scholarly journals Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Niels A. Zondervan ◽  
Vitor A. P. Martins dos Santos ◽  
Maria Suarez-Diez ◽  
Edoardo Saccenti
Keyword(s):  
Necrotizing Fasciitis ◽  
Streptococcus Pyogenes ◽  
Large Scale ◽  
Protein Domain ◽  
Zoonotic Potential ◽  
Biological Processes ◽  
Skin Infections ◽  
Genomic Information ◽  
Host Tropism ◽  
Life Threatening

Abstract Background Staphylococcus and Streptococcus species can cause many different diseases, ranging from mild skin infections to life-threatening necrotizing fasciitis. Both genera consist of commensal species that colonize the skin and nose of humans and animals, and of which some can display a pathogenic phenotype. Results We compared 235 Staphylococcus and 315 Streptococcus genomes based on their protein domain content. We show the relationships between protein persistence and essentiality by integrating essentiality predictions from two metabolic models and essentiality measurements from six large-scale transposon mutagenesis experiments. We identified clusters of strains within species based on proteins associated to similar biological processes. We built Random Forest classifiers that predicted the zoonotic potential. Furthermore, we identified shared attributes between of Staphylococcus aureus and Streptococcus pyogenes that allow them to cause necrotizing fasciitis. Conclusions Differences observed in clustering of strains based on functional groups of proteins correlate with phenotypes such as host tropism, capability to infect multiple hosts and drug resistance. Our method provides a solid basis towards large-scale prediction of phenotypes based on genomic information.

Skin and Soft Tissue Infections

2015 ◽  
Author(s):  
Daniel J. Pallin
Keyword(s):  
Soft Tissue ◽  
Necrotizing Fasciitis ◽  
Bacterial Infections ◽  
Methicillin Resistant Staphylococcus Aureus ◽  
Skin Infections ◽  
Soft Tissue Infections ◽  
Protective Mechanisms ◽  
Contact Precautions ◽  
Life Threatening ◽  
Plantar Warts

The skin is the largest organ of the human body, and has diverse functions including protection from infection, temperature regulation, sensation, and immunologic and hormonal functions. Skin infections occur when the skin’s protective mechanisms fail. Some infections may be life-threatening (eg, necrotizing fasciitis) or may require the patient to be placed on contact precautions; thus, the initial goals of assessment of patients with skin and soft tissue infections are to assess the patient’s stability and to determine whether precautions are necessary to protect others. This review covers the pathophysiology, stabilization and assessment, diagnosis and treatment, and disposition and outcomes for a variety of skin and soft tissue infections. Figures show an algorithm for treatment of bacterial infections of the skin, and photographs of  various infections including necrotizing fasciitis, cellulitis, an abscess caused by methicillin-resistant Staphylococcus aureus, a furuncle, a carbuncle, nonbullous and bullous impetigo, echythma, folliculitis, anthrax lesion, tinea corporis, condyloma acuminatum, and plantar warts. Tables list cellulitis treatment with particular exposures, the dermatophytoses, and yeast infections of skin and mucous membranes. This review contains 16 highly rendered figures, 3 tables, and 32 references.

scholarly journals Transcriptomic profiling of Streptococcus pyogenes M1T1 strain in a mouse model of necrotizing fasciitis

2019 ◽  
Author(s):  
Yujiro Hirose ◽  
Masaya Yamaguchi ◽  
Daisuke Okuzaki ◽  
Daisuke Motooka ◽  
Hiroshi Hamamoto ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mouse Model ◽  
Necrotizing Fasciitis ◽  
Streptococcus Pyogenes ◽  
Treatment Strategies ◽  
Rna Seq ◽  
Novel Treatment ◽  
Genes Encoding ◽  
Life Threatening ◽  
Novel Treatment Strategies

AbstractStreptococcus pyogenes is a major cause of necrotizing fasciitis, a life-threatening subcutaneous soft-tissue infection. At the host infection site, the local environment and interaction between host and bacteria affect bacterial gene-expression profiles, but the S. pyogenes gene-expression pattern in necrotizing fasciitis remains unknown. In this study, we used a mouse model of necrotizing fasciitis and performed RNA-sequencing (RNA-seq) analysis of S. pyogenes M1T1 strain 5448 by using infected hindlimbs obtained at 24, 48, and 96 h post-infection. The RNA-seq analysis identified 483 bacterial genes whose expression was consistently altered in the infected hindlimbs as compared to their expression under in vitro conditions. The consistently enriched genes during infection included 306 genes encoding molecules involved in virulence, carbohydrate utilization, amino acid metabolism, trace-metal transport and vacuolar ATPase transport system. Surprisingly, drastic upregulation of 3 genes, encoding streptolysin S precursor (sagA), cysteine protease (speB), and secreted DNase (spd), was noted in the mouse model of necrotizing fasciitis (log2 fold-change values: >6.0, >9.4, and >7.1, respectively). Conversely, the consistently downregulated genes included 177 genes, containing genes associated with oxidative-stress response and cell division. These results suggest that S. pyogenes in necrotizing fasciitis changes its metabolism, decreases cell proliferation, and upregulates the expression of major toxins. Our findings could provide critical information for developing novel treatment strategies and vaccines for necrotizing fasciitis.Author summaryