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Zhang X, Huang X, Zheng P, Liu E, Bai S, Chen S, Pang Y, Xiao X, Yang H, Guo J. Changes in oral, skin, and gut microbiota in children with atopic dermatitis: a case-control study. Front Microbiol 2024; 15:1442126. [PMID: 39211320 PMCID: PMC11358084 DOI: 10.3389/fmicb.2024.1442126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024] Open
Abstract
Introduction Atopic dermatitis (AD) is a common clinical recurrent atopic disease in dermatology, most seen in children and adolescents. In recent years, AD has been found to be closely associated with microbial communities. Methods To explore the synergistic effects between colonizing bacteria from different sites and AD, we comparatively analyzed the skin, oral, and gut microbiota of children with AD (50 individuals) and healthy children (50 individuals) by 16S rRNA gene sequencing. Twenty samples were also randomly selected from both groups for metabolic and macrogenomic sequencing. Results The results of our sequencing study showed reduced microbiota diversity in the oral, skin, and gut of children with AD (P < 0.05). Metabolomics analysis showed that serotonergic synapse, arachidonic acid metabolism, and steroid biosynthesis were downregulated at all three loci in the oral, skin, and gut of children with AD (P < 0.05). Macrogenomic sequencing analysis showed that KEGG functional pathways of the three site flora were involved in oxidative phosphorylation, ubiquitin-mediated proteolysis, mRNA surveillance pathway, ribosome biogenesis in eukaryotes, proteasome, basal transcription factors, peroxisome, MAPK signaling pathway, mitophagy, fatty acid elongation, and so on (P < 0.05). Discussion The combined microbial, metabolic, and macrogenetic analyses identified key bacteria, metabolites, and pathogenic pathways that may be associated with AD development. We provides a more comprehensive and in-depth understanding of the role of the microbiota at different sites in AD patients, pointing to new directions for future diagnosis, treatment and prognosis.
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Affiliation(s)
- Xueer Zhang
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaomin Huang
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Pai Zheng
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - E. Liu
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Sixian Bai
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shuoyu Chen
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yaobin Pang
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xinyu Xiao
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Huifang Yang
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jing Guo
- Department of Dermatology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Yu T, Xu X, Liu Y, Wang X, Wu S, Qiu Z, Liu X, Pan X, Gu C, Wang S, Dong L, Li W, Yao X. Multi-omics signatures reveal genomic and functional heterogeneity of Cutibacterium acnes in normal and diseased skin. Cell Host Microbe 2024; 32:1129-1146.e8. [PMID: 38936370 DOI: 10.1016/j.chom.2024.06.002] [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: 12/20/2023] [Revised: 04/19/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024]
Abstract
Cutibacterium acnes is the most abundant bacterium of the human skin microbiome since adolescence, participating in both skin homeostasis and diseases. Here, we demonstrate individual and niche heterogeneity of C. acnes from 1,234 isolate genomes. Skin disease (atopic dermatitis and acne) and body site shape genomic differences of C. acnes, stemming from horizontal gene transfer and selection pressure. C. acnes harbors characteristic metabolic functions, fewer antibiotic resistance genes and virulence factors, and a more stable genome compared with Staphylococcus epidermidis. Integrated genome, transcriptome, and metabolome analysis at the strain level unveils the functional characteristics of C. acnes. Consistent with the transcriptome signature, C. acnes in a sebum-rich environment induces toxic and pro-inflammatory effects on keratinocytes. L-carnosine, an anti-oxidative stress metabolite, is up-regulated in the C. acnes metabolome from atopic dermatitis and attenuates skin inflammation. Collectively, our study reveals the joint impact of genes and the microenvironment on C. acnes function.
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Affiliation(s)
- Tianze Yu
- Department of Dermatology, Shanghai Institute of Dermatology, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Xiaoqiang Xu
- Department of Dermatology, Shanghai Institute of Dermatology, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Yang Liu
- 01life Institute, Shenzhen 518000, China
| | - Xiaokai Wang
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong 999077, China
| | - Shi Wu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Zhuoqiong Qiu
- Department of Dermatology, Shanghai Institute of Dermatology, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Xiaochun Liu
- Department of Allergy and Rheumatology, Hospital for Skin Diseases, Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China
| | - Xiaoyu Pan
- Department of Dermatology, Shanghai Institute of Dermatology, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Chaoying Gu
- Department of Dermatology, Shanghai Institute of Dermatology, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Shangshang Wang
- Department of Dermatology, Shanghai Institute of Dermatology, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Lixin Dong
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong 999077, China.
| | - Wei Li
- Department of Dermatology, Shanghai Institute of Dermatology, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China.
| | - Xu Yao
- Department of Allergy and Rheumatology, Hospital for Skin Diseases, Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China.
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3
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Lee DH, Lee K, Kim YS, Cha CJ. Comprehensive genomic landscape of antibiotic resistance in Staphylococcus epidermidis. mSystems 2024; 9:e0022624. [PMID: 38727238 PMCID: PMC11237394 DOI: 10.1128/msystems.00226-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/04/2024] [Indexed: 06/19/2024] Open
Abstract
Staphylococcus epidermidis, a common commensal bacterium found on human skin, can cause infections in clinical settings, and the presence of antibiotic resistance genes (ARGs) impedes the treatment of S. epidermidis infections. However, studies characterizing the ARGs in S. epidermidis with regard to genomic and ecological diversities are limited. Thus, we performed a comprehensive and comparative analysis of 405 high-quality S. epidermidis genomes, including those of 35 environmental isolates from the Han River, to investigate the genomic diversity of antibiotic resistance in this pathogen. Comparative genomic analysis revealed the prevalence of ARGs in S. epidermidis genomes associated with multi-locus sequence types. The genes encoding dihydrofolate reductase (dfrC) and multidrug efflux pump (norA) were genome-wide core ARGs. β-Lactam class ARGs were also highly prevalent in the S. epidermidis genomes, which was consistent with the resistance phenotype observed in river isolates. Furthermore, we identified chloramphenicol acetyltransferase genes (cat) in the plasmid-like sequences of the six river isolates, which have not been reported previously in S. epidermidis genomes. These genes were identical to those harbored by the Enterococcus faecium plasmids and associated with the insertion sequence 6 family transposases, homologous to those found in Staphylococcus aureus plasmids, suggesting the possibility of horizontal gene transfer between these Gram-positive pathogens. Comparison of the ARG and virulence factor profiles between S. epidermidis and S. aureus genomes revealed that these two species were clearly distinguished, suggesting genomic demarcation despite ecological overlap. Our findings provide a comprehensive understanding of the genomic diversity of antibiotic resistance in S. epidermidis. IMPORTANCE A comprehensive understanding of the antibiotic resistance gene (ARG) profiles of the skin commensal bacterium and opportunistic pathogen Staphylococcus epidermidis needs to be documented from a genomic point of view. Our study encompasses a comparative analysis of entire S. epidermidis genomes from various habitats, including those of 35 environmental isolates from the Han River sequenced in this study. Our results shed light on the distribution and diversity of ARGs within different S. epidermidis multi-locus sequence types, providing valuable insights into the ecological and genetic factors associated with antibiotic resistance. A comparison between S. epidermidis and Staphylococcus aureus revealed marked differences in ARG and virulence factor profiles, despite their overlapping ecological niches.
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Affiliation(s)
- Do-Hoon Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, South Korea
| | - Kihyun Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, South Korea
| | - Yong-Seok Kim
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, South Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, South Korea
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Eisenbraun EL, Vulpis TD, Prosser BN, Horswill AR, Blackwell HE. Synthetic Peptides Capable of Potent Multigroup Staphylococcal Quorum Sensing Activation and Inhibition in Both Cultures and Biofilm Communities. J Am Chem Soc 2024; 146:15941-15954. [PMID: 38832917 PMCID: PMC11321086 DOI: 10.1021/jacs.4c02694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
The pathogen Staphylococcus epidermidis uses a chemical signaling process, i.e., quorum sensing (QS), to form robust biofilms and cause human infection. Many questions remain about QS in S. epidermidis, as it uses this intercellular communication pathway to both negatively and positively regulate virulence traits. Herein, we report synthetic multigroup agonists and antagonists of the S. epidermidis accessory gene regulator (agr) QS system capable of potent superactivation and complete inhibition, respectively. These macrocyclic peptides maintain full efficacy across the three major agr specificity groups, and their activity can be "mode-switched" from agonist to antagonist via subtle residue-specific structural changes. We describe the design and synthesis of these non-native peptides and demonstrate that they can appreciably decrease biofilm formation on abiotic surfaces, underscoring the potential for agr agonism as a route to block S. epidermidis virulence. Additionally, we show that both the S. epidermidis agonists and antagonists are active in S. aureus, another common pathogen with a related agr system, yet only as antagonists. This result not only revealed one of the most potent agr inhibitors known in S. aureus but also highlighted differences in the mechanisms of agr agonism and antagonism between these related bacteria. Finally, our investigations reveal unexpected inhibitory behavior for certain S. epidermidis agr agonists at sub-activating concentrations, an observation that can be leveraged for the design of future probes with enhanced potencies. Together, these peptides provide a powerful tool set to interrogate the role of QS in S. epidermidis infections and in Staphylococcal pathogenicity in general.
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Affiliation(s)
- Emma L. Eisenbraun
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Ave., Madison, WI 53706, USA
| | - Troy D. Vulpis
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Ave., Madison, WI 53706, USA
| | - Brendan N. Prosser
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Ave., Madison, WI 53706, USA
| | - Alexander R. Horswill
- Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA
| | - Helen E. Blackwell
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Ave., Madison, WI 53706, USA
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5
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Fisher CR, Masters TL, Johnson S, Greenwood-Quaintance KE, Chia N, Abdel MP, Patel R. Comparative transcriptomic analysis of Staphylococcus epidermidis associated with periprosthetic joint infection under in vivo and in vitro conditions. Int J Med Microbiol 2024; 315:151620. [PMID: 38579524 PMCID: PMC11214590 DOI: 10.1016/j.ijmm.2024.151620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 01/19/2024] [Accepted: 03/26/2024] [Indexed: 04/07/2024] Open
Abstract
Staphylococcus epidermidis is part of the commensal microbiota of the skin and mucous membranes, though it can also act as a pathogen in certain scenarios, causing a range of infections, including periprosthetic joint infection (PJI). Transcriptomic profiling may provide insights into mechanisms by which S. epidermidis adapts while in a pathogenic compared to a commensal state. Here, a total RNA-sequencing approach was used to profile and compare the transcriptomes of 19 paired PJI-associated S. epidermidis samples from an in vivo clinical source and grown in in vitro laboratory culture. Genomic comparison of PJI-associated and publicly available commensal-state isolates were also compared. Of the 1919 total transcripts found, 145 were from differentially expressed genes (DEGs) when comparing in vivo or in vitro samples. Forty-two transcripts were upregulated and 103 downregulated in in vivo samples. Of note, metal sequestration-associated genes, specifically those related to staphylopine activity (cntA, cntK, cntL, and cntM), were upregulated in a subset of clinical in vivo compared to laboratory grown in vitro samples. About 70% of the total transcripts and almost 50% of the DEGs identified have not yet been annotated. There were no significant genomic differences between known commensal and PJI-associated S. epidermidis isolates, suggesting that differential genomics may not play a role in S. epidermidis pathogenicity. In conclusion, this study provides insights into phenotypic alterations employed by S epidermidis to adapt to infective and non-infected microenvironments, potentially informing future therapeutic targets for related infections.
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Affiliation(s)
- Cody R Fisher
- Mayo Clinic Graduate School of Biomedical Sciences, Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA; Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Thao L Masters
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Stephen Johnson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Kerryl E Greenwood-Quaintance
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicholas Chia
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Matthew P Abdel
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN 55905, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.
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Ionescu MA, Tatu AL, Busila C, Axente ER, Badalato N, Feuilloley MGJ, Asquier E, Martínez JD, Lefeuvre L. Microbiome Modulation in Acne Patients and Clinical Correlations. Life (Basel) 2024; 14:688. [PMID: 38929671 PMCID: PMC11204784 DOI: 10.3390/life14060688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND The imbalance of skin microbiota in acne can induce changes leading to induction or to aggravation of chronic inflammatory lesions; complex mechanisms are involved. Cutibacterium acnes (C. acnes) ribotypes RT4 and RT5 express more biofilm and are associated with inflammatory acne lesions. C. acnes RT6 is a non-acne ribotype, beneficial for the skin. OBJECTIVES In an open clinical trial, acne adults were included and assessed clinically at baseline and at month 2 using the Investigator Global Assessment of Acne (IGA) score. A topical emulsion was applied twice daily for 2 months (M2) in each included patient. In the same series of acne patients, skin swab samples were collected from acne patients at baseline and M2 from lesional and non-lesional skin; skin swabs were collected for the metagenomic long-read analysis of microbiota. MATERIALS AND METHODS Acne patients with a gravity score IGA of >1<3 were included in this pilot study. An emulsion of O/W formulated with vegetal extract of Umbelliferae associated with a polysaccharide at 1% was applied twice daily for 2 months. At baseline and M2 clinical assessments were made; skin swab samples were also taken for microbiota analysis from lesional and non-lesional skin in each included patient. Extractions of genomic DNA (gDNA) from swab samples from baseline and from M2 were made, followed by full-length (V1-V9) amplification of the 16S rDNA and sequencing of amplicon libraries for strain-level bacterial community profiling. RESULTS In a series of 32 adult acne patients, the mean initial IGA scale was 3.1; at M2 the IGA scale was 1.5 (p < 0.001). The mean decrease in acne lesions was by 63%. Microbiome metagenomic long-read analysis in these series was mainly dominated by C. acnes followed by Staphylococcus epidermidis (S. epidermidis). The density of C. acnes ribotypes RT6 (non-acne strain) was increased at M2 compared to baseline and the density of ribotypes C. acnes RT1 to RT5 was decreased at M2, compared to baseline (p < 0.0001). S. epidermidis ribotypes (1 to 36) were non significantly increased at M2, compared to baseline (p < 0.1). CONCLUSIONS In a series of 32 acne patients that applied an emulsion based on vegetal extract of Umbelliferae and a polysaccharide at 1% twice daily, a significant clinical improvement in IGA scale for acne lesions was seen at M2, compared to baseline (p < 0.0001). The clinical improvement was correlated with an improvement in skin microbiome at M2 compared to baseline, indicated by the increase in the relative abundance of non-acne strain of C. acnes ribotype 6 and of the decrease in the relative abundance of acne strains ribotypes C. acnes RT1 to RT5.
