are not related to a greater proliferation of the Taiaçu strain, as there were no significant differences in the rickettsial load in mice tissues inoculated with either strain. The present study is the first step to experimentally assess differences in fatality rates of RMSF in two different regions of the American continent.
Collapse
|
36
|
Williams SC, Frew JW, Krueger JG. A systematic review and critical appraisal of metagenomic and culture studies in hidradenitis suppurativa. Exp Dermatol 2020; 30:1388-1397. [PMID: 32614993 DOI: 10.1111/exd.14141] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/11/2020] [Accepted: 06/25/2020] [Indexed: 12/15/2022]
Abstract
Hidradenitis suppurativa (HS), also known as acne inversa, is a chronic inflammatory skin disease with still largely unknown pathogenesis. While infectious organisms have been identified in lesions of the disease since the 1980s, questions remain over the role that bacteria and microbiome play. Recent studies using 16S ribosomal RNA gene sequencing and larger culture-based studies have begun to paint a clearer picture of the microbial world of HS. With this systematic review, we summarize all the work that has been done to date in HS bacteriology, analyse potential pitfalls and limitations of the current studies, and address future directions of investigation. This systematic review attempted to collate and analyse all bacteriology studies done to date. This review was prospectively registered with PROSPERO (1670769) performed in line with the PRISMA checklist. Twenty two studies were identified comprising 862 individual HS patients for culture studies and 206 HS patients for 16S rRNA gene sequencing studies. Methodology tended to be varied, with different sampling, culturing and sequencing methods as well as amount of analysis and stratification of patients. Bacteria identified as elevated in HS lesions in sequencing studies as well as grown from HS lesions in culture studies are identified and discussed. These primarily included the anerobic Gram-negative bacilli Prevotella, Porphyromonas and Fusibacterium, the Gram-positive bacilli Corynebacterium, and the Gram-positive cocci Staphylococcus, Streptococcus and Parvimonas. Potential interactions, as well as work in other disease models with related bacteria are also discussed. Areas of further investigation include in vitro studies of interactions between bacteria and keratinocytes, gut and oral microbiome studies and deep sequencing studies for virulence and phage factors.
Collapse
Affiliation(s)
- Samuel C Williams
- Laboratory of Investigative Dermatology, Rockefeller University, New York, New York.,Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, Weill Cornell Medical School, New York, New York
| | - John W Frew
- Laboratory of Investigative Dermatology, Rockefeller University, New York, New York
| | - James G Krueger
- Laboratory of Investigative Dermatology, Rockefeller University, New York, New York
| |
Collapse
|
37
|
Abstract
S. enterica is a major foodborne pathogen, which can be transmitted via several distinct routes from animals and environmental sources to human hosts. Multiple subspecies and serotypes of S. enterica exhibit considerable differences in virulence, host specificity, and colonization. This study provides detailed insights into the dynamics of recombination and its contributions to S. enterica subspecies evolution. Widespread recombination within the species means that new adaptations arising in one lineage can be rapidly transferred to another lineage. We therefore predict that recombination has been an important factor in the emergence of several major disease-causing strains from diverse genomic backgrounds and their ability to adapt to disparate environments. Salmonella is responsible for many nontyphoidal foodborne infections and enteric (typhoid) fever in humans. Of the two Salmonella species, Salmonella enterica is highly diverse and includes 10 known subspecies and approximately 2,600 serotypes. Understanding the evolutionary processes that generate the tremendous diversity in Salmonella is important in reducing and controlling the incidence of disease outbreaks and the emergence of virulent strains. In this study, we aim to elucidate the impact of homologous recombination in the diversification of S. enterica subspecies. Using a data set of previously published 926 Salmonella genomes representing the 10 S. enterica subspecies and Salmonella bongori, we calculated a genus-wide pan-genome composed of 84,041 genes and the S. enterica pan-genome of 81,371 genes. The size of the accessory genomes varies between 12,429 genes in S. enterica subsp. arizonae (subsp. IIIa) to 33,257 genes in S. enterica subsp. enterica (subsp. I). A total of 12,136 genes in the Salmonella pan-genome show evidence of recombination, representing 14.44% of the pan-genome. We identified genomic hot spots of recombination that include genes associated with flagellin and the synthesis of methionine and thiamine pyrophosphate, which are known to influence host adaptation and virulence. Last, we uncovered within-species heterogeneity in rates of recombination and preferential genetic exchange between certain donor and recipient strains. Frequent but biased recombination within a bacterial species may suggest that lineages vary in their response to environmental selection pressure. Certain lineages, such as the more uncommon non-enterica subspecies (non-S. enterica subsp. enterica), may also act as a major reservoir of genetic diversity for the wider population. IMPORTANCES. enterica is a major foodborne pathogen, which can be transmitted via several distinct routes from animals and environmental sources to human hosts. Multiple subspecies and serotypes of S. enterica exhibit considerable differences in virulence, host specificity, and colonization. This study provides detailed insights into the dynamics of recombination and its contributions to S. enterica subspecies evolution. Widespread recombination within the species means that new adaptations arising in one lineage can be rapidly transferred to another lineage. We therefore predict that recombination has been an important factor in the emergence of several major disease-causing strains from diverse genomic backgrounds and their ability to adapt to disparate environments.
