scholarly journals Comparative genomic and pan-genomic characteristion of Staphylococcus epidermidis from different sources unveils the molecular basis and potential biomarkers of pathogenic strains

2021 ◽  
Author(s):  
Shudan Lin ◽  
Bianjin Sun ◽  
Xinrui Shi ◽  
Yi Xu ◽  
Yunfeng Gu ◽  
...  
Keyword(s):  
Staphylococcus Epidermidis ◽  
Biofilm Formation ◽  
Ocular Trauma ◽  
Bloodstream Infections ◽  
Common Species ◽  
Comparative Genomic ◽  
Whole Genomes ◽  
Genomic Analyses ◽  
Different Sources ◽  
Potential Biomarkers

Coagulase-negative Staphylococcus (CoNS) is the most common pathogen causing traumatic endophthalmitis, Staphylococcus epidermidis is the most common species which colonizes human skin, eye surfaces and nasal cavity and is the main cause of nosocomial infection, specially foreign body-related bloodstream infections (FBR-BSIs). Although some studies have reported the genome characteristics of S. epidermidis, a comprehensive understanding of its pathogenicity and the genome of ocular trauma-sourced strains is still lacking. In this study, we sequenced, analyzed and reported the whole genomes of 11 ocular trauma-sourced samples of S. epidermis that caused traumatic endophthalmitis. By integrating publicly available genomes, we obtained a total of 187 S. epidermis samples from healthy and diseased eyes, skin, respiratory tract and blood. Combined with pangenome, phylogenetic and comparative genomic analyses, our study supported that S. epidermidis, regardless of niche source, exhibits two founder lineages with different pathogenicities. Moreover, we identified potential biomarkers associated with the virulence of S. epidermis, namely, essD, uhpt, sdrF, sdrG, fbe and icaABCDR. The essD and uhpt genes have high homology with esaD and hpt in Staphylococcus aureus, showing that the genomes of S. epidermidis and S. aureus may have communicated during evolution, while the sdrF, sdrG, fbe, and icaABCDR genes are related to biofilm formation. Compared to S. epidermidis from blood sources, ocular-sourced strains causing intraocular infection had no direct relationship with biofilm formation. In conclusion, this study not only provided additional data resources for studies on S. epidermidis is, but also improved understanding of the evolution and pathogenicity of different source strains.

scholarly journals Comparative Genomic and Pan-Genomic Characterization of Staphylococcus epidermidis From Different Sources Unveils the Molecular Basis and Potential Biomarkers of Pathogenic Strains

2021 ◽  
Vol 12 ◽  
Author(s):  
Shudan Lin ◽  
Bianjin Sun ◽  
Xinrui Shi ◽  
Yi Xu ◽  
Yunfeng Gu ◽  
...  
Keyword(s):  
Staphylococcus Epidermidis ◽  
Biofilm Formation ◽  
Ocular Trauma ◽  
Bloodstream Infections ◽  
Common Species ◽  
Comparative Genomic ◽  
Whole Genomes ◽  
Genomic Characterization ◽  
Different Sources ◽  
Potential Biomarkers

Coagulase-negative Staphylococcus (CoNS) is the most common pathogen causing traumatic endophthalmitis. Among which, Staphylococcus epidermidis is the most common species that colonizes human skin, eye surfaces, and nasal cavity. It is also the main cause of nosocomial infection, specially foreign body-related bloodstream infections (FBR-BSIs). Although some studies have reported the genome characteristics of S. epidermidis, the genome of ocular trauma-sourced S. epidermidis strain and a comprehensive understanding of its pathogenicity are still lacking. Our study sequenced, analyzed, and reported the whole genomes of 11 ocular trauma-sourced samples of S. epidermidis that caused traumatic endophthalmitis. By integrating publicly available genomes, we obtained a total of 187 S. epidermidis samples from healthy and diseased eyes, skin, respiratory tract, and blood. Combined with pan-genome, phylogenetic, and comparative genomic analyses, our study showed that S. epidermidis, regardless of niche source, exhibits two founder lineages with different pathogenicity. Moreover, we identified several potential biomarkers associated with the virulence of S. epidermidis, including essD, uhpt, sdrF, sdrG, fbe, and icaABCDR. EssD and uhpt have high homology with esaD and hpt in Staphylococcus aureus, showing that the genomes of S. epidermidis and S. aureus may have communicated during evolution. SdrF, sdrG, fbe, and icaABCDR are related to biofilm formation. Compared to S. epidermidis from blood sources, ocular-sourced strains causing intraocular infection had no direct relationship with biofilm formation. In conclusion, this study provided additional data resources for studies on S. epidermidis and improved our understanding of the evolution and pathogenicity among strains of different sources.