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Affiliation(s)
- Marius-Anton Ionescu
- Dermatology Department, University Hospital “Saint Louis”, University of Paris, 75010 Paris, France;
| | - Alin Laurentiu Tatu
- Clinical Medical Department, Faculty of Medicine and Pharmacy, “Dunarea de Jos” University, 800008 Galati, Romania
- “Sfanta Cuvioasa Parascheva” Hospital of Infectious Diseases, 800179 Galati, Romania
- Multidisciplinary Integrated Center of Dermatological Interface Research MIC-DIR (Centrul Integrat Multidisciplinar de Cercetare de Interfata Dermatologica—CIM-CID), “Dunărea de Jos” University, 800201 Galati, Romania
| | - Camelia Busila
- Clinical Medical Department, Faculty of Medicine and Pharmacy, “Dunarea de Jos” University, 800008 Galati, Romania
- “Sf. Ioan” Emergency Clinical Paediatric Hospital, 800487 Galati, Romania
| | - Elena Roxana Axente
- Faculty of Medicine and Pharmacy, “Dunarea de Jos” University, 35 AI I Cuza St., 800010 Galati, Romania;
| | | | | | - Estelle Asquier
- Laboratoires Dermatologiques d’Uriage, 92200 Neuilly sur-Seine, France; (E.A.); (L.L.)
| | - José Dario Martínez
- Department of Internal Medicine, Faculty of Medicine, Hospital Universitario José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey 64460, Mexico;
| | - Luc Lefeuvre
- Laboratoires Dermatologiques d’Uriage, 92200 Neuilly sur-Seine, France; (E.A.); (L.L.)
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Mancuso CP, Baker JS, Qu E, Tripp AD, Balogun IO, Lieberman TD. Intraspecies warfare restricts strain coexistence in human skin microbiomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.592803. [PMID: 38765968 PMCID: PMC11100718 DOI: 10.1101/2024.05.07.592803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Determining why only a fraction of encountered or applied bacterial strains engraft in a given person's microbiome is crucial for understanding and engineering these communities1. Previous work has established that metabolism can determine colonization success in vivo2-4, but relevance of bacterial warfare in preventing engraftment has been less explored. Here, we demonstrate that intraspecies warfare presents a significant barrier to strain transmission in the skin microbiome by profiling 14,884 pairwise interactions between Staphylococcus epidermidis cultured from eighteen human subjects from six families. We find that intraspecies antagonisms are abundant; these interactions are mechanistically diverse, independent of the relatedness between strains, and consistent with rapid evolution via horizontal gene transfer. Ability to antagonize more strains is associated with reaching a higher fraction of the on-person S. epidermidis community. Moreover, antagonisms are significantly depleted among strains residing on the same person relative to random assemblages. Two notable exceptions, in which bacteria evolved to become sensitive to antimicrobials found on the same host, are explained by mutations that provide phage resistance, contextualizing the importance of warfare among other lethal selective pressures. Taken together, our results emphasize that accounting for intraspecies bacterial warfare is essential to the design of long-lasting probiotic therapeutics.
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Affiliation(s)
- Christopher P. Mancuso
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
| | - Jacob S. Baker
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
| | - Evan Qu
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
| | - A. Delphine Tripp
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Systems Biology, Harvard University; Cambridge, MA 02138, USA
| | - Ishaq O. Balogun
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
| | - Tami D. Lieberman
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA 02142, USA
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Lee J, Mannan AA, Miyano T, Irvine AD, Tanaka RJ. In Silico Elucidation of Key Drivers of Staphyloccocus aureus- Staphyloccocus epidermidis-Induced Skin Damage in Atopic Dermatitis Lesions. JID INNOVATIONS 2024; 4:100269. [PMID: 38766490 PMCID: PMC11101946 DOI: 10.1016/j.xjidi.2024.100269] [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: 06/07/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 05/22/2024] Open
Abstract
Staphylococcus aureus (SA) colonizes and can damage skin in atopic dermatitis lesions, despite being commonly found with Staphylococcus epidermidis (SE), a commensal that can inhibit SA's virulence and kill SA. In this study, we developed an in silico model, termed a virtual skin site, describing the dynamic interplay between SA, SE, and the skin barrier in atopic dermatitis lesions to investigate the mechanisms driving skin damage by SA and SE. We generated 106 virtual skin sites by varying model parameters to represent different skin physiologies and bacterial properties. In silico analysis revealed that virtual skin sites with no skin damage in the model were characterized by parameters representing stronger SA and SE growth attenuation than those with skin damage. This inspired an in silico treatment strategy combining SA-killing with an enhanced SA-SE growth attenuation, which was found through simulations to recover many more damaged virtual skin sites to a non-damaged state, compared with SA-killing alone. This study demonstrates that in silico modelling can help elucidate the key factors driving skin damage caused by SA-SE colonization in atopic dermatitis lesions and help propose strategies to control it, which we envision will contribute to the design of promising treatments for clinical studies.
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Affiliation(s)
- Jamie Lee
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Ahmad A. Mannan
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Takuya Miyano
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Alan D. Irvine
- Clinical Medicine, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Reiko J. Tanaka
- Department of Bioengineering, Imperial College London, London, United Kingdom
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Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Rose SMSF, Tran TDB, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas PB, Zhou Y, Sodergren E, Weinstock GM, Snyder MP. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Cell Host Microbe 2024; 32:506-526.e9. [PMID: 38479397 PMCID: PMC11022754 DOI: 10.1016/j.chom.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/23/2024] [Accepted: 02/20/2024] [Indexed: 03/26/2024]
Abstract
To understand the dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune, and clinical markers of microbiomes from four body sites in 86 participants over 6 years. We found that microbiome stability and individuality are body-site specific and heavily influenced by the host. The stool and oral microbiome are more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. We identify individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlate across body sites, suggesting systemic dynamics influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals show altered microbial stability and associations among microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease.
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Affiliation(s)
- Xin Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford, CA 94305, USA; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Xiaotao Shen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA
| | - Jethro S Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7FY, UK
| | - Daniel J Spakowicz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Division of Medical Oncology, Ohio State University Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Columbus, OH 43210, USA
| | | | - Wenyu Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA
| | - Monica Avina
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander Honkala
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Faye Chleilat
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shirley Jingyi Chen
- Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kexin Cha
- Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shana Leopold
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Chenchen Zhu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lei Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Shanghai Institute of Immunology, Shanghai Jiao Tong University, Shanghai 200240, PRC
| | - Lin Lyu
- Shanghai Institute of Immunology, Shanghai Jiao Tong University, Shanghai 200240, PRC
| | - Daniel Hornburg
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Si Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xinyue Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chao Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PRC
| | - Liuyiqi Jiang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PRC
| | - Lihua Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ruiqi Jian
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew W Brooks
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Meng Wang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peng Gao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | | | - Hoan Nguyen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Alessandra Celli
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bo-Young Hong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Woody L Hunt School of Dental Medicine, Texas Tech University Health Science Center, El Paso, TX 79905, USA
| | - Eddy J Bautista
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Corporación Colombiana de Investigación Agropecuaria (Agrosavia), Headquarters-Mosquera, Cundinamarca 250047, Colombia
| | - Yair Dorsett
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Medicine, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Paula B Kavathas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yanjiao Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Medicine, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Erica Sodergren
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford, CA 94305, USA; Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA.
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10
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Tian H, Wang L, Hardy R, Kozhaya L, Placek L, Fleming E, Oh J, Unutmaz D, Yao X. Bioassay-Driven, Fractionation-Empowered, Focused Metabolomics for Discovering Bacterial Activators of Aryl Hydrocarbon Receptor. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:518-526. [PMID: 38308645 DOI: 10.1021/jasms.3c00386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2024]
Abstract
Aryl hydrocarbon receptor (AhR) is a transcription factor that regulates gene expression upon ligand activation, enabling microbiota-dependent induction, training, and function of the host immune system. A spectrum of metabolites, encompassing indole and tryptophan derivatives, have been recognized as activators. This work introduces an integrated, mass spectrometry-centric workflow that employs a bioassay-guided, fractionation-based methodology for the identification of AhR activators derived from human bacterial isolates. By leveraging the workflow efficiency, the complexities inherent in metabolomics profiling are significantly reduced, paving the way for an in-depth and focused mass spectrometry analysis of bioactive fractions isolated from bacterial culture supernatants. Validation of AhR activator candidates used multiple criteria─MS/MS of the synthetic reference compound, bioassay of AhR activity, and elution time confirmation using a C-13 isotopic reference─and was demonstrated for N-formylkynurenine (NFK). The workflow reported provides a roadmap update for improved efficiency of identifying bioactive metabolites using mass spectrometry-based metabolomics. Mass spectrometry datasets are accessible at the National Metabolomics Data Repository (PR001479, Project DOI: 10.21228/M8JM7Q).
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Affiliation(s)
- Huidi Tian
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Lei Wang
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Rachel Hardy
- The Jackson Laboratory, 10 Discovery Drive, Farmington, Connecticut 06032, United States
| | - Lina Kozhaya
- The Jackson Laboratory, 10 Discovery Drive, Farmington, Connecticut 06032, United States
| | - Lindsey Placek
- The Jackson Laboratory, 10 Discovery Drive, Farmington, Connecticut 06032, United States
| | - Elizabeth Fleming
- The Jackson Laboratory, 10 Discovery Drive, Farmington, Connecticut 06032, United States
| | - Julia Oh
- The Jackson Laboratory, 10 Discovery Drive, Farmington, Connecticut 06032, United States
| | - Derya Unutmaz
- The Jackson Laboratory, 10 Discovery Drive, Farmington, Connecticut 06032, United States
| | - Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
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11
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Fang GY, Wu FH, Mu XJ, Jiang YJ, Liu XQ. Monitoring longitudinal antimicrobial resistance trends of Staphylococcus aureus strains worldwide over the past 100 years to decipher its evolution and transmission. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133136. [PMID: 38056258 DOI: 10.1016/j.jhazmat.2023.133136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 11/19/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
Staphylococcus aureus inhabits diverse habitats including food waste and wastewater treatment plants. Cases of S. aureus-induced infection are commonly reported worldwide. The emergence of antimicrobial resistance (AMR) of S. aureus is a growing public health threat worldwide. Here, we longitudinally monitored global trends in antibiotic resistance genes (ARGs) of 586 S. aureus strains, isolated between 1884 and 2022. The ARGs in S. aureus exhibited a significant increase over time (P < 0.0001). Mobile genetic elements play a crucial role in the transfer of ARGs in S. aureus strains. The structural equation model results revealed a significant correlation between the human development index and rising antibiotic consumption, which subsequently leads to an indirect escalation of AMR in S. aureus strains. Lastly, a machine learning algorithm successfully predicted the AMR risk of global terrestrial S. aureus with over 70% accuracy. Overall, these findings provided valuable insights for managing AMR in S. aureus.
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Affiliation(s)
- Guan-Yu Fang
- College of Food and Health, Zhejiang A&F University, Hangzhou 311300, PR China; National Grain Industry (High-Quality Rice Storage in Temperate and Humid Region) Technology Innovation Center, Zhejiang A&F University, Hangzhou 311300, PR China.
| | - Feng-Hua Wu
- College of Food and Health, Zhejiang A&F University, Hangzhou 311300, PR China; National Grain Industry (High-Quality Rice Storage in Temperate and Humid Region) Technology Innovation Center, Zhejiang A&F University, Hangzhou 311300, PR China
| | - Xiao-Jing Mu
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, PR China
| | - Yu-Jian Jiang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, PR China
| | - Xing-Quan Liu
- College of Food and Health, Zhejiang A&F University, Hangzhou 311300, PR China; National Grain Industry (High-Quality Rice Storage in Temperate and Humid Region) Technology Innovation Center, Zhejiang A&F University, Hangzhou 311300, PR China.