Collapse
|
38
|
Semple SL, Bols NC, Lumsden JS, Dixon B. Understanding the pathogenesis of Flavobacterium psychrophilum using the rainbow trout monocyte/macrophage-like cell line, RTS11, as an infection model. Microb Pathog 2019; 139:103910. [PMID: 31809795 DOI: 10.1016/j.micpath.2019.103910] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/28/2019] [Accepted: 12/02/2019] [Indexed: 02/05/2023]
Abstract
The life cycle of Flavobacterium psychrophilum (Fp), the causative agent of bacterial coldwater disease (BCWD) and rainbow trout fry syndrome (RTFS), appears to involve interactions with spleen and head kidney macrophages. To develop an in vitro model for studying this, F. psychrophilum was incubated with a rainbow trout splenic monocyte/macrophage-like cell line (RTS11) and fundamental macrophage functions evaluated. The animal cell basal medium, L15, supplemented with bovine serum (FBS) supports RTS11 maintenance, and surprisingly, L15 with 2% FBS (L15/FBS) also supported F. psychrophilum growth. L15/FBS in which the bacteria had been grown is referred to as F. psychrophilum conditioned medium (FpCM). Adding FpCM to RTS11 cultures caused a small, yet significant, percentage of cells to die, many cells to become more diffuse, and phagocytosis to be temporarily reduced. FpCM also significantly stimulated transcript expression for pro-inflammatory cytokines (IL-1β, TNFα and IL-6) and the anti-inflammatory cytokine (IL-10) after one day of exposure but this upregulation rapidly declined over time. Adding live F. psychrophilum to RTS11 cultures also altered the cellular morphology and stimulated cytokine expression more profoundly than FpCM. Additionally, the phagocytic activity of RTS11 was also significantly impaired by live F. psychrophilum, but not to the same extent as when exposed to FpCM. Adding heat-killed bacteria to RTS11 cultures elicited few changes. These bacteria/RTS11 co-cultures should be useful for gaining a deeper understanding of the pathogenesis of F. psychrophilum and may aid in the development of effective measures to prevent infection and spread of this troublesome disease.
Collapse
Affiliation(s)
- Shawna L Semple
- University of Waterloo, Department of Biology, Waterloo, Canada
| | - Niels C Bols
- University of Waterloo, Department of Biology, Waterloo, Canada
| | - John S Lumsden
- University of Guelph, Ontario Veterinary College, Department of Pathobiology, Guelph, Canada
| | - Brian Dixon
- University of Waterloo, Department of Biology, Waterloo, Canada.