scholarly journals Molecular comparison of bacterial isolates from blood with strains colonizing pharynx and intestine in immunocompromised patients with sepsis

2003 ◽  
Vol 52 (6) ◽  
pp. 527-530 ◽  
Author(s):  
Koichi Murono ◽  
Yoshiki Hirano ◽  
Shin Koyano ◽  
Kiminari Ito ◽  
Kenji Fujieda
Keyword(s):  
Staphylococcus Epidermidis ◽  
Intestinal Tract ◽  
Bloodstream Infections ◽  
Haematopoietic Stem Cell ◽  
Immunocompromised Patients ◽  
Viridans Streptococci ◽  
Blood Isolate ◽  
Genomic Analyses ◽  
Molecular Comparison ◽  
Culture Positive

Most causative organisms of sepsis in immunocompromised patients are the same species as those that colonize their own nasopharynx or intestinal tract. To determine whether the strains recovered from blood originate mainly from patients’ own flora, isolates from blood and throat and/or stool were investigated by genomic analyses. Surveillance cultures of throat and stool were taken prospectively from cancer patients being treated with intensive chemotherapy followed by haematopoietic stem-cell transplantation. In those cases of sepsis in which the isolate from blood was the same species as that from the throat and/or stool, the genomic profiles of the isolates were compared by PFGE. Ten cases of blood culture-positive sepsis were documented in six of 14 subjects during a 2 year period; isolates of Pseudomonas aeruginosa, Staphylococcus epidermidis, Enterococcus sp., viridans streptococci and Fusobacterium sp. were recovered from blood. In five of seven cases in which the blood isolate was the same species as that from the throat or stool, the genotypes of the isolates from both sites were identical. In the majority of immunocompromised patients, the causative organisms of bloodstream infections originated mainly from their own flora.

The phenotypic and genotypic characteristics of biofilm formation and SCCmec typing of Staphylococcus epidermidis isolated from different sources

Gene Reports ◽  
2019 ◽  
Vol 17 ◽  
pp. 100444 ◽  
Author(s):  
Nima Mohammadzadeh ◽  
Fathollah Teymouri ◽  
Shabnam Razavi ◽  
Meysam Hasannejad-Bibalan ◽  
Abed Zahedi Bialvaei ◽  
...  
Keyword(s):  
Staphylococcus Epidermidis ◽  
Biofilm Formation ◽  
Sccmec Typing ◽  
Genotypic Characteristics ◽  
Different Sources

scholarly journals Small Molecules Produced by Commensal Staphylococcus epidermidis Disrupt Formation of Biofilms by Staphylococcus aureus

2019 ◽  
Vol 86 (5) ◽  
Author(s):  
Thaís Glatthardt ◽  
Juliana Curityba de Mello Campos ◽  
Raiane Cardoso Chamon ◽  
Thiago Freitas de Sá Coimbra ◽  
Giulia de Almeida Rocha ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Staphylococcus Epidermidis ◽  
Biofilm Formation ◽  
Bloodstream Infections ◽  
Proteinase K ◽  
Antibiofilm Activity ◽  
Skin Microbiome ◽  
Chronic Infections ◽  
Content Type ◽  
Treatment And Prevention