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12
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Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Schüssler-Fiorenza Rose SM, Binh Tran TD, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas P, Zhou Y, Sodergren E, Weinstock GM, Snyder MP. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.577565. [PMID: 38352363 PMCID: PMC10862915 DOI: 10.1101/2024.02.01.577565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
To understand dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune and clinical markers of microbiomes from four body sites in 86 participants over six years. We found that microbiome stability and individuality are body-site-specific and heavily influenced by the host. The stool and oral microbiome were more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. Also, we identified individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlated across body sites, suggesting systemic coordination influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals showed altered microbial stability and associations between microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease. Study Highlights The stability of the human microbiome varies among individuals and body sites.Highly individualized microbial genera are more stable over time.At each of the four body sites, systematic interactions between the environment, the host and bacteria can be detected.Individuals with insulin resistance have lower microbiome stability, a more diversified skin microbiome, and significantly altered host-microbiome interactions.
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13
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Baker JS, Qu E, Mancuso CP, Tripp AD, Conwill A, Lieberman TD. Highly-resolved within-species dynamics in the human facial skin microbiome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.575018. [PMID: 38260404 PMCID: PMC10802602 DOI: 10.1101/2024.01.10.575018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Human facial skin microbiomes (FSMs) on adults are dominated by just two bacterial species, Cutibacterium acnes and Staphylococcus epidermidis. Underlying this apparent simplicity, each FSM harbors multiple strains of both species whose assembly dynamics on individuals are unknown. Here, we use 4,055 isolate genomes and 360 metagenomes to trace the dynamics of strains on individuals and their transmission. Strains are shared amongst family members of all ages, but each individual harbors unique strain consortia. Strain stability changes upon formation of the adult-type FSM: S. epidermidis lineage turnover slows, and the rate of C. acnes colonization increases before stabilizing, suggesting this transitional window could facilitate engraftment of therapeutic strains. Our work reveals previously undetectable community dynamics and informs the design of therapeutic interventions.
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Affiliation(s)
- Jacob S. Baker
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Evan Qu
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Christopher P. Mancuso
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - A. Delphine Tripp
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Systems Biology, Harvard University; Cambridge, MA 02138, USA
| | - Arolyn Conwill
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Tami D. Lieberman
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA 02139, USA
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14
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Rath A, Kieninger B, Caplunik-Pratsch A, Fritsch J, Mirzaliyeva N, Holzmann T, Bender JK, Werner G, Schneider-Brachert W. Concerning emergence of a new vancomycin-resistant Enterococcus faecium strain ST1299/CT1903/vanA at a tertiary university centre in South Germany. J Hosp Infect 2024; 143:25-32. [PMID: 37852539 DOI: 10.1016/j.jhin.2023.10.008] [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: 08/08/2023] [Revised: 09/22/2023] [Accepted: 10/08/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND vanB-carrying vancomycin-resistant Enterococcus faecium (VREfm) of the sequence types 80 (ST80) and ST117 have dominated Germany in the past. In 2020, our hospital witnessed a sharp increase in the proportion of vanA-positive VREfm. AIM To attempt to understand these dynamics through whole-genome sequencing (WGS) and analysis of nosocomial transmissions. METHODS At our hospital, the first VREfm isolate per patient, treated during 2020, was analysed retrospectively using specific vanA/vanB PCR, WGS, multi-locus sequence typing (MLST), and core-genome (cg) MLST. Epidemiologic links between VRE-positive patients were assessed using hospital occupancy data. FINDINGS Isolates from 319 out of 356 VREfm patients were available for WGS, of which 181 (56.7%) fulfilled the ECDC definition for nosocomial transmission. The high load of nosocomial cases is reflected in the overall high clonality rate with only three dominating sequence (ST) and complex types (CT), respectively: the new emerging strain ST1299 (100% vanA, 77.4% CT1903), and the well-known ST80 (90.0% vanB, 81.0% CT1065) and ST117 (78.0% vanB, 65.0% CT71). The ST1299 isolates overall, and the subtype CT1903 in particular, showed high isolate clonality, which demonstrates impressively high spreading potential. Overall, 152 out of 319 isolates had an allelic cgMLST difference of ≤3 to another, including 91 (59.6%) ST1299. Occupancy data identified shared rooms (3.7%), shared departments (6.2%), and VRE-colonized prior room occupants (0.6%) within 30 days before diagnosis as solid epidemiological links. CONCLUSION A new emerging VREfm clone, ST1299/CT1903/vanA, dominated our institution in 2020 and has been an important driver of the increasing VREfm rates.
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Affiliation(s)
- A Rath
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany.
| | - B Kieninger
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - A Caplunik-Pratsch
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - J Fritsch
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - N Mirzaliyeva
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - T Holzmann
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
| | - J K Bender
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - G Werner
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - W Schneider-Brachert
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
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15
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Zhou Y, Xu X, Liu Y, Wang A, Luo Y, Liu X, Wang X, Li W, Yao X. Heterogeneous Regulation of StaphylococcusAureus by Different StaphylococcusEpidermidisagr Types in Atopic Dermatitis. J Invest Dermatol 2023; 143:2484-2493.e11. [PMID: 37271450 DOI: 10.1016/j.jid.2023.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/15/2023] [Accepted: 05/02/2023] [Indexed: 06/06/2023]
Abstract
The skin commensal Staphylococcus epidermidis exhibits a protective role in skin inflammation; however, the exact functions of S. epidermidis and their mechanisms in atopic dermatitis (AD) are not fully understood. Here, whole-genome sequencing was conducted on strains of S. epidermidis isolated from pediatric patients with AD and revealed significant strain-level heterogeneity in functional genes. Specific sequence analysis of S. epidermidis identified four types of accessory gene regulator (agr) according to locus variations in the agr operon, which was consistent with the metagenomic data of the contextual microbiota. The number of S. epidermidisagr type I was slightly decreased among AD isolates, whereas agr type IV was hardly detected in AD isolates. Functional experiments showed that strains of S. epidermidisagr types I and IV, but not types II and III, inhibited the expression of S. aureusagr-mediated virulence factors in vitro, suppressed S. aureus epidermal colonization, and attenuated skin inflammation in a mouse model. The delineation of genome signatures of S. epidermidis at the strain level in AD and the quorum-sensing interference between S. epidermidisagr type IV and S. aureus provide a foundation for the modulation of the skin microbiota and the treatment of AD.
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Affiliation(s)
- Yuan Zhou
- Department of Allergy and Rheumatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Xiaoqiang Xu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China
| | - Yang Liu
- 01 Life Institute, Shenzhen, China
| | - Ao Wang
- Department of Allergy and Rheumatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Yang Luo
- Department of Allergy and Rheumatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Xiaochun Liu
- Department of Allergy and Rheumatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Xiaokai Wang
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, China
| | - Wei Li
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China
| | - Xu Yao
- Department of Allergy and Rheumatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China.
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16
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Joglekar P, Conlan S, Lee-Lin SQ, Deming C, Kashaf SS, Kong HH, Segre JA. Integrated genomic and functional analyses of human skin-associated Staphylococcus reveal extensive inter- and intra-species diversity. Proc Natl Acad Sci U S A 2023; 120:e2310585120. [PMID: 37956283 PMCID: PMC10666031 DOI: 10.1073/pnas.2310585120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/11/2023] [Indexed: 11/15/2023] Open
Abstract
Human skin is stably colonized by a distinct microbiota that functions together with epidermal cells to maintain a protective physical barrier. Staphylococcus, a prominent genus of the skin microbiota, participates in colonization resistance, tissue repair, and host immune regulation in strain-specific manners. To unlock the potential of engineering skin microbial communities, we aim to characterize the diversity of this genus within the context of the skin environment. We reanalyzed an extant 16S rRNA amplicon dataset obtained from distinct body sites of healthy volunteers, providing a detailed biogeographic depiction of staphylococcal species that colonize our skin. S. epidermidis, S. capitis, and S. hominis were the most abundant staphylococcal species present in all volunteers and were detected at all body sites. Pan-genome analysis of isolates from these three species revealed that the genus-core was dominated by central metabolism genes. Species-restricted-core genes encoded known host colonization functions. The majority (~68%) of genes were detected only in a fraction of isolate genomes, underscoring the immense strain-specific gene diversity. Conspecific genomes grouped into phylogenetic clades, exhibiting body site preference. Each clade was enriched for distinct gene sets that are potentially involved in site tropism. Finally, we conducted gene expression studies of select isolates showing variable growth phenotypes in skin-like medium. In vitro expression revealed extensive intra- and inter-species gene expression variation, substantially expanding the functional diversification within each species. Our study provides an important resource for future ecological and translational studies to examine the role of shared and strain-specific staphylococcal genes within the skin environment.
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Affiliation(s)
- Payal Joglekar
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Shih-Queen Lee-Lin
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Clay Deming
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Sara Saheb Kashaf
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | | | - Heidi H. Kong
- Cutaneous Microbiome and Inflammation Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD20892
| | - Julia A. Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
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17
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Sreekumaran S, Premnath M, Prathyush PR, Mathew J, Nath CC, Paul N, Abraham SS, Radhakrishnan EK. Predicting Human Risk with Multidrug Resistant Enterobacter hormaechei MS2 having MCR 9 Gene Isolated from the Feces of Healthy Broiler Through Whole-Genome Sequence-Based Analysis. Curr Microbiol 2023; 81:8. [PMID: 37966536 DOI: 10.1007/s00284-023-03492-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 09/14/2023] [Indexed: 11/16/2023]
Abstract
The zoonotic spread of antimicrobial resistance (AMR) and the associated infections are becoming a major threat to the human population worldwide. Strategies to identify the potential pathogen dissemination by seemingly healthy livestock are at a nascent stage and it is of significant importance to monitor environmental evolution of AMR. In this study, a multidrug resistant strain (MDR) of Enterobacter hormaechei MS2 isolated from the feces of healthy broiler chicken has been characterized by whole-genome sequencing-based method. Here, the isolate was primarily subjected to antimicrobial susceptibility testing followed genome sequencing and analysis. From the antimicrobial susceptibility testing result, the strain was found to be resistant to multiple classes of drugs including the colistin which is an important last resort drug used to treat infectious diseases. The resistome prediction of genomic data further revealed the presence of 7 perfect and 26 strict hits including those for MCR-9 and FosA2. The pathogenicity prediction has also demonstrated the strain to have the potential to be a human pathogen with 0.72 probability. The phylogenetic analysis has also supported the zoonotic potential of the strain due to its clustering with isolates from both human and livestock-associated host groups. The results of the study suggest the need for a strong surveillance system to identify the opportunistic zoonotic pathogens to prevent a silent AMR menace mediated by them. Carriage of multi-drug resistant strains in the livestock gut microbiome is also a serious concern as it has high AMR transmissibility through contact and supply chain activities.
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Affiliation(s)
- Sreejith Sreekumaran
- School of Biosciences, Mahatma Gandhi University, PD Hills (PO), Kottayam, Kerala, 686 560, India
| | - Manjusha Premnath
- School of Biosciences, Mahatma Gandhi University, PD Hills (PO), Kottayam, Kerala, 686 560, India
| | - P R Prathyush
- State Institute of Animal Diseases, Thiruvananthapuram, Kerala, 695 563, India
| | - Jyothis Mathew
- School of Biosciences, Mahatma Gandhi University, PD Hills (PO), Kottayam, Kerala, 686 560, India
| | - Chitra C Nath
- Department of Microbiology, Government Medical College, Kottayam, Kerala, 686 008, India
| | - Nimmy Paul
- Department of Microbiology, Government Medical College, Kottayam, Kerala, 686 008, India
| | | | - E K Radhakrishnan
- School of Biosciences, Mahatma Gandhi University, PD Hills (PO), Kottayam, Kerala, 686 560, India.
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18
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Li Z, Ju Y, Xia J, Zhang Z, Zhen H, Tong X, Sun Y, Lu H, Zong Y, Chen P, Cai K, Wang Z, Yang H, Wang J, Wang J, Hou Y, Jin X, Zhang T, Zhang W, Xu X, Xiao L, Guo R, Nie C. Integrated Human Skin Bacteria Genome Catalog Reveals Extensive Unexplored Habitat-Specific Microbiome Diversity and Function. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300050. [PMID: 37548643 PMCID: PMC10558695 DOI: 10.1002/advs.202300050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 07/08/2023] [Indexed: 08/08/2023]
Abstract
The skin is the largest organ in the human body. Various skin environments on its surface constitutes a complex ecosystem. One of the characteristics of the skin micro-ecosystem is low biomass, which greatly limits a comprehensive identification of the microbial species through sequencing. In this study, deep-shotgun sequencing (average 21.5 Gigabyte (Gb)) from 450 facial samples and publicly available skin metagenomic datasets of 2069 samples to assemble a Unified Human Skin Genome (UHSG) catalog is integrated. The UHSG encompasses 813 prokaryotic species derived from 5779 metagenome-assembled genomes, among which 470 are novel species covering 20 phyla with 1385 novel assembled genomes. Based on the UHSG, the core functions of the skin microbiome are described and the differences in amino acid metabolism, carbohydrate metabolism, and drug resistance functions among different phyla are identified. Furthermore, analysis of secondary metabolites of the near-complete genomes further find 1220 putative novel secondary metabolites, several of which are found in previously unknown genomes. Single nucleotide variant (SNV) reveals a possible skin protection mechanism: the negative selection process of the skin environment to conditional pathogens. UHSG offers a convenient reference database that will facilitate a more in-depth understanding of the role of skin microorganisms in the skin.