| |
Collapse
|
39
|
A Complete Genome Screening Program of Clinical Methicillin-Resistant Staphylococcus aureus Isolates Identifies the Origin and Progression of a Neonatal Intensive Care Unit Outbreak. J Clin Microbiol 2019; 57:JCM.01261-19. [PMID: 31578260 PMCID: PMC6879278 DOI: 10.1128/jcm.01261-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/23/2019] [Indexed: 01/17/2023] Open
Abstract
Whole-genome sequencing (WGS) of Staphylococcus aureus is increasingly used as part of infection prevention practices. In this study, we established a long-read technology-based WGS screening program of all first-episode methicillin-resistant Staphylococcus aureus (MRSA) blood infections at a major urban hospital. Whole-genome sequencing (WGS) of Staphylococcus aureus is increasingly used as part of infection prevention practices. In this study, we established a long-read technology-based WGS screening program of all first-episode methicillin-resistant Staphylococcus aureus (MRSA) blood infections at a major urban hospital. A survey of 132 MRSA genomes assembled from long reads enabled detailed characterization of an outbreak lasting several months of a CC5/ST105/USA100 clone among 18 infants in a neonatal intensive care unit (NICU). Available hospital-wide genome surveillance data traced the origins of the outbreak to three patients admitted to adult wards during a 4-month period preceding the NICU outbreak. The pattern of changes among complete outbreak genomes provided full spatiotemporal resolution of its progression, which was characterized by multiple subtransmissions and likely precipitated by equipment sharing between adults and infants. Compared to other hospital strains, the outbreak strain carried distinct mutations and accessory genetic elements that impacted genes with roles in metabolism, resistance, and persistence. This included a DNA recognition domain recombination in the hsdS gene of a type I restriction modification system that altered DNA methylation. Transcriptome sequencing (RNA-Seq) profiling showed that the (epi)genetic changes in the outbreak clone attenuated agr gene expression and upregulated genes involved in stress response and biofilm formation. Overall, our findings demonstrate the utility of long-read sequencing for hospital surveillance and for characterizing accessory genomic elements that may impact MRSA virulence and persistence.
Collapse
|
40
|
Górski A, Międzybrodzki R, Jończyk-Matysiak E, Żaczek M, Borysowski J. Phage-specific diverse effects of bacterial viruses on the immune system. Future Microbiol 2019; 14:1171-1174. [PMID: 31535921 PMCID: PMC6802706 DOI: 10.2217/fmb-2019-0222] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Andrzej Górski
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology & Experimental Therapy, Polish Academy of Sciences (HIIET PAS), R Weigla 12, 53-114 Wrocław, Poland.,Phage Therapy Unit, Hirszfeld Institute of Immunology & Experimental Therapy, Polish Academy of Sciences (HIIET PAS), R Weigla 12, 53-114 Wrocław, Poland
| | - Ryszard Międzybrodzki
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology & Experimental Therapy, Polish Academy of Sciences (HIIET PAS), R Weigla 12, 53-114 Wrocław, Poland.,Phage Therapy Unit, Hirszfeld Institute of Immunology & Experimental Therapy, Polish Academy of Sciences (HIIET PAS), R Weigla 12, 53-114 Wrocław, Poland.,Department of Clinical Immunology, Transplantation Institute, Medical University of Warsaw, Nowogrodzka 59, 02-006 Warsaw, Poland
| | - Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology & Experimental Therapy, Polish Academy of Sciences (HIIET PAS), R Weigla 12, 53-114 Wrocław, Poland
| | - Maciej Żaczek
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology & Experimental Therapy, Polish Academy of Sciences (HIIET PAS), R Weigla 12, 53-114 Wrocław, Poland
| | - Jan Borysowski
- Department of Clinical Immunology, Transplantation Institute, Medical University of Warsaw, Nowogrodzka 59, 02-006 Warsaw, Poland
| |
Collapse
|
41
|
Jang YJ, Kim WK, Han DH, Lee K, Ko G. Lactobacillus fermentum species ameliorate dextran sulfate sodium-induced colitis by regulating the immune response and altering gut microbiota. Gut Microbes 2019; 10:696-711. [PMID: 30939976 PMCID: PMC6866707 DOI: 10.1080/19490976.2019.1589281] [Citation(s) in RCA: 164] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We evaluated immunometabolic functions of novel Lactobacillus fermentum strains (KBL374 and KBL375) isolated from feces of healthy Koreans. The levels of inflammatory cytokines, such as interleukin (IL)-2, interferon-γ, IL-4, IL-13, and IL-17A, were decreased, and that of the anti-inflammatory cytokine IL-10 was increased, in human peripheral blood mononuclear cells (PBMCs) treated with the L. fermentum KBL374 or KBL375 strain. When these strains were orally administered to mice with dextran sulfate sodium (DSS)-induced colitis, both L. fermentum KBL374 and KBL375 showed beneficial effects on body weight, disease activity index score, colon length, cecal weight, and histological scores. Furthermore, both L. fermentum KBL374 and KBL375 modulated the innate immune response by improving gut barrier function and reducing leukocyte infiltration. Consistent with the PBMC data, both L. fermentum KBL374- and KBL375-treated DSS mice demonstrated decreased Th1-, Th2-, and Th17-related cytokine levels and increased IL-10 in the colon compared with the DSS control mice. Administration of L. fermentum KBL374 or KBL375 to mice increased the CD4+CD25+Foxp3+Treg cell population in mesenteric lymph nodes. Additionally, L. fermentum KBL374 or KBL375 administration reshaped and increased the diversity of the gut microbiota. In particular, L. fermentum KBL375 increased the abundance of beneficial microorganisms, such as Lactobacillus spp. and Akkermansia spp. Both L. fermentum KBL374 and KBL375 may alleviate inflammatory diseases, such as inflammatory bowel disease, in the gut by regulating immune responses and altering the composition of gut microbiota.