ABSTRACT The microbiota influences host health through several mechanisms, including protecting it from pathogen colonization. Staphylococcus epidermidis is one of the most frequently found species in the skin microbiota, and its presence can limit the development of pathogens such as Staphylococcus aureus. S. aureus causes diverse types of infections ranging from skin abscesses to bloodstream infections. Given the increasing prevalence of S. aureus drug-resistant strains, it is imperative to search for new strategies for treatment and prevention. Thus, we investigated the activity of molecules produced by a commensal S. epidermidis isolate against S. aureus biofilms. We showed that molecules present in S. epidermidis cell-free conditioned media (CFCM) caused a significant reduction in biofilm formation in most S. aureus clinical isolates, including all 4 agr types and agr-defective strains, without any impact on growth. S. epidermidis molecules also disrupted established S. aureus biofilms and reduced the antibiotic concentration required to eliminate them. Preliminary characterization of the active compound showed that its activity is resistant to heat, protease inhibitors, trypsin, proteinase K, and sodium periodate treatments, suggesting that it is not proteinaceous. RNA sequencing revealed that S. epidermidis-secreted molecules modulate the expression of hundreds of S. aureus genes, some of which are associated with biofilm production. Biofilm formation is one of the main virulence factors of S. aureus and has been associated with chronic infections and antimicrobial resistance. Therefore, molecules that can counteract this virulence factor may be promising alternatives as novel therapeutic agents to control S. aureus infections. IMPORTANCE S. aureus is a leading agent of infections worldwide, and its main virulence characteristic is the ability to produce biofilms on surfaces such as medical devices. Biofilms are known to confer increased resistance to antimicrobials and to the host immune responses, requiring aggressive antibiotic treatment and removal of the infected surface. Here, we investigated a new source of antibiofilm compounds, the skin microbiome. Specifically, we found that a commensal strain of S. epidermidis produces molecules with antibiofilm activity, leading to a significant decrease of S. aureus biofilm formation and to a reduction of previously established biofilms. The molecules potentiated the activity of antibiotics and affected the expression of hundreds of S. aureus genes, including those associated with biofilm formation. Our research highlights the search for compounds that can aid us in the fight against S. aureus infections.

scholarly journals Inhibitory effects of ultrasound irradiation on Staphylococcus epidermidis biofilm

2021 ◽  
Author(s):  
Harumi Koibuchi ◽  
Yasutomo Fujii ◽  
Yusuke Sato’o ◽  
Takashi Mochizuki ◽  
Toshiyuki Yamada ◽  
...  
Keyword(s):  
Staphylococcus Epidermidis ◽  
Biofilm Formation ◽  
Bloodstream Infections ◽  
Ultrasound Irradiation ◽  
Bottom Surface ◽  
Bacterial Biofilms ◽  
Inhibitory Effects ◽  
Lower Intensity ◽  
Remarkable Effect ◽  
Continuous Waves

Abstract Purpose We aimed to investigate whether low-intensity continuous and pulsed wave ultrasound (US) irradiation can inhibit the formation of Staphylococcus epidermidis biofilms, for potential application in the treatment of catheter-related bloodstream infections (CRBSI). Methods S. epidermidis biofilms that formed on the bottom surfaces of 6-well plates were irradiated on the bottom surface using the sound cell incubator system for different intervals of time. Results US irradiation with continuous waves for 24 h notably inhibited biofilm formation (p < 0.01), but the same US irradiation for 12 h had no remarkable effect. Further, double US irradiation with pulsed waves for 20 min inhibited biofilm formation by 33.6%, nearly two-fold more than single US irradiation, which reduced it by 17.9%. Conclusion US irradiation of a lower intensity (ISATA = 6–29 mW/cm2) than used in a previous study and lower than recommended by the Food and Drug Administration shows potential for preventing CRBSI caused by bacterial biofilms.

scholarly journals Involvement of the Iron-Regulated Loci hts and fhuC in Biofilm Formation and Survival of Staphylococcus epidermidis within the Host

2022 ◽  
Author(s):  
Fernando Oliveira ◽  
Tânia Lima ◽  
Alexandra Correia ◽  
Ana Margarida Silva ◽  
Cristina Soares ◽  
...  
Keyword(s):  
Staphylococcus Epidermidis ◽  
Biofilm Formation ◽  
Bloodstream Infections ◽  
Central Line ◽  
Nosocomial Pathogens ◽  
Content Type ◽  
Iron Restriction

Staphylococcus epidermidis is one of the most important nosocomial pathogens and a major cause of central line-associated bloodstream infections. Once in the bloodstream, this bacterium must surpass severe iron restriction in order to survive and establish infection.

scholarly journals Fluid Flow Induces Biofilm Formation in Staphylococcus epidermidis Polysaccharide Intracellular Adhesin-Positive Clinical Isolates