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19
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Demiselle J, Meyer P, Lavigne T, Kaurin J, Merdji H, Schenck M, Studer A, Janssen-Langenstein R, Helms J, Hoellinger B, Castelain V, Grillon A, Schneider F, Meziani F, Clere-Jehl R. Staphylococcus epidermidis bloodstream infections are a cause of septic shock in intensive care unit patients. Int J Infect Dis 2023; 135:45-48. [PMID: 37517512 DOI: 10.1016/j.ijid.2023.07.014] [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: 04/30/2023] [Revised: 06/16/2023] [Accepted: 07/18/2023] [Indexed: 08/01/2023] Open
Abstract
OBJECTIVES Staphylococcus epidermidis (SE) is a supposedly low-virulence agent, which may cause proven bloodstream infections (BSIs), with little-known consequences on intensive care unit (ICU) patients. We aimed at studying ICU patients diagnosed with BSIs caused by SE (SE-BSIs). METHODS We constituted a retrospective cohort in two medical ICUs. SE-BSIs were defined by two or more independent SE-positive blood cultures of the same strain, within 48 hours, without concurrent infection. RESULTS We included 59 patients; 58% were men (n = 34), with median age of 67 (interquartile range 60-74) years and a simplified acute physiology score II of 59 (36-74) points, and 56% were immunocompromised (n = 33). Among the 37 (63%) patients requiring norepinephrine initiation or increase at the onset of SE-BSI versus patients not requiring vasopressors (37%; n = 22), concomitant arterial lactate levels reached 2.8 (1.9-5.8) versus 1.5 (1.3-2.2) mmol/l (P <0.01), whereas the mean blood pressure was 49 (42-54) versus 61 (56-65) mm Hg (P = 0.01) and the mortality was 46% (n = 17) vs 14% (n = 3) at day 28 (P = 0.01), respectively. Regarding antibiotics, the susceptibility rates toward linezolid and vancomycin were 71% (n = 41/58) and 100% (n = 54/54), respectively. At the time of SE-BSI, all but one patient had a central venous access device. CONCLUSION This work highlights SE-BSIs as a cause of septic shock, mostly in immunocompromised ICU patients, with increasing concerns about resistance to antibiotics and central line management.
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Affiliation(s)
- Julien Demiselle
- Université de Strasbourg (UNISTRA), Faculté de Médecine, Hôpitaux Universitaires de Strasbourg, Service de Médecine Intensive-Réanimation, Nouvel Hôpital Civil, 1 place de l'hôpital, 67000 Strasbourg, France; INSERM, UMR_S1260, Regenerative Nanomedicine (RNM), CRBS, Centre de Recherche en Biomédecine de Strasbourg, Université de Strasbourg, 1 rue Eugène Boeckel, 67000 Strasbourg, France
| | - Pierre Meyer
- Service d'Anesthésie-Réanimation, Nouvel Hôpital Civil, Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, 67000 Strasbourg, France
| | - Thierry Lavigne
- Hygiène Hospitalière et Médecine Préventive, Pôle de Santé Publique, Hôpital Civil, Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, 67000 Strasbourg, France
| | - Julian Kaurin
- Université de Strasbourg (UNISTRA), Faculté de Médecine, Hôpitaux Universitaires de Strasbourg, Service de Médecine Intensive-Réanimation, Nouvel Hôpital Civil, 1 place de l'hôpital, 67000 Strasbourg, France
| | - Hamid Merdji
- Université de Strasbourg (UNISTRA), Faculté de Médecine, Hôpitaux Universitaires de Strasbourg, Service de Médecine Intensive-Réanimation, Nouvel Hôpital Civil, 1 place de l'hôpital, 67000 Strasbourg, France; INSERM, UMR_S1260, Regenerative Nanomedicine (RNM), CRBS, Centre de Recherche en Biomédecine de Strasbourg, Université de Strasbourg, 1 rue Eugène Boeckel, 67000 Strasbourg, France
| | - Maleka Schenck
- Université de Strasbourg (UNISTRA), Faculté de Médecine, Hôpitaux Universitaires de Strasbourg, Service de Médecine Intensive-Réanimation, Hôpital de Hautepierre, 1 avenue Molière, 67200 Strasbourg, France
| | - Antoine Studer
- Université de Strasbourg (UNISTRA), Faculté de Médecine, Hôpitaux Universitaires de Strasbourg, Service de Médecine Intensive-Réanimation, Nouvel Hôpital Civil, 1 place de l'hôpital, 67000 Strasbourg, France
| | - Ralf Janssen-Langenstein
- Université de Strasbourg (UNISTRA), Faculté de Médecine, Hôpitaux Universitaires de Strasbourg, Service de Médecine Intensive-Réanimation, Hôpital de Hautepierre, 1 avenue Molière, 67200 Strasbourg, France
| | - Julie Helms
- Université de Strasbourg (UNISTRA), Faculté de Médecine, Hôpitaux Universitaires de Strasbourg, Service de Médecine Intensive-Réanimation, Nouvel Hôpital Civil, 1 place de l'hôpital, 67000 Strasbourg, France; INSERM, UMR_S1260, Regenerative Nanomedicine (RNM), CRBS, Centre de Recherche en Biomédecine de Strasbourg, Université de Strasbourg, 1 rue Eugène Boeckel, 67000 Strasbourg, France
| | - Baptiste Hoellinger
- Université de Strasbourg (UNISTRA), Faculté de Médecine, Hôpitaux Universitaires de Strasbourg, Service de Maladies Infectieuses et Tropicales, Nouvel Hôpital Civil, 1 place de l'hôpital, 67000 Strasbourg, France
| | - Vincent Castelain
- Université de Strasbourg (UNISTRA), Faculté de Médecine, Hôpitaux Universitaires de Strasbourg, Service de Médecine Intensive-Réanimation, Hôpital de Hautepierre, 1 avenue Molière, 67200 Strasbourg, France
| | - Antoine Grillon
- UR7290, Virulence bactérienne précoce, Fédération de Médecine Translationnelle de Strasbourg, Université de Strasbourg, Institut de bactériologie, 3 rue Koeberlé, 67000, Strasbourg, France
| | - Francis Schneider
- Université de Strasbourg (UNISTRA), Faculté de Médecine, Hôpitaux Universitaires de Strasbourg, Service de Médecine Intensive-Réanimation, Hôpital de Hautepierre, 1 avenue Molière, 67200 Strasbourg, France
| | - Ferhat Meziani
- Université de Strasbourg (UNISTRA), Faculté de Médecine, Hôpitaux Universitaires de Strasbourg, Service de Médecine Intensive-Réanimation, Nouvel Hôpital Civil, 1 place de l'hôpital, 67000 Strasbourg, France; INSERM, UMR_S1260, Regenerative Nanomedicine (RNM), CRBS, Centre de Recherche en Biomédecine de Strasbourg, Université de Strasbourg, 1 rue Eugène Boeckel, 67000 Strasbourg, France
| | - Raphaël Clere-Jehl
- Université de Strasbourg (UNISTRA), Faculté de Médecine, Hôpitaux Universitaires de Strasbourg, Service de Médecine Intensive-Réanimation, Hôpital de Hautepierre, 1 avenue Molière, 67200 Strasbourg, France; Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM (French National Institute of Health and Medical Research), UMR_S1109, Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, 1 place de l'hôpital, 67000 Strasbourg, France.
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20
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Badrane H, Cheng S, Dupont CL, Hao B, Driscoll E, Morder K, Liu G, Newbrough A, Fleres G, Kaul D, Espinoza JL, Clancy CJ, Nguyen MH. Genotypic diversity and unrecognized antifungal resistance among populations of Candida glabrata from positive blood cultures. Nat Commun 2023; 14:5918. [PMID: 37739935 PMCID: PMC10516878 DOI: 10.1038/s41467-023-41509-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 09/07/2023] [Indexed: 09/24/2023] Open
Abstract
The longstanding model is that most bloodstream infections (BSIs) are caused by a single organism. We perform whole genome sequencing of five-to-ten strains from blood culture (BC) bottles in each of ten patients with Candida glabrata BSI. We demonstrate that BCs contain mixed populations of clonal but genetically diverse strains. Genetically distinct strains from two patients exhibit phenotypes that are potentially important during BSIs, including differences in susceptibility to antifungal agents and phagocytosis. In both patients, the clinical microbiology lab recovered a fluconazole-susceptible index strain, but we identify mixed fluconazole-susceptible and -resistant populations. Diversity in drug susceptibility is likely clinically relevant, as fluconazole-resistant strains were subsequently recovered by the clinical laboratory during persistent or relapsing infections. In one patient, unrecognized respiration-deficient small colony variants are fluconazole-resistant and significantly attenuated for virulence during murine candidiasis. Our data suggest a population-based model of C. glabrata genotypic and phenotypic diversity during BSIs.
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Affiliation(s)
| | | | | | - Binghua Hao
- University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | - Guojun Liu
- University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | - Drishti Kaul
- J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | | | - Cornelius J Clancy
- University of Pittsburgh, Pittsburgh, PA, USA
- VA Pittsburgh Healthcare System, Pittsburgh, PA, USA
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21
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Zhou W, Fleming E, Legendre G, Roux L, Latreille J, Gendronneau G, Forestier S, Oh J. Skin microbiome attributes associate with biophysical skin ageing. Exp Dermatol 2023; 32:1546-1556. [PMID: 37350224 PMCID: PMC11128091 DOI: 10.1111/exd.14863] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/07/2023] [Accepted: 06/10/2023] [Indexed: 06/24/2023]
Abstract
Two major arms of skin ageing are changes in the skin's biophysical conditions and alterations in the skin microbiome. This work partitioned both arms to study their interaction in detail. Leveraging the resolution provided by shotgun metagenomics, we explored how skin microbial species, strains and gene content interact with the biophysical traits of the skin during ageing. With a dataset well-controlled for confounding factors, we found that skin biophysical traits, especially the collagen diffusion coefficient, are associated with the composition and the functional potential of the skin microbiome, including the abundance of bacterial strains found in nosocomial infections and the abundance of antibiotic resistance genes. Our findings reveal important associations between skin biophysical features and ageing-related changes in the skin microbiome and generate testable hypotheses for the mechanisms of such associations.
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Affiliation(s)
- Wei Zhou
- The Jackson Laboratory, Farmington CT, USA
| | | | | | - Lauriane Roux
- Biology and Clinical Department, Chanel F&B, Pantin, France
| | | | | | | | - Julia Oh
- The Jackson Laboratory, Farmington CT, USA
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22
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Kim G, Lee Y, You JS, Hwang W, Hwang J, Kim HY, Kim J, Jo A, Park IH, Ali M, Kim J, Shin JS, Kwon HK, Kim HJ, Yoon SS. A Moonlighting Protein Secreted by a Nasal Microbiome Fortifies the Innate Host Defense Against Bacterial and Viral Infections. Immune Netw 2023; 23:e31. [PMID: 37670809 PMCID: PMC10475824 DOI: 10.4110/in.2023.23.e31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/06/2023] [Accepted: 06/19/2023] [Indexed: 09/07/2023] Open
Abstract
Evidence suggests that the human respiratory tract, as with the gastrointestinal tract, has evolved to its current state in association with commensal microbes. However, little is known about how the airway microbiome affects the development of airway immune system. Here, we uncover a previously unidentified mode of interaction between host airway immunity and a unique strain (AIT01) of Staphylococcus epidermidis, a predominant species of the nasal microbiome. Intranasal administration of AIT01 increased the population of neutrophils and monocytes in mouse lungs. The recruitment of these immune cells resulted in the protection of the murine host against infection by Pseudomonas aeruginosa, a pathogenic bacterium. Interestingly, an AIT01-secreted protein identified as GAPDH, a well-known bacterial moonlighting protein, mediated this protective effect. Intranasal delivery of the purified GAPDH conferred significant resistance against other Gram-negative pathogens (Klebsiella pneumoniae and Acinetobacter baumannii) and influenza A virus. Our findings demonstrate the potential of a native nasal microbe and its secretory protein to enhance innate immune defense against airway infections. These results offer a promising preventive measure, particularly relevant in the context of global pandemics.