Collapse
Affiliation(s)
- You Jin Jang
- Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Woon-Ki Kim
- Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Dae Hee Han
- Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Kiuk Lee
- Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Gwangpyo Ko
- Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea,N-Bio, Seoul National University, Seoul, Republic of Korea,KoBioLabs, Inc., Seoul, Republic of Korea,Center for Human and Environmental Microbiome, Seoul National University, Seoul, Republic of Korea,Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea,CONTACT GwangPyo Ko Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| |
Collapse
|
42
|
Park CJ, Andam CP. Within-Species Genomic Variation and Variable Patterns of Recombination in the Tetracycline Producer Streptomyces rimosus. Front Microbiol 2019; 10:552. [PMID: 30949149 PMCID: PMC6437091 DOI: 10.3389/fmicb.2019.00552] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/04/2019] [Indexed: 01/09/2023] Open
Abstract
Streptomyces rimosus is best known as the primary source of the tetracycline class of antibiotics, most notably oxytetracycline, which have been widely used against many gram-positive and gram-negative pathogens and protozoan parasites. However, despite the medical and agricultural importance of S. rimosus, little is known of its evolutionary history and genome dynamics. In this study, we aim to elucidate the pan-genome characteristics and phylogenetic relationships of 32 S. rimosus genomes. The S. rimosus pan-genome contains more than 22,000 orthologous gene clusters, and approximately 8.8% of these genes constitutes the core genome. A large part of the accessory genome is composed of 9,646 strain-specific genes. S. rimosus exhibits an open pan-genome (decay parameter α = 0.83) and high gene diversity between strains (genomic fluidity φ = 0.12). We also observed strain-level variation in the distribution and abundance of biosynthetic gene clusters (BGCs) and that each individual S. rimosus genome has a unique repertoire of BGCs. Lastly, we observed variation in recombination, with some strains donating or receiving DNA more often than others, strains that tend to frequently recombine with specific partners, genes that often experience recombination more than others, and variable sizes of recombined DNA sequences. We conclude that the high levels of inter-strain genomic variation in S. rimosus is partly explained by differences in recombination among strains. These results have important implications on current efforts for natural drug discovery, the ecological role of strain-level variation in microbial populations, and addressing the fundamental question of why microbes have pan-genomes.
Collapse
Affiliation(s)
- Cooper J Park
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Cheryl P Andam
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| |
Collapse
|
43
|
Abstract
The discovery and characterization of the prokaryotic CRISPR-Cas immune system has led to a revolution in genome editing and engineering technologies. Despite the fact that most applications emerged after the discovery of the type II-A CRISPR-Cas9 system of Streptococcus pyogenes, its biological importance in this organism has received little attention. Here, we provide a comprehensive overview of the current knowledge about CRISPR-Cas systems from S. pyogenes. We discuss how the interplay between CRISPR-mediated immunity and horizontal gene transfer might have modeled the evolution of this pathogen. We review the current literature about the CRISPR-Cas systems present in S. pyogenes (types I-C and II-A), and describe their distinctive biochemical and functional features. Finally, we summarize the main biotechnological applications that have arisen from the discovery of the CRISPR-Cas9 system in S. pyogenes.