2012 ◽  
Vol 78 (16) ◽  
pp. 5890-5896 ◽  
Author(s):  
Westbrook M. Weaver ◽  
Vladana Milisavljevic ◽  
Jeff F. Miller ◽  
Dino Di Carlo
Keyword(s):  
Fluid Flow ◽  
Staphylococcus Epidermidis ◽  
Biofilm Formation ◽  
Hospital Costs ◽  
Bloodstream Infections ◽  
Clinical Isolates ◽  
Content Type ◽  
Biofilm Structure

ABSTRACTStaphylococcus epidermidisis a common cause of catheter-related bloodstream infections, resulting in significant morbidity and mortality and increased hospital costs. The ability to form biofilms plays a crucial role in pathogenesis; however, not all clinical isolates form biofilms under normalin vitroconditions. Strains containing theicaoperon can display significant phenotypic variation with respect to polysaccharide intracellular adhesin (PIA)-based biofilm formation, including the induction of biofilms upon environmental stress. Using a parallel microfluidic approach to investigate flow as an environmental signal forS. epidermidisbiofilm formation, we demonstrate that fluid shear alone induces PIA-positive biofilms of certain clinical isolates and influences biofilm structure. These findings suggest an important role of the catheter microenvironment, particularly fluid flow, in the establishment ofS. epidermidisinfections by PIA-dependent biofilm formation.

scholarly journals The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Josué Barrera-Redondo ◽  
Guillermo Sánchez-de la Vega ◽  
Jonás A. Aguirre-Liguori ◽  
Gabriela Castellanos-Morales ◽  
Yocelyn T. Gutiérrez-Guerrero ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Population Level ◽  
Growth Hormones ◽  
Comparative Genomic ◽  
Structural Variants ◽  
Closely Related Species ◽  
Level Data ◽  
Genomic Analyses ◽  
Genotype By Sequencing ◽  
Regulation Of Growth

AbstractDespite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study Cucurbita domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of C. argyrosperma across Mexico. We also assembled the first high-quality wild Cucurbita genome. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We found evidence of gene flow between the domesticated and wild subspecies, which likely alleviated the effects of the domestication bottleneck. We uncovered candidate domestication genes that are involved in the regulation of growth hormones, plant defense mechanisms, seed development, and germination. The presence of shared selected alleles with the closely related species Cucurbita moschata suggests domestication-related introgression between both taxa.

Complete chloroplast genomes of Leptodermis scabrida complex: comparative genomic analyses and phylogenetic relationships

Gene ◽  
2021 ◽  
pp. 145715
Author(s):  
Ying Zhang ◽  
Zhengfeng Wang ◽  
Yanan Guo ◽  
Sheng Chen ◽  
Xianyi Xu ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Comparative Genomic ◽  
Chloroplast Genomes ◽  
Genomic Analyses

scholarly journals Motility activity, slime production, biofilm formation and genetic typing by ERIC-PCR for Pseudomonas aeruginosa strains isolated from bovine and other sources (human and environment)

2014 ◽  
Vol 17 (2) ◽  
pp. 321-329 ◽  
Author(s):  
K. Wolska ◽  
P. Szweda ◽  
K. Lada ◽  
E. Rytel ◽  
K. Gucwa ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Bovine Mastitis ◽  
Twitching Motility ◽  
Phenotypic Properties ◽  
Biofilm Production ◽  
Abiotic Surfaces ◽  
Hospital Patients ◽  
Relationship Of ◽  
Initial Biofilm ◽  
Different Sources

AbstractThe molecular-typing strategy, ERIC-PCR was used in an attempt to determine the genomic relationship of 28 P. aeruginosa strains isolated from faeces of healthy bovine, bovine mastitis and from faeces of hospital patients as well as from environment. ERIC-PCR fingerprinting revealed large molecular differentiation within this group of isolates. Twenty two out of 28 strains tested generated unique patterns of DNA bands and only three genotypes consisted of two isolates each were identified. We also tested the P. aeruginosa isolates for their ability to form a biofilm on abiotic surfaces including polyvinylchloride and polystyrene. Different biofilm-forming abilities were demonstrated among strains; however, most of them (64.3%) showed moderate-biofilm forming ability. The strains with increased swimming and twitching motility displayed elevated biofilm formation. However, a negative correlation was found between slime and initial biofilm production. On the basis of the results obtained, we suggest that there are no major differences in phenotypic properties between P. aeruginosa strains isolated from different sources

Sign in / Sign up

Export Citation Format

Share Document