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Affiliation(s)
- Gwanghee Kim
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea
- Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
- BioMe Inc., Seoul 02455, Korea
| | - Yoojin Lee
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea
- Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jin Sun You
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea
- Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Wontae Hwang
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea
- Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jeewon Hwang
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea
- Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Hwa Young Kim
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea
- Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jieun Kim
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Ara Jo
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul 03080, Korea
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul 03080, Korea
| | - In ho Park
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Mohammed Ali
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea
- Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jongsun Kim
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jeon-Soo Shin
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea
- Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Ho-Keun Kwon
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea
- Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Hyun Jik Kim
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul 03080, Korea
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul 03080, Korea
| | - Sang Sun Yoon
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea
- Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
- BioMe Inc., Seoul 02455, Korea
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea
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23
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Williams P, Hill P, Bonev B, Chan WC. Quorum-sensing, intra- and inter-species competition in the staphylococci. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001381. [PMID: 37578829 PMCID: PMC10482373 DOI: 10.1099/mic.0.001381] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/31/2023] [Indexed: 08/15/2023]
Abstract
In Gram-positive bacteria such as Staphylococcus aureus and the coagulase-negative staphylococci (CoNS), the accessory gene regulator (agr) is a highly conserved but polymorphic quorum-sensing system involved in colonization, virulence and biofilm development. Signalling via agr depends on the interaction of an autoinducing peptide (AIP) with AgrC, a transmembrane sensor kinase that, once phosphorylated activates the response regulator AgrA. This in turn autoinduces AIP biosynthesis and drives target gene expression directly via AgrA or via the post-transcriptional regulator, RNAIII. In this review we describe the molecular mechanisms underlying the agr-mediated generation of, and response to, AIPs and the molecular basis of AIP-dependent activation and inhibition of AgrC. How the environment impacts on agr functionality is considered and the consequences of agr dysfunction for infection explored. We also discuss the concept of AIP-driven competitive interference between S. aureus and the CoNS and its anti-infective potential.
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Affiliation(s)
- Paul Williams
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Phil Hill
- School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Boyan Bonev
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Weng C. Chan
- School of Pharmacy, Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
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24
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Joglekar P, Conlan S, Lee-Lin SQ, Deming C, Kashaf SS, Kong HH, Segre JA. Integrated genomic and functional analyses of human skin-associated Staphylococcus reveals extensive inter- and intra-species diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.22.546190. [PMID: 37503282 PMCID: PMC10370188 DOI: 10.1101/2023.06.22.546190] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Human skin is stably colonized by a distinct microbiota that functions together with epidermal cells to maintain a protective physical barrier. Staphylococcus, a prominent genus of the skin microbiota, participates in colonization resistance, tissue repair, and host immune regulation in strain specific manners. To unlock the potential of engineering skin microbial communities, we aim to fully characterize the functional diversity of this genus within the context of the skin environment. We conducted metagenome and pan-genome analyses of isolates obtained from distinct body sites of healthy volunteers, providing a detailed biogeographic depiction of staphylococcal species that colonize our skin. S. epidermidis, S. capitis, and S. hominis were the most abundant species present in all volunteers and were detected at all body sites. Pan-genome analysis of these three species revealed that the genus-core was dominated by central metabolism genes. Species-specific core genes were enriched in host colonization functions. The majority (~68%) of genes were detected only in a fraction of isolate genomes, underscoring the immense strain-specific gene diversity. Conspecific genomes grouped into phylogenetic clades, exhibiting body site preference. Each clade was enriched for distinct gene-sets that are potentially involved in site tropism. Finally, we conducted gene expression studies of select isolates showing variable growth phenotypes in skin-like medium. In vitro expression revealed extensive intra- and inter-species gene expression variation, substantially expanding the functional diversification within each species. Our study provides an important resource for future ecological and translational studies to examine the role of shared and strain-specific staphylococcal genes within the skin environment.
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Affiliation(s)
- Payal Joglekar
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
| | - Shih-Queen Lee-Lin
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
| | - Clay Deming
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
| | - Sara Saheb Kashaf
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
| | | | - Heidi H. Kong
- Cutaneous Microbiome and Inflammation Section, NIAMS, NIH, Bethesda, Maryland, USA
| | - Julia A. Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
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25
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Landemaine L, Da Costa G, Fissier E, Francis C, Morand S, Verbeke J, Michel ML, Briandet R, Sokol H, Gueniche A, Bernard D, Chatel JM, Aguilar L, Langella P, Clavaud C, Richard ML. Staphylococcus epidermidis isolates from atopic or healthy skin have opposite effect on skin cells: potential implication of the AHR pathway modulation. Front Immunol 2023; 14:1098160. [PMID: 37304256 PMCID: PMC10250813 DOI: 10.3389/fimmu.2023.1098160] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 05/04/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction Staphylococcus epidermidis is a commensal bacterium ubiquitously present on human skin. This species is considered as a key member of the healthy skin microbiota, involved in the defense against pathogens, modulating the immune system, and involved in wound repair. Simultaneously, S. epidermidis is the second cause of nosocomial infections and an overgrowth of S. epidermidis has been described in skin disorders such as atopic dermatitis. Diverse isolates of S. epidermidis co-exist on the skin. Elucidating the genetic and phenotypic specificities of these species in skin health and disease is key to better understand their role in various skin conditions. Additionally, the exact mechanisms by which commensals interact with host cells is partially understood. We hypothesized that S. epidermidis isolates identified from different skin origins could play distinct roles on skin differentiation and that these effects could be mediated by the aryl hydrocarbon receptor (AhR) pathway. Methods For this purpose, a library of 12 strains originated from healthy skin (non-hyperseborrheic (NH) and hyperseborrheic (H) skin types) and disease skin (atopic (AD) skin type) was characterized at the genomic and phenotypic levels. Results and discussion Here we showed that strains from atopic lesional skin alter the epidermis structure of a 3D reconstructed skin model whereas strains from NH healthy skin do not. All strains from NH healthy skin induced AhR/OVOL1 path and produced high quantities of indole metabolites in co-culture with NHEK; especially indole-3-aldehyde (IAld) and indole-3-lactic acid (ILA); while AD strains did not induce AhR/OVOL1 path but its inhibitor STAT6 and produced the lowest levels of indoles as compared to the other strains. As a consequence, strains from AD skin altered the differentiation markers FLG and DSG1. The results presented here, on a library of 12 strains, showed that S. epidermidis originated from NH healthy skin and atopic skin have opposite effects on the epidermal cohesion and structure and that these differences could be linked to their capacity to produce metabolites, which in turn could activate AHR pathway. Our results on a specific library of strains provide new insights into how S. epidermidis may interact with the skin to promote health or disease.
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Affiliation(s)
- Leslie Landemaine
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Gregory Da Costa
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
| | - Elsa Fissier
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
| | - Carine Francis
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | | | | | - Marie-Laure Michel
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
| | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Harry Sokol
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
- Sorbonne Université, INSERM UMRS-938, Centre de Recherche Saint-Antoine, Assistance Publique - Hôpitaux de Paris (AP-HP), Paris, France
| | | | | | - Jean-Marc Chatel
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
| | - Luc Aguilar
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Philippe Langella
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
| | - Cecile Clavaud
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Mathias L. Richard
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
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26
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Saheb Kashaf S, Harkins CP, Deming C, Joglekar P, Conlan S, Holmes CJ, Almeida A, Finn RD, Segre JA, Kong HH. Staphylococcal diversity in atopic dermatitis from an individual to a global scale. Cell Host Microbe 2023; 31:578-592.e6. [PMID: 37054678 PMCID: PMC10151067 DOI: 10.1016/j.chom.2023.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/08/2022] [Accepted: 03/10/2023] [Indexed: 04/15/2023]
Abstract
Atopic dermatitis (AD) is a multifactorial, chronic relapsing disease associated with genetic and environmental factors. Among skin microbes, Staphylococcus aureus and Staphylococcus epidermidis are associated with AD, but how genetic variability and staphylococcal strains shape the disease remains unclear. We investigated the skin microbiome of an AD cohort (n = 54) as part of a prospective natural history study using shotgun metagenomic and whole genome sequencing, which we analyzed alongside publicly available data (n = 473). AD status and global geographical regions exhibited associations with strains and genomic loci of S. aureus and S. epidermidis. In addition, antibiotic prescribing patterns and within-household transmission between siblings shaped colonizing strains. Comparative genomics determined that S. aureus AD strains were enriched in virulence factors, whereas S. epidermidis AD strains varied in genes involved in interspecies interactions and metabolism. In both species, staphylococcal interspecies genetic transfer shaped gene content. These findings reflect the staphylococcal genomic diversity and dynamics associated with AD.
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Affiliation(s)
- Sara Saheb Kashaf
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Catriona P Harkins
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Clay Deming
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Payal Joglekar
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cassandra J Holmes
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandre Almeida
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Julia A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Heidi H Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Badrane H, Cheng S, Dupont CL, Hao B, Driscoll E, Morder K, Liu G, Newbrough A, Fleres G, Kaul D, Espinoza JL, Clancy CJ, Nguyen MH. Genotypic diversity and unrecognized antifungal resistance among populations of Candida glabrata from positive blood cultures. RESEARCH SQUARE 2023:rs.3.rs-2706400. [PMID: 37066226 PMCID: PMC10104189 DOI: 10.21203/rs.3.rs-2706400/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The longstanding paradigm is that most bloodstream infections (BSIs) are caused by a single organism. We performed whole genome sequencing of five-to-ten strains from blood culture (BC) bottles in each of ten patients with Candida glabrata BSI. We demonstrated that BCs contained mixed populations of clonal but genetically diverse strains. Genetically distinct strains from two patients exhibited phenotypes that were potentially important during BSIs, including differences in susceptibility to antifungal agents and phagocytosis. In both patients, the clinical microbiology lab recovered a fluconazole-susceptible index strain, but we identified mixed fluconazole-susceptible and â€"resistant populations. Diversity in drug susceptibility was likely clinically relevant, as fluconazole-resistant strains were subsequently recovered by the clinical laboratory during persistent or relapsing infections. In one patient, unrecognized respiration-deficient small colony variants were fluconazole-resistant and significantly attenuated for virulence during murine candidiasis. Our data suggest a new population-based paradigm of C. glabrata genotypic and phenotypic diversity during BSIs.
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Affiliation(s)
| | - Shaoji Cheng
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Binghua Hao
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | | | - Guojun Liu
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | | | | | | | - Cornelius J Clancy
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
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Dinic M, Verpile R, Meng J, Marjanovic J, Burgess JL, Plano L, Hower S, Thaller SR, Banerjee S, Lev-Tov H, Tomic-Canic M, Pastar I. Chronic wound microenvironment mediates selection of biofilm-forming multi drug resistant Staphylococcus epidermidis with capability to impair healing. RESEARCH SQUARE 2023:rs.3.rs-2562300. [PMID: 36824891 PMCID: PMC9949177 DOI: 10.21203/rs.3.rs-2562300/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Venous leg ulcers (VLU) are the most common chronic wounds characterized by bacterial biofilms and perturbed microbiome. Staphylococcus epidermidis is primarily known as skin commensal beneficial for the host, however, some strains can form biofilms and cause infections. By employing shotgun metagenomic sequencing we show that genetic signatures of antimicrobial resistance, adhesion and biofilm formation in VLU isolates correlate with in vitro bacterial traits. We demonstrate that the capability of chronic wound isolates to form biofilms and elicit IL-8 and IL-1β expression in human ex vivo wounds, correlates with the non-healing outcomes in patients with VLU. In contrast, commensal strains were incapable of surviving in the human ex vivo wounds. We show that major fitness traits of S. epidermis from VLU involve genes for resistance to methicillin and mupirocin, while the biofilm formation relied on the minimal number of genetic elements responsible for bacterial binding to fibronectin and fibrinogen. This underscores the importance of the emergence of treatment resistant virulent lineages in patients with non-healing wounds.
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Affiliation(s)
- Miroslav Dinic
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
- Group for Probiotics and Microbiota-Host Interaction, Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Rebecca Verpile
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jingjing Meng
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jelena Marjanovic
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jamie L Burgess
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Lisa Plano
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Suzanne Hower
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Seth R Thaller
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Santanu Banerjee
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Hadar Lev-Tov
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Marjana Tomic-Canic
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Irena Pastar
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
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29
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Smythe P, Wilkinson HN. The Skin Microbiome: Current Landscape and Future Opportunities. Int J Mol Sci 2023; 24:3950. [PMID: 36835363 PMCID: PMC9963692 DOI: 10.3390/ijms24043950] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/11/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023] Open
Abstract
Our skin is the largest organ of the body, serving as an important barrier against the harsh extrinsic environment. Alongside preventing desiccation, chemical damage and hypothermia, this barrier protects the body from invading pathogens through a sophisticated innate immune response and co-adapted consortium of commensal microorganisms, collectively termed the microbiota. These microorganisms inhabit distinct biogeographical regions dictated by skin physiology. Thus, it follows that perturbations to normal skin homeostasis, as occurs with ageing, diabetes and skin disease, can cause microbial dysbiosis and increase infection risk. In this review, we discuss emerging concepts in skin microbiome research, highlighting pertinent links between skin ageing, the microbiome and cutaneous repair. Moreover, we address gaps in current knowledge and highlight key areas requiring further exploration. Future advances in this field could revolutionise the way we treat microbial dysbiosis associated with skin ageing and other pathologies.