Collapse
Affiliation(s)
- Anaïs Le Rhun
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany
| | - Andrés Escalera-Maurer
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
| | - Majda Bratovič
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
| | - Emmanuelle Charpentier
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
| |
Collapse
|
44
|
Hafner A, Kolbe U, Freund I, Castiglia V, Kovarik P, Poth T, Herster F, Weigand MA, Weber ANR, Dalpke AH, Eigenbrod T. Crucial Role of Nucleic Acid Sensing via Endosomal Toll-Like Receptors for the Defense of Streptococcus pyogenes in vitro and in vivo. Front Immunol 2019; 10:198. [PMID: 30846984 PMCID: PMC6394247 DOI: 10.3389/fimmu.2019.00198] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 01/23/2019] [Indexed: 12/13/2022] Open
Abstract
Streptococcus pyogenes is a major human pathogen causing a variety of diseases ranging from common pharyngitis to life-threatening soft tissue infections and sepsis. Microbial nucleic acids, especially bacterial RNA, have recently been recognized as a major group of pathogen-associated molecular patterns (PAMPs) involved in the detection of Streptococcus pyogenes via endosomal Toll-like receptors (TLRs) in vitro. However, the individual contribution and cooperation between TLRs as well as cell-type and strain specific differences in dependency on nucleic acid detection during S. pyogenes infection in vitro have not been clarified in detail. Moreover, the role of particularly bacterial RNA for the defense of S. pyogenes infection in vivo remains poorly defined. In this study, we report that in all investigated innate immune cells involved in the resolution of bacterial infections, including murine macrophages, dendritic cells and neutrophils, recognition of S. pyogenes strain ATCC12344 is almost completely dependent on nucleic acid sensing via endosomal TLRs at lower MOIs, whereas at higher MOIs, detection via TLR2 plays an additional, yet redundant role. We further demonstrate that different S. pyogenes strains display a considerable inter-strain variability with respect to their nucleic acid dependent recognition. Moreover, TLR13-dependent recognition of S. pyogenes RNA is largely non-redundant in bone marrow-derived macrophages (BMDMs), but less relevant in neutrophils and bone marrow-derived myeloid dendritic cells (BMDCs) for the induction of an innate immune response in vitro. In vivo, we show that a loss of nucleic acid sensing blunts early recognition of S. pyogenes, leading to a reduced local containment of the bacterial infection with subsequent pronounced systemic inflammation at later time points. Thus, our results argue for a crucial role of nucleic acid sensing via endosomal TLRs in defense of S. pyogenes infection both in vitro and in vivo.
Collapse
Affiliation(s)
- Anna Hafner
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Ulrike Kolbe
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
| | - Isabel Freund
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
| | - Virginia Castiglia
- Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Pavel Kovarik
- Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Tanja Poth
- Center for Model System and Comparative Pathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Franziska Herster
- Department of Immunology, Interfaculty Institute of Cell Biology, Eberhard-Karls-University, Tübingen, Germany
| | - Markus A. Weigand
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Alexander N. R. Weber
- Department of Immunology, Interfaculty Institute of Cell Biology, Eberhard-Karls-University, Tübingen, Germany
| | - Alexander H. Dalpke
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
- Institute of Medical Microbiology and Hygiene, Technical University Dresden, Dresden, Germany
| | - Tatjana Eigenbrod
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
| |
Collapse
|
45
|
Yi J, Simpanya MF, Settles EW, Shannon AB, Hernandez K, Pristo L, Keener ME, Hornstra H, Busch JD, Soffler C, Brett PJ, Currie BJ, Bowen RA, Tuanyok A, Keim P. Caprine humoral response to Burkholderia pseudomallei antigens during acute melioidosis from aerosol exposure. PLoS Negl Trop Dis 2019; 13:e0006851. [PMID: 30811382 PMCID: PMC6411198 DOI: 10.1371/journal.pntd.0006851] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 03/11/2019] [Accepted: 01/09/2019] [Indexed: 11/29/2022] Open
Abstract
Burkholderia pseudomallei causes melioidosis, a common source of pneumonia and sepsis in Southeast Asia and Northern Australia that results in high mortality rates. A caprine melioidosis model of aerosol infection that leads to a systemic infection has the potential to characterize the humoral immune response. This could help identify immunogenic proteins for new diagnostics and vaccine candidates. Outbred goats may more accurately mimic human infection, in contrast to the inbred mouse models used to date. B. pseudomallei infection was delivered as an intratracheal aerosol. Antigenic protein profiling was generated from the infecting strain MSHR511. Humoral immune responses were analyzed by ELISA and western blot, and the antigenic proteins were identified by mass spectrometry. Throughout the course of the infection the assay results demonstrated a much greater humoral response with IgG antibodies, in both breadth and quantity, compared to IgM antibodies. Pre-infection sera showed multiple immunogenic proteins already reactive for IgG (7-20) and IgM (0-12) in most of the goats despite no previous exposure to B. pseudomallei. After infection, the number of IgG reactive proteins showed a marked increase as the disease progressed. Early stage infection (day 7) showed immune reaction to chaperone proteins (GroEL, EF-Tu, and DnaK). These three proteins were detected in all serum samples after infection, with GroEL immunogenically dominant. Seven common reactive antigens were selected for further analysis using ELISA. The heat shock protein GroEL1 elicited the strongest goat antibody immune response compared to the other six antigens. Most of the six antigens showed the peak IgM reactivity at day 14, whereas the IgG reactivity increased further as the disease progressed. An overall MSHR511 proteomic comparison between the goat model and human sera showed that many immune reactive proteins are common between humans and goats with melioidosis.
Collapse
Affiliation(s)
- Jinhee Yi
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Mukoma F. Simpanya
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Erik W. Settles
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Austin B. Shannon
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Karen Hernandez
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Lauren Pristo
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Mitchell E. Keener
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Heidie Hornstra
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Joseph D. Busch
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Carl Soffler
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Paul J. Brett
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, United States of America
| | - Bart J. Currie
- Menzies School of Health Research and Infectious Diseases Department, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Richard A. Bowen
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Apichai Tuanyok
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| |
Collapse
|
46
|
Górski A, Bollyky PL, Przybylski M, Borysowski J, Międzybrodzki R, Jończyk-Matysiak E, Weber-Dąbrowska B. Perspectives of Phage Therapy in Non-bacterial Infections. Front Microbiol 2019; 9:3306. [PMID: 30687285 PMCID: PMC6333649 DOI: 10.3389/fmicb.2018.03306] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 12/19/2018] [Indexed: 12/18/2022] Open
Abstract
While the true value of phage therapy (PT) in human bacterial infections still awaits formal confirmation by clinical trials, new data have been accumulating indicating that in the future PT may be applied in the treatment of non-bacterial infections. Thus, "phage guests" may interact with eukaryotic cells and such interactions with cells of the immune system may protect human health (Guglielmi, 2017) and cause clinically useful immunomodulatory and anti-inflammatory effects when administered for therapeutic purposes (Górski et al., 2017; Van Belleghem et al., 2017). Recently, a vision of how these effects could translate into advances in novel means of therapy in a variety of human pathologies secondary to immune disturbances and allergy was presented (Górski et al., 2018a). In this article we present what is currently known about anti-microbial effects of phage which are not directly related to their antibacterial action and how these findings could be applied in the future in treatment of viral and fungal infections.