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Affiliation(s)
- Paisleigh Smythe
- Centre for Biomedicine, Hull York Medical School, University of Hull, Hull HU6 7RX, UK
- Skin Research Centre, Hull York Medical School, University of York, York YO10 5DD, UK
| | - Holly N. Wilkinson
- Centre for Biomedicine, Hull York Medical School, University of Hull, Hull HU6 7RX, UK
- Skin Research Centre, Hull York Medical School, University of York, York YO10 5DD, UK
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30
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Swaney MH, Nelsen A, Sandstrom S, Kalan LR. Sweat and Sebum Preferences of the Human Skin Microbiota. Microbiol Spectr 2023; 11:e0418022. [PMID: 36602383 PMCID: PMC9927561 DOI: 10.1128/spectrum.04180-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/06/2022] [Indexed: 01/06/2023] Open
Abstract
The microorganisms inhabiting human skin must overcome numerous challenges that typically impede microbial growth, including low pH, osmotic pressure, and low nutrient availability. Yet the skin microbiota thrive on the skin and have adapted to these stressful conditions. The limited nutrients available for microbial use in this unique niche include those from host-derived sweat, sebum, and corneocytes. Here, we have developed physiologically relevant, synthetic skin-like growth media composed of compounds present in sweat and sebum. We find that skin-associated bacterial species exhibit unique growth profiles at different concentrations of artificial sweat and sebum. Most strains evaluated demonstrate a preference for high sweat concentrations, while the sebum preference is highly variable, suggesting that the capacity for sebum utilization may be a driver of the skin microbial community structure. In particular, the prominent skin commensal Staphylococcus epidermidis exhibits the strongest preference for sweat while growing equally well across sebum concentrations. Conversely, the growth of Corynebacterium kefirresidentii, another dominant skin microbiome member, is dependent on increasing concentrations of both sweat and sebum but only when sebum is available, suggesting a lipid requirement of this species. Furthermore, we observe that strains with similar growth profiles in the artificial media cluster by phylum, suggesting that phylogeny is a key factor in sweat and sebum use. Importantly, these findings provide an experimental rationale for why different skin microenvironments harbor distinct microbiome communities. In all, our study further emphasizes the importance of studying microorganisms in an ecologically relevant context, which is critical for our understanding of their physiology, ecology, and function on the skin. IMPORTANCE The human skin microbiome is adapted to survive and thrive in the harsh environment of the skin, which is low in nutrient availability. To study skin microorganisms in a system that mimics the natural skin environment, we developed and tested a physiologically relevant, synthetic skin-like growth medium that is composed of compounds found in the human skin secretions sweat and sebum. We find that most skin-associated bacterial species tested prefer high concentrations of artificial sweat but that artificial sebum concentration preference varies from species to species, suggesting that sebum utilization may be an important contributor to skin microbiome composition. This study demonstrates the utility of a skin-like growth medium, which can be applied to diverse microbiological systems, and underscores the importance of studying microorganisms in an ecologically relevant context.
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Affiliation(s)
- Mary Hannah Swaney
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin, Madison, Wisconsin, USA
| | - Amanda Nelsen
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Shelby Sandstrom
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Lindsay R. Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
- Department of Medicine, Division of Infectious Disease, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
- M. G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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Bromfield JI, Hugenholtz P, Frazer IH, Khosrotehrani K, Chandra J. Targeting Staphylococcus aureus dominated skin dysbiosis in actinic keratosis to prevent the onset of cutaneous squamous cell carcinoma: Outlook for future therapies? Front Oncol 2023; 13:1091379. [PMID: 36816953 PMCID: PMC9933124 DOI: 10.3389/fonc.2023.1091379] [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: 11/08/2022] [Accepted: 01/17/2023] [Indexed: 02/05/2023] Open
Abstract
Cutaneous squamous cell carcinoma (cSCC) and its premalignant precursor, actinic keratosis (AK), present a global health burden that is continuously increasing despite extensive efforts to promote sun safety. Chronic UV exposure is a recognized risk factor for the development of AK and cSCC. However, increasing evidence suggests that AK and cSCC is also associated with skin microbiome dysbiosis and, in particular, an overabundance of the bacterium Staphylococcus aureus (S. aureus). Studies have shown that S. aureus-derived toxins can contribute to DNA damage and lead to chronic upregulation of proinflammatory cytokines that may affect carcinogenesis. Eradication of S. aureus from AK lesions and restoration of a healthy microbiome may therefore represent a therapeutic opportunity to alter disease progression. Whilst antibiotics can reduce the S. aureus load, antibiotic resistant S. aureus pose an increasing global public health threat. The use of specific topically delivered probiotics has been used experimentally in other skin conditions to restore eubiosis, and could therefore also present a non-invasive treatment approach to decrease S. aureus colonization and restore a healthy skin microbiome on AK lesions. This article reviews mechanisms by which S. aureus may contribute to cutaneous carcinogenesis, and discusses hypotheses and theories that explore the therapeutic potential of specific bacterial species which compete with S. aureus in an attempt to restore microbial eubiosis in skin.
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Affiliation(s)
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Ian Hector Frazer
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, Australia
| | - Kiarash Khosrotehrani
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, Australia
- Department of Dermatology, Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Janin Chandra
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, Australia
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32
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Staphylococcus epidermidis and its dual lifestyle in skin health and infection. Nat Rev Microbiol 2023; 21:97-111. [PMID: 36042296 PMCID: PMC9903335 DOI: 10.1038/s41579-022-00780-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2022] [Indexed: 01/20/2023]
Abstract
The coagulase-negative bacterium Staphylococcus epidermidis is a member of the human skin microbiota. S. epidermidis is not merely a passive resident on skin but actively primes the cutaneous immune response, maintains skin homeostasis and prevents opportunistic pathogens from causing disease via colonization resistance. However, it is now appreciated that S. epidermidis and its interactions with the host exist on a spectrum of potential pathogenicity derived from its high strain-level heterogeneity. S. epidermidis is the most common cause of implant-associated infections and is a canonical opportunistic biofilm former. Additional emerging evidence suggests that some strains of S. epidermidis may contribute to the pathogenesis of common skin diseases. Here, we highlight new developments in our understanding of S. epidermidis strain diversity, skin colonization dynamics and its multifaceted interactions with the host and other members of the skin microbiota.
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33
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Ma S, Li H. Statistical and Computational Methods for Microbial Strain Analysis. Methods Mol Biol 2023; 2629:231-245. [PMID: 36929080 DOI: 10.1007/978-1-0716-2986-4_11] [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] [Indexed: 03/17/2023]
Abstract
Microbial strains are interpreted as a lineage derived from a recent ancestor that have not experienced "too many" recombination events and can be successfully retrieved with culture-independent techniques using metagenomic sequencing. Such a strain variability has been increasingly shown to display additional phenotypic heterogeneities that affect host health, such as virulence, transmissibility, and antibiotics resistance. New statistical and computational methods have recently been developed to track the strains in samples based on shotgun metagenomics data either based on reference genome sequences or Metagenome-assembled genomes (MAGs). In this paper, we review some recent statistical methods for strain identifications based on frequency counts at a set of single nucleotide variants (SNVs) within a set of single-copy marker genes. These methods differ in terms of whether reference genome sequences are needed, how SNVs are called, what methods of deconvolution are used and whether the methods can be applied to multiple samples. We conclude our review with areas that require further research.
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Affiliation(s)
- Siyuan Ma
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Hongzhe Li
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA.
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34
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Murray GGR, Chaguza C. Zooming into the structure of the microbiome. Nat Rev Microbiol 2023; 21:5. [PMID: 36451022 DOI: 10.1038/s41579-022-00834-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
- Gemma G R Murray
- Wellcome Sanger Institute, Cambridge, UK.,University College London, London, UK
| | - Chrispin Chaguza
- Wellcome Sanger Institute, Cambridge, UK. .,University College London, London, UK. .,Yale School of Public Health, New Haven, CT, USA.
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35
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Cheng S, Fleres G, Chen L, Liu G, Hao B, Newbrough A, Driscoll E, Shields RK, Squires KM, Chu TY, Kreiswirth BN, Nguyen MH, Clancy CJ. Within-Host Genotypic and Phenotypic Diversity of Contemporaneous Carbapenem-Resistant Klebsiella pneumoniae from Blood Cultures of Patients with Bacteremia. mBio 2022; 13:e0290622. [PMID: 36445082 PMCID: PMC9765435 DOI: 10.1128/mbio.02906-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 12/02/2022] Open
Abstract
It is unknown whether bacterial bloodstream infections (BSIs) are commonly caused by single organisms or mixed microbial populations. We hypothesized that contemporaneous carbapenem-resistant Klebsiella pneumoniae (CRKP) strains from blood cultures of individual patients are genetically and phenotypically distinct. We determined short-read whole-genome sequences of 10 sequence type 258 (ST258) CRKP strains from blood cultures in each of 6 patients (Illumina HiSeq). Strains clustered by patient by core genome and pan-genome phylogeny. In 5 patients, there was within-host strain diversity by gene mutations, presence/absence of antibiotic resistance or virulence genes, and/or plasmid content. Accessory gene phylogeny revealed strain diversity in all 6 patients. Strains from 3 patients underwent long-read sequencing for genome completion (Oxford Nanopore) and phenotypic testing. Genetically distinct strains within individuals exhibited significant differences in carbapenem and other antibiotic responses, capsular polysaccharide (CPS) production, mucoviscosity, and/or serum killing. In 2 patients, strains differed significantly in virulence during mouse BSIs. Genetic or phenotypic diversity was not observed among strains recovered from blood culture bottles seeded with index strains from the 3 patients and incubated in vitro at 37°C. In conclusion, we identified genotypic and phenotypic variant ST258 CRKP strains from blood cultures of individual patients with BSIs, which were not detected by the clinical laboratory or in seeded blood cultures. The data suggest a new paradigm of CRKP population diversity during BSIs, at least in some patients. If validated for BSIs caused by other bacteria, within-host microbial diversity may have implications for medical, microbiology, and infection prevention practices and for understanding antibiotic resistance and pathogenesis. IMPORTANCE The long-standing paradigm for pathogenesis of bacteremia is that, in most cases, a single organism passes through a bottleneck and establishes itself in the bloodstream (single-organism hypothesis). In keeping with this paradigm, standard practice in processing positive microbiologic cultures is to test single bacterial strains from morphologically distinct colonies. This study is the first genome-wide analysis of within-host diversity of Klebsiella pneumoniae strains recovered from individual patients with bloodstream infections (BSIs). Our finding that positive blood cultures comprised genetically and phenotypically heterogeneous carbapenem-resistant K. pneumoniae strains challenges the single-organism hypothesis and suggests that at least some BSIs are caused by mixed bacterial populations that are unrecognized by the clinical laboratory. The data support a model of pathogenesis in which pressures in vivo select for strain variants with particular antibiotic resistance or virulence attributes and raise questions about laboratory protocols and treatment decisions directed against single strains.
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Affiliation(s)
- Shaoji Cheng
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Liang Chen
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
| | - Guojun Liu
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Binghua Hao
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | | | | | - Ryan K. Shields
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | | | - Ting-yu Chu
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
| | - Barry N. Kreiswirth
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
| | - M. Hong Nguyen
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Cornelius J. Clancy
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
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36
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Spoto M, Riera Puma JP, Fleming E, Guan C, Ondouah Nzutchi Y, Kim D, Oh J. Large-Scale CRISPRi and Transcriptomics of Staphylococcus epidermidis Identify Genetic Factors Implicated in Lifestyle Versatility. mBio 2022; 13:e0263222. [PMID: 36409086 PMCID: PMC9765180 DOI: 10.1128/mbio.02632-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022] Open
Abstract
Staphylococcus epidermidis is a ubiquitous human commensal skin bacterium that is also one of the most prevalent nosocomial pathogens. The genetic factors underlying this remarkable lifestyle plasticity are incompletely understood, mainly due to the difficulties of genetic manipulation, precluding high-throughput functional profiling of this species. To probe the versatility of S. epidermidis to survive across a diversity of environmental conditions, we developed a large-scale CRISPR interference (CRISPRi) screen complemented by transcriptional profiling (RNA sequencing) across 24 diverse conditions and piloted a droplet-based CRISPRi approach to enhance throughput and sensitivity. We identified putative essential genes, importantly revealing amino acid metabolism as crucial to survival across diverse environments, and demonstrated the importance of trace metal uptake for survival under multiple stress conditions. We identified pathways significantly enriched and repressed across our range of stress and nutrient-limited conditions, demonstrating the considerable plasticity of S. epidermidis in responding to environmental stressors. Additionally, we postulate a mechanism by which nitrogen metabolism is linked to lifestyle versatility in response to hyperosmotic challenges, such as those encountered on human skin. Finally, we examined the survival of S. epidermidis under acid stress and hypothesize a role for cell wall modification as a vital component of the survival response under acidic conditions. Taken together, this study integrates large-scale CRISPRi and transcriptomics data across multiple environments to provide insights into a keystone member of the human skin microbiome. Our results additionally provide a valuable benchmarking analysis for CRISPRi screens and are a rich resource for other staphylococcal researchers. IMPORTANCE Staphylococcus epidermidis is a bacteria that broadly inhabits healthy human skin, yet it is also a common cause of skin infections and bloodstream infections associated with implanted medical devices. Because human skin has many different types of S. epidermidis, each containing different genes, our goal is to determine how these different genes allow S. epidermidis to switch from healthy growth in the skin to being an infectious pathogen. Understanding this switch is critical to developing new strategies to prevent and treat S. epidermidis infections.