Collapse
Affiliation(s)
- Andrzej Górski
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland.,Department of Clinical Immunology, Medical University of Warsaw, Warsaw, Poland
| | - Paul L Bollyky
- Division of Infectious Diseases, Department of Medicine, Stanford University Medical School, Stanford, CA, United States.,Immunology Program, Stanford University, Stanford, CA, United States
| | - Maciej Przybylski
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland
| | - Jan Borysowski
- Department of Clinical Immunology, Medical University of Warsaw, Warsaw, Poland
| | - Ryszard Międzybrodzki
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland.,Department of Clinical Immunology, Medical University of Warsaw, Warsaw, Poland
| | - Ewa Jończyk-Matysiak
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Beata Weber-Dąbrowska
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| |
Collapse
|
47
|
O’Brien VP, Dorsey DA, Hannan TJ, Hultgren SJ. Host restriction of Escherichia coli recurrent urinary tract infection occurs in a bacterial strain-specific manner. PLoS Pathog 2018; 14:e1007457. [PMID: 30543708 PMCID: PMC6292575 DOI: 10.1371/journal.ppat.1007457] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 11/05/2018] [Indexed: 11/29/2022] Open
Abstract
Urinary tract infections (UTI) are extremely common and can be highly recurrent, with 1-2% of women suffering from six or more recurrent episodes per year. The high incidence of recurrent UTI, including recurrent infections caused by the same bacterial strain that caused the first infection, suggests that at least some women do not mount a protective adaptive immune response to UTI. Here we observed in a mouse model of cystitis (bladder infection) that infection with two different clinical uropathogenic Escherichia coli (UPEC) isolates, UTI89 or CFT073, resulted in different kinetics of bacterial clearance and different susceptibility to same-strain recurrent infection. UTI89 and CFT073 both caused infections that persisted for at least two weeks in similar proportions of mice, but whereas UTI89 infections could persist indefinitely, CFT073 infections began to clear two weeks after inoculation and were uniformly cleared within eight weeks. Mice with a history of CFT073 cystitis lasting four weeks were protected against recurrent CFT073 infection after antibiotic therapy, but were not protected against challenge with UTI89. In contrast, mice with a history of UTI89 cystitis lasting four weeks were highly susceptible to challenge infection with either strain after antibiotic treatment. We found that depletion of CD4+ and CD8+ T cell subsets impaired the ability of the host to clear CFT073 infections and rendered mice with a history of CFT073 cystitis lasting four weeks susceptible to recurrent CFT073 cystitis upon challenge. Our findings demonstrate the complex interplay between the broad genetic diversity of UPEC and the host innate and adaptive immune responses during UTI. A better understanding of these host-pathogen interactions is urgently needed for effective drug and vaccine development in the era of increasing antibiotic resistance.
Collapse
Affiliation(s)
- Valerie P. O’Brien
- Department of Molecular Microbiology and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Denise A. Dorsey
- Department of Molecular Microbiology and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Thomas J. Hannan
- Department of Molecular Microbiology and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Scott J. Hultgren
- Department of Molecular Microbiology and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
| |
Collapse
|
48
|
Nazir Z, Afridi SG, Shah M, Shams S, Khan A. Reverse vaccinology and subtractive genomics-based putative vaccine targets identification for Burkholderia pseudomallei Bp1651. Microb Pathog 2018; 125:219-229. [PMID: 30243554 DOI: 10.1016/j.micpath.2018.09.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/16/2018] [Accepted: 09/18/2018] [Indexed: 12/16/2022]
Abstract
The Burkholderia pseudomallei is a unique bio-threat and causative agent of melioidosis. The B. pseudomallei Bp1651 strain has been isolated from a chronic cystic fibrosis patient. The genome-level DNA sequences information of this strain has recently been published. Unfortunately, there is no commercial vaccine available till date to combat B. pseudomallei infection. The genome-wide prioritization approaches are widely used for the identification of potential therapeutic candidates against pathogens. In the present study, we utilized the recently available annotated genomic information of B. pseudomallei Bp1651 through subtractive genomics and reverse-vaccinology strategies to identify its potential vaccine targets. The analyses identified more than 60 pathogen-specific, human host non-homologous proteins that may prioritize in future studies to investigate therapeutic targets for B. pseudomallei Bp1651. The potential B and T-cells antigenic determinant peptides from these pathogen-specific proteins were cataloged using antigenicity and epitope prediction tools. The analyses unveiled a promising antigenic peptide "FQWEFSLSV" from protein-export membrane protein (SecF) of Bp1651 strain, which was predicted to interact with multiple class I and class II MHC alleles with IC50 value < 100 nM. The molecular docking analysis verified favorable molecular interaction of this lead antigenic peptide with the ligand-binding pocket residues of HLA A*02:06 human host immune cell surface receptor. This peptide is predicted to be a suitable epitope capable to elicit the cell-mediated immune response against the B. pseudomallei pathogen. The putative epitopes and proteins identified in this study may be promising vaccine targets against Bp1651 as well as other pathogenic strains of B. pseudomallei.