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Affiliation(s)
- Michelle Spoto
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
- The University of Connecticut Health Center, Farmington, Connecticut, USA
| | | | - Elizabeth Fleming
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Changhui Guan
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | | | - Dean Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Julia Oh
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
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37
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Engineering a "detect and destroy" skin probiotic to combat methicillin-resistant Staphylococcus aureus. PLoS One 2022; 17:e0276795. [PMID: 36520793 PMCID: PMC9754240 DOI: 10.1371/journal.pone.0276795] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/13/2022] [Indexed: 12/23/2022] Open
Abstract
The prevalence and virulence of pathogens such as methicillin-resistant Staphylococcus (S.) aureus (MRSA), which can cause recurrent skin infections, are of significant clinical concern. Prolonged antibiotic exposure to treat or decolonize S. aureus contributes to development of antibiotic resistance, as well as depletion of the microbiome, and its numerous beneficial functions. We hypothesized an engineered skin probiotic with the ability to selectively deliver antimicrobials only in the presence of the target organism could provide local bioremediation of pathogen colonization. We constructed a biosensing S. epidermidis capable of detecting the presence of S. aureus quorum sensing autoinducer peptide and producing lysostaphin in response. Here, we demonstrate in vitro activity of this biosensor and present and discuss challenges to deployment of this and other engineered topical skin probiotics.
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38
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Mitterer JA, Frank BJH, Gardete-Hartmann S, Panzenboeck LF, Simon S, Krepler P, Hofstaetter JG. Changes of the microbiological spectrum and antibiotic resistance pattern in postoperative spinal implant infections with multiple culture-positive revision surgeries. Spine J 2022; 22:1934-1943. [PMID: 35853535 DOI: 10.1016/j.spinee.2022.07.086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/27/2022] [Accepted: 07/11/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND CONTEXT In severe cases of postoperative spinal implant infections (PSII) multiple revision surgeries may be needed. Little is known if changes in the microbiological spectrum and antibiotic resistance pattern occur between revision surgeries. PURPOSE Analysis of the microbiological spectrum and antibiotic resistance pattern in patients with multiple revision surgeries for the treatment of PSII STUDY DESIGN: Retrospective database analysis. PATIENT SAMPLE Between 01/2011 and 12/2018, 103 patients underwent 248 revision surgeries for the treatment of PSII. Twenty patients (19.4%) who underwent multiple revision surgeries for PSII were included in this study. OUTCOME MEASURES Microbiological spectrum, antibiotic resistance pattern. METHODS A retrospective analysis of a prospectively maintained single center spine infection database was performed with a minimum follow-up of 3 years. Overall, 20 patients (six male/14 female) underwent 82 revisions for PSII (median 3; range 2-12). There were 55 of 82 (67.1%) procedures with a positive microbiological result. Microbiological analysis was performed on tissue and implant sonication fluid. Changes in microbial spectrum and antibiotic resistance pattern between surgeries were evaluated using Chi-Square and Fisher's exact test. RESULTS In total, 74 microorganisms (83.3% gram-positive; 10.8% gram-negative) were identified. The most common microorganisms were Staphylococcus epidermidis (18.9%) and Cutibacterium acnes (18.9%). All S. epidermidis identified were methicillin-resistant (MRSE). Overall, there were 15 of 55 (27.3%) polymicrobial infections. The microbiological spectrum changed in 57.1% (20/35) between the revision stages over the entire PSII period. In 42.9% (15/35) the microorganism persisted between the revision surgeries stages. Overall, changes of the antibiotic resistance pattern were seen in 17.4% (8/46) of the detected microorganisms, comparing index revision and all subsequent re-revisions. Moreover, higher resistance rates were found for moxifloxacin and for ciprofloxacin at first re-revision surgery compared with index PSII revision. Resistances against vancomycin increased from 4.5% (1/23) at index PSII revision to 7.7% (2/26) at first re-revision surgery. CONCLUSIONS Changes of the microbiological spectrum and the resistance pattern can occur in patients with severe PSII who require multiple revision surgeries. It is important to consider these findings in the antimicrobial treatment of PSII. The microbiological analysis of intraoperative tissue samples should be performed at every revision procedure for PSII.
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Affiliation(s)
- Jennyfer A Mitterer
- Michael Ogon Laboratory for Orthopaedic Research, Orthopaedic Hospital Speising, Vienna, Austria
| | - Bernhard J H Frank
- Michael Ogon Laboratory for Orthopaedic Research, Orthopaedic Hospital Speising, Vienna, Austria; Second Department, Orthopaedic Hospital Speising, Vienna, Austria
| | - Susana Gardete-Hartmann
- Michael Ogon Laboratory for Orthopaedic Research, Orthopaedic Hospital Speising, Vienna, Austria
| | - Lukas F Panzenboeck
- Michael Ogon Laboratory for Orthopaedic Research, Orthopaedic Hospital Speising, Vienna, Austria; Third Department, Orthopaedic Hospital Speising, Vienna, Austria
| | - Sebastian Simon
- Michael Ogon Laboratory for Orthopaedic Research, Orthopaedic Hospital Speising, Vienna, Austria; Second Department, Orthopaedic Hospital Speising, Vienna, Austria
| | - Petra Krepler
- Michael Ogon Laboratory for Orthopaedic Research, Orthopaedic Hospital Speising, Vienna, Austria; Third Department, Orthopaedic Hospital Speising, Vienna, Austria
| | - Jochen G Hofstaetter
- Michael Ogon Laboratory for Orthopaedic Research, Orthopaedic Hospital Speising, Vienna, Austria; Second Department, Orthopaedic Hospital Speising, Vienna, Austria.
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39
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Caldwell R, Zhou W, Oh J. Strains to go: interactions of the skin microbiome beyond its species. Curr Opin Microbiol 2022; 70:102222. [PMID: 36242896 PMCID: PMC9701184 DOI: 10.1016/j.mib.2022.102222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/07/2022] [Accepted: 09/14/2022] [Indexed: 01/25/2023]
Abstract
An extraordinary biodiversity of bacteria, fungi, viruses, and even small multicellular eukaryota inhabit the human skin. Genomic innovations have accelerated characterization of this biodiversity both at a species as well as the subspecies, or strain level, which further imparts a tremendous genetic diversity to an individual's skin microbiome. In turn, these advances portend significant species- and strain-specificity in the skin microbiome's functional impact on cutaneous immunity, barrier integrity, aging, and other skin physiologic processes. Future advances in defining strain diversity, spatial distribution, and metabolic diversity for major skin species will be foundational for understanding the microbiome's essentiality to the skin ecosystem and for designing topical therapeutics that leverage or target the skin microbiome.
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Affiliation(s)
- Ryan Caldwell
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - Wei Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - Julia Oh
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States.
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40
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Brás S, França A. Transcriptome Mining to Identify Molecular Markers for the Diagnosis of Staphylococcus epidermidis Bloodstream Infections. Antibiotics (Basel) 2022; 11:1596. [PMID: 36421239 PMCID: PMC9687011 DOI: 10.3390/antibiotics11111596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/08/2022] [Accepted: 11/09/2022] [Indexed: 12/01/2023] Open
Abstract
Bloodstream infections caused by Staphylococcus epidermidis are often misdiagnosed since no diagnostic marker found so far can unequivocally discriminate "true" infection from sample contamination. While attempts have been made to find genomic and/or phenotypic differences between invasive and commensal isolates, possible changes in the transcriptome of these isolates under in vivo-mimicking conditions have not been investigated. Herein, we characterized the transcriptome, by RNA sequencing, of three clinical and three commensal isolates after 2 h of exposure to whole human blood. Bioinformatics analysis was used to rank the genes with the highest potential to distinguish invasive from commensal isolates and among the ten genes identified as candidates, the gene SERP2441 showed the highest potential. A collection of 56 clinical and commensal isolates was then used to validate, by quantitative PCR, the discriminative power of the selected genes. A significant variation was observed among isolates, and the discriminative power of the selected genes was lost, undermining their potential use as markers. Nevertheless, future studies should include an RNA sequencing characterization of a larger collection of isolates, as well as a wider range of conditions to increase the chances of finding further candidate markers for the diagnosis of bloodstream infections caused by S. epidermidis.
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Affiliation(s)
- Susana Brás
- LIBRO—Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Angela França
- LIBRO—Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS–Associate Laboratory, Braga and Guimarães, Portugal
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41
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Rodríguez‐Pastor R, Shafran Y, Knossow N, Gutiérrez R, Harrus S, Zaman L, Lenski RE, Barrick JE, Hawlena H. A road map for in vivo evolution experiments with blood-borne parasitic microbes. Mol Ecol Resour 2022; 22:2843-2859. [PMID: 35599628 PMCID: PMC9796859 DOI: 10.1111/1755-0998.13649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 03/14/2022] [Accepted: 05/13/2022] [Indexed: 01/07/2023]
Abstract
Laboratory experiments in which blood-borne parasitic microbes evolve in their animal hosts offer an opportunity to study parasite evolution and adaptation in real time and under natural settings. The main challenge of these experiments is to establish a protocol that is both practical over multiple passages and accurately reflects natural transmission scenarios and mechanisms. We provide a guide to the steps that should be considered when designing such a protocol, and we demonstrate its use via a case study. We highlight the importance of choosing suitable ancestral genotypes, treatments, number of replicates per treatment, types of negative controls, dependent variables, covariates, and the timing of checkpoints for the experimental design. We also recommend specific preliminary experiments to determine effective methods for parasite quantification, transmission, and preservation. Although these methodological considerations are technical, they also often have conceptual implications. To this end, we encourage other researchers to design and conduct in vivo evolution experiments with blood-borne parasitic microbes, despite the challenges that the work entails.
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Affiliation(s)
- Ruth Rodríguez‐Pastor
- Jacob Blaustein Center for Scientific Cooperation, The Jacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevMidreshet Ben‐GurionIsrael
| | - Yarden Shafran
- Mitrani Department of Desert Ecology, Swiss Institute for Dryland Environmental and Energy Research, The Jacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevMidreshet Ben‐GurionIsrael
| | - Nadav Knossow
- Mitrani Department of Desert Ecology, Swiss Institute for Dryland Environmental and Energy Research, The Jacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevMidreshet Ben‐GurionIsrael
| | - Ricardo Gutiérrez
- Koret School of Veterinary Medicine, Faculty of Agricultural, Nutritional and Environmental SciencesThe Hebrew University of JerusalemRehovotIsrael
| | - Shimon Harrus
- Koret School of Veterinary Medicine, Faculty of Agricultural, Nutritional and Environmental SciencesThe Hebrew University of JerusalemRehovotIsrael
| | - Luis Zaman
- Department of Ecology and Evolutionary Biology, The Center for the Study of Complex Systems (CSCS)University of MichiganAnn ArborMichiganUSA
| | - Richard E. Lenski
- Department of Microbiology and Molecular GeneticsMichigan State UniversityEast LansingMichiganUSA
| | - Jeffrey E. Barrick
- Department of Molecular BiosciencesThe University of Texas AustinAustinTexasUSA
| | - Hadas Hawlena
- Mitrani Department of Desert Ecology, Swiss Institute for Dryland Environmental and Energy Research, The Jacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevMidreshet Ben‐GurionIsrael
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42
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Lieberman TD. Detecting bacterial adaptation within individual microbiomes. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210243. [PMID: 35989602 PMCID: PMC9393564 DOI: 10.1098/rstb.2021.0243] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/17/2022] [Indexed: 12/11/2022] Open
Abstract
The human microbiome harbours a large capacity for within-person adaptive mutations. Commensal bacterial strains can stably colonize a person for decades, and billions of mutations are generated daily within each person's microbiome. Adaptive mutations emerging during health might be driven by selective forces that vary across individuals, vary within an individual, or are completely novel to the human population. Mutations emerging within individual microbiomes might impact the immune system, the metabolism of nutrients or drugs, and the stability of the community to perturbations. Despite this potential, relatively little attention has been paid to the possibility of adaptive evolution within complex human-associated microbiomes. This review discusses the promise of studying within-microbiome adaptation, the conceptual and technical limitations that may have contributed to an underappreciation of adaptive de novo mutations occurring within microbiomes to date, and methods for detecting recent adaptive evolution. This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.
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Affiliation(s)
- Tami D. Lieberman
- Department of Civil and Environmental Engineering, Institute for Medical Engineering and Science,Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute, Cambridge, MA, USA
- Ragon Institute, Cambridge, MA, USA
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43
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Larson PJ, Zhou W, Santiago A, Driscoll S, Fleming E, Voigt AY, Chun OK, Grady JJ, Kuchel GA, Robison JT, Oh J. Associations of the skin, oral and gut microbiome with aging, frailty and infection risk reservoirs in older adults. NATURE AGING 2022; 2:941-955. [PMID: 36398033 PMCID: PMC9667708 DOI: 10.1038/s43587-022-00287-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/30/2022] [Indexed: 01/25/2023]
Abstract
Older adults represent a vulnerable population with elevated risk for numerous morbidities. To explore the association of the microbiome with aging and age-related susceptibilities including frailty and infectious disease risk, we conducted a longitudinal study of the skin, oral, and gut microbiota in 47 community- or skilled nursing facility-dwelling older adults vs. younger adults. We found that microbiome changes were not associated with chronological age so much as frailty: we identified prominent changes in microbiome features associated with susceptibility to pathogen colonization and disease risk, including diversity, stability, heterogeneity, and biogeographic determinism, which were moreover associated with a loss of Cutibacterium (C.) acnes in the skin microbiome. Strikingly, the skin microbiota were also the primary reservoir for antimicrobial resistance, clinically important pathobionts, and nosocomial strains, suggesting a potential role particularly for the skin microbiome in disease risk and dissemination of multidrug resistant pathogens.