Collapse
Affiliation(s)
- Zarghoona Nazir
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Khyber Pakhtunkhwa, Pakistan
| | - Sahib Gul Afridi
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Khyber Pakhtunkhwa, Pakistan
| | - Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University Multan, Punjab, Pakistan
| | - Sulaiman Shams
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Khyber Pakhtunkhwa, Pakistan
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Khyber Pakhtunkhwa, Pakistan.
| |
Collapse
|
49
|
Kalan LR, Brennan MB. The role of the microbiome in nonhealing diabetic wounds. Ann N Y Acad Sci 2018; 1435:79-92. [PMID: 30003536 DOI: 10.1111/nyas.13926] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 06/12/2018] [Accepted: 06/18/2018] [Indexed: 12/17/2022]
Abstract
Wound healing is a highly coordinated and complex process, and there can be devastating consequences if it is interrupted. It is believed that, in combination with host factors, microorganisms in a wound bed can not only impair wound healing but can lead to stalled, chronic wounds. It is hypothesized that the wound microbiota persists in chronic wounds as a biofilm, recalcitrant to antibiotic and mechanical intervention. Cultivation-based methods are the gold standard for identification of pathogens residing in wounds. However, these methods are biased against fastidious organisms, and do not capture the full extent of microbial diversity in chronic wounds. Thus, the link between specific microbes and impaired healing remains tenuous. This is partially because local infection and, more specifically, the formation of a biofilm, is difficult to diagnose. This has led to research efforts aimed at understanding if biofilm formation delays healing and leads to persistent and chronic infection. Circumventing challenges associated with culture-based estimations, advances in high-throughput sequencing analysis has revealed that chronic wounds are host to complex, diverse microbiomes comprising multiple species of bacteria and fungi. Here, we discuss how the use of genomic methodologies to study wound microbiomes has advanced the current understanding of infection and biofilm formation in chronic wounds.
Collapse
Affiliation(s)
- Lindsay R Kalan
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin.,Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin
| | - Meghan B Brennan
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin
| |
Collapse
|
50
|
Qian Y, Yang X, Xu S, Wu C, Qin N, Chen SD, Xiao Q. Detection of Microbial 16S rRNA Gene in the Blood of Patients With Parkinson's Disease. Front Aging Neurosci 2018; 10:156. [PMID: 29881345 PMCID: PMC5976788 DOI: 10.3389/fnagi.2018.00156] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/07/2018] [Indexed: 01/16/2023] Open
Abstract
Emerging evidence suggests that the microbiota present in feces plays a role in Parkinson's disease (PD). However, the alterations of the microbiome in the blood of PD patients remain unknown. To test this hypothesis, we conducted this case-control study to explore the microbiota compositions in the blood of Chinese PD patients. Microbiota communities in the blood of 45 patients and their healthy spouses were investigated using high-throughput Illumina HiSeq sequencing targeting the V3-V4 region of 16S ribosomal RNA (rRNA) gene. The relationships between the microbiota in the blood and PD clinical characteristics were analyzed. No difference was detected in the structure and richness between PD patients and healthy controls. The following genera were enriched in the blood of PD patients: Isoptericola, Cloacibacterium, Enhydrobacter and Microbacterium; whereas genus Limnobacter was enriched in the healthy controls after adjusting for age, gender, body mass index (BMI) and constipation. Additionally, the findings regarding these genera were validated in another independent group of 58 PD patients and 57 healthy controls using real-time PCR targeting genus-specific 16S rRNA genes. Furthermore, not only the genera Cloacibacterium and Isoptericola (which were identified as enriched in PD patients) but also the genera Paludibacter and Saccharofermentans were positively associated with disease duration. Some specific genera in the blood were related to mood disorders. We believe this is the first report to provide direct evidence to support the hypothesis that the identified microbiota in the blood are associated with PD. Additionally, some microbiota in the blood are closely associated with the clinical characteristics of PD. Elucidating these differences in blood microbiomes will provide a foundation to improve our understanding of the role of microbiota in the pathogenesis of PD.
Collapse
Affiliation(s)
- Yiwei Qian
- Department of Neurology & Collaborative Innovation Center for Brain Science, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaodong Yang
- Department of Neurology & Collaborative Innovation Center for Brain Science, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shaoqing Xu
- Department of Neurology & Collaborative Innovation Center for Brain Science, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chunyan Wu
- Department of Bioinformatics, Realbio Genomics Institute, Shanghai, China
| | - Nan Qin
- Department of Bioinformatics, Realbio Genomics Institute, Shanghai, China
| | - Sheng-Di Chen
- Department of Neurology & Collaborative Innovation Center for Brain Science, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qin Xiao
- Department of Neurology & Collaborative Innovation Center for Brain Science, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|