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Affiliation(s)
- Peter J. Larson
- UCONN Health (University of Connecticut), Farmington, CT
- The Jackson Laboratory, Farmington, CT
| | - Wei Zhou
- The Jackson Laboratory, Farmington, CT
| | - Alba Santiago
- UCONN Health (University of Connecticut), Farmington, CT
| | - Sarah Driscoll
- UCONN Health (University of Connecticut), Farmington, CT
| | | | | | | | - James J. Grady
- UCONN Health (University of Connecticut), Farmington, CT
| | | | | | - Julia Oh
- The Jackson Laboratory, Farmington, CT
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44
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Voigt AY, Emiola A, Johnson JS, Fleming ES, Nguyen H, Zhou W, Tsai KY, Fink C, Oh J. Skin Microbiome Variation with Cancer Progression in Human Cutaneous Squamous Cell Carcinoma. J Invest Dermatol 2022; 142:2773-2782.e16. [PMID: 35390349 PMCID: PMC9509417 DOI: 10.1016/j.jid.2022.03.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 12/13/2022]
Abstract
The skin microbiome plays a critical role in skin homeostasis and disorders. UVR is the major cause of nonmelanoma skin cancer, but other risk factors, including immune suppression, chronic inflammation, and antibiotic usage, suggest the microbiome as an additional, unexplored risk factor and potential disease biomarker. The overarching goal was to study the skin microbiome in squamous cell carcinoma (SCC) and premalignant actinic keratosis compared with that in healthy skin to identify skin cancer‒associated changes in the skin microbiome. We performed a high-resolution analysis of shotgun metagenomes of actinic keratosis and SCC in healthy skin, revealing the microbial community shifts specific to actinic keratosis and SCC. Most prominently, the relative abundance of pathobiont Staphylococcus aureus was increased at the expense of commensal Cutibacterium acnes in SCC compared with that in healthy skin, and enrichment of functional pathways in SCC reflected this shift. Notably, C. acnes associated with lesional versus healthy skin differed at the strain level, suggesting the specific functional changes associated with its depletion in SCC. Our study revealed a transitional microbial dysbiosis from healthy skin to actinic keratosis to SCC, supporting further investigation of the skin microbiome for use as a biomarker and providing hypotheses for studies investigating how these microbes might influence skin cancer progression.
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Affiliation(s)
- Anita Y Voigt
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Akintunde Emiola
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Jethro S Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA; Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | | | - Hoan Nguyen
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Wei Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Kenneth Y Tsai
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA; Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Christine Fink
- Department of Dermatology, Venereology, and Allergology, University Medical Center, Ruprecht-Karl University of Heidelberg, Heidelberg, Germany
| | - Julia Oh
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.
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45
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Ahle CM, Stødkilde K, Poehlein A, Bömeke M, Streit WR, Wenck H, Reuter JH, Hüpeden J, Brüggemann H. Interference and co-existence of staphylococci and Cutibacterium acnes within the healthy human skin microbiome. Commun Biol 2022; 5:923. [PMID: 36071129 PMCID: PMC9452508 DOI: 10.1038/s42003-022-03897-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/25/2022] [Indexed: 12/12/2022] Open
Abstract
Human skin is populated by trillions of microbes collectively called the skin microbiome. Staphylococcus epidermidis and Cutibacterium acnes are among the most abundant members of this ecosystem, with described roles in skin health and disease. However, knowledge regarding the health beneficial effects of these ubiquitous skin residents is still limited. Here, we profiled the staphylococcal and C. acnes landscape across four different skin sites of 30 individuals (120 skin samples) using amplicon-based next-generation sequencing. Relative abundance profiles obtained indicated the existence of phylotype-specific co-existence and exclusion scenarios. Co-culture experiments with 557 staphylococcal strains identified 30 strains exhibiting anti-C. acnes activities. Notably, staphylococcal strains were found to selectively exclude acne-associated C. acnes and co-exist with healthy skin-associated phylotypes, through regulation of the antimicrobial activity. Overall, these findings highlight the importance of skin-resident staphylococci and suggest that selective microbial interference is a contributor to healthy skin homeostasis. The dynamic interaction between the common resident skin microbes Staphylococcus epidermidis and Cutibacterium acnes is uncovered, showing that S. epidermidis can selectively exclude acne-associated C. acnes strains from the human skin.
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Affiliation(s)
- Charlotte Marie Ahle
- Beiersdorf AG, Research & Development, Front End Innovation, 20245, Hamburg, Germany. .,Department of Microbiology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany.
| | | | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, 37073, Göttingen, Germany
| | - Mechthild Bömeke
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, 37073, Göttingen, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, 22609, Hamburg, Germany
| | - Horst Wenck
- Beiersdorf AG, Research & Development, Front End Innovation, 20245, Hamburg, Germany
| | - Jörn Hendrik Reuter
- Beiersdorf AG, Research & Development, Front End Innovation, 20245, Hamburg, Germany
| | - Jennifer Hüpeden
- Beiersdorf AG, Research & Development, Front End Innovation, 20245, Hamburg, Germany
| | - Holger Brüggemann
- Department of Biomedicine, Aarhus University, 8000, Aarhus, Denmark.
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46
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Keystone taxa: an emerging area of microbiome research for future disease diagnosis and health safety in human. Microbiol Res 2022. [DOI: 10.1016/j.micres.2022.127203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Lee AJ, Reiter T, Doing G, Oh J, Hogan DA, Greene CS. Using genome-wide expression compendia to study microorganisms. Comput Struct Biotechnol J 2022; 20:4315-4324. [PMID: 36016717 PMCID: PMC9396250 DOI: 10.1016/j.csbj.2022.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 08/07/2022] [Accepted: 08/07/2022] [Indexed: 11/30/2022] Open
Abstract
A gene expression compendium is a heterogeneous collection of gene expression experiments assembled from data collected for diverse purposes. The widely varied experimental conditions and genetic backgrounds across samples creates a tremendous opportunity for gaining a systems level understanding of the transcriptional responses that influence phenotypes. Variety in experimental design is particularly important for studying microbes, where the transcriptional responses integrate many signals and demonstrate plasticity across strains including response to what nutrients are available and what microbes are present. Advances in high-throughput measurement technology have made it feasible to construct compendia for many microbes. In this review we discuss how these compendia are constructed and analyzed to reveal transcriptional patterns.
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Affiliation(s)
- Alexandra J. Lee
- Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA, USA
| | - Taylor Reiter
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Denver, CO, USA
| | - Georgia Doing
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Julia Oh
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth, Hanover, NH, USA
| | - Casey S. Greene
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Denver, CO, USA
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48
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Ide K, Saeki T, Arikawa K, Yoda T, Endoh T, Matsuhashi A, Takeyama H, Hosokawa M. Exploring strain diversity of dominant human skin bacterial species using single-cell genome sequencing. Front Microbiol 2022; 13:955404. [PMID: 35992707 PMCID: PMC9389210 DOI: 10.3389/fmicb.2022.955404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 07/06/2022] [Indexed: 12/03/2022] Open
Abstract
To understand the role of the skin commensal bacterial community in skin health and the spread of pathogens, it is crucial to identify genetic differences in the bacterial strains corresponding to human individuals. A culture-independent genomics approach is an effective tool for obtaining massive high-quality bacterial genomes. Here we present a single-cell genome sequencing to obtain comprehensive whole-genome sequences of uncultured skin bacteria from skin swabs. We recovered 281 high-quality (HQ) and 244 medium-quality single-amplified genomes (SAGs) of multiple skin bacterial species from eight individuals, including cohabiting group. Single-cell sequencing outperformed in the genome recovery from the same skin swabs, showing 10-fold non-redundant strain genomes compared to the shotgun metagenomic sequencing and binning approach. We then focused on the abundant skin bacteria and identified intra-species diversity, especially in 47 Moraxella osloensis derived HQ SAGs, characterizing the strain-level heterogeneity at mobile genetic element profiles, including plasmids and prophages. Even between the cohabiting individual hosts, they have unique skin bacterial strains in the same species, which shows microdiversity in each host. Genetic and functional differences between skin bacterial strains are predictive of in vivo competition to adapt bacterial genome to utilize the sparse nutrients available on the skin or produce molecules that inhibit the colonization of other microbes or alter their behavior. Thus, single-cell sequencing provides a large number of genomes of higher resolution and quality than conventional metagenomic analysis and helps explore the skin commensal bacteria at the strain level, linking taxonomic and functional information.
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Affiliation(s)
- Keigo Ide
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- bitBiome, Inc., Tokyo, Japan
| | | | | | | | | | | | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Tokyo, Japan
| | - Masahito Hosokawa
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- bitBiome, Inc., Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Tokyo, Japan
- *Correspondence: Masahito Hosokawa,
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49
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Abstract
Staphylococcus hominis is frequently isolated from human skin, and we hypothesize that it may protect the cutaneous barrier from opportunistic pathogens. We determined that S. hominis makes six unique autoinducing peptide (AIP) signals that inhibit the major virulence factor accessory gene regulator (agr) quorum sensing system of Staphylococcus aureus. We solved and confirmed the structures of three novel AIP signals in conditioned medium by mass spectrometry and then validated synthetic AIP activity against all S. aureus agr classes. Synthetic AIPs also inhibited the conserved agr system in a related species, Staphylococcus epidermidis. We determined the distribution of S. hominis agr types on healthy human skin and found S. hominis agr-I and agr-II were highly represented across subjects. Further, synthetic AIP-II was protective in vivo against S. aureus-associated dermonecrotic or epicutaneous injury. Together, these findings demonstrate that a ubiquitous colonizer of human skin has a fundamentally protective role against opportunistic damage. IMPORTANCE Human skin is home to a variety of commensal bacteria, including many species of coagulase-negative staphylococci (CoNS). While it is well established that the microbiota as a whole maintains skin homeostasis and excludes pathogens (i.e., colonization resistance), relatively little is known about the unique contributions of individual CoNS species to these interactions. Staphylococcus hominis is the second most frequently isolated CoNS from healthy skin, and there is emerging evidence to suggest that it may play an important role in excluding pathogens, including Staphylococcus aureus, from colonizing or infecting the skin. Here, we identified that S. hominis makes 6 unique peptide inhibitors of the S. aureus global virulence factor regulation system (agr). Additionally, we found that one of these peptides can prevent topical or necrotic S. aureus skin injury in a mouse model. Our results demonstrate a specific and broadly protective role for this ubiquitous, yet underappreciated skin commensal.
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50
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Teichmann P, Both A, Wolz C, Hornef MW, Rohde H, Yazdi AS, Burian M. The Staphylococcus epidermidis Transcriptional Profile During Carriage. Front Microbiol 2022; 13:896311. [PMID: 35558117 PMCID: PMC9087046 DOI: 10.3389/fmicb.2022.896311] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/08/2022] [Indexed: 11/29/2022] Open
Abstract
The virulence factors of the opportunistic human pathogen Staphylococcus epidermidis have been a main subject of research. In contrast, limited information is available on the mechanisms that allow the bacterium to accommodate to the conditions during carriage, a prerequisite for pathogenicity. Here, we tested the hypothesis that the adaptation of S. epidermidis at different anatomical sites is reflected by differential gene regulation. We used qPCR to profile S. epidermidis gene expression in vivo in nose and skin swabs of 11 healthy individuals. Despite some heterogeneity between individuals, significant site-specific differences were detected. For example, expression of the S. epidermidis regulator sarA was found similarly in the nose and on the skin of all individuals. Also, genes encoding colonization and immune evasion factors (sdrG, capC, and dltA), as well as the sphingomyelinase encoding gene sph, were expressed at both anatomical sites. In contrast, expression of the global regulator agr was almost inactive in the nose but readily present on the skin. A similar site-specific expression profile was also identified for the putative chitinase-encoding SE0760. In contrast, expression of the autolysine-encoding gene sceD and the wall teichoic acid (WTA) biosynthesis gene tagB were more pronounced in the nose as compared to the skin. In summary, our analysis identifies site-specific gene expression patterns of S. epidermidis during colonization. In addition, the observed expression signature was significantly different from growth in vitro. Interestingly, the strong transcription of sphingomyelinase together with the low expression of genes encoding the tricarboxylic acid cycle (TCA) suggests very good nutrient supply in both anatomical niches, even on the skin where one might have suspected a rather lower nutrient supply compared to the nose.
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Affiliation(s)
- Pascâl Teichmann
- Department of Dermatology and Allergology, RWTH University Hospital Aachen, Aachen, Germany
| | - Anna Both
- Institute of Medical Microbiology, Virology and Hygiene, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Christiane Wolz
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Mathias W Hornef
- Institute of Medical Microbiology, RWTH University Hospital Aachen, Aachen, Germany
| | - Holger Rohde
- Institute of Medical Microbiology, Virology and Hygiene, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Amir S Yazdi
- Department of Dermatology and Allergology, RWTH University Hospital Aachen, Aachen, Germany
| | - Marc Burian
- Department of Dermatology and Allergology, RWTH University Hospital Aachen, Aachen, Germany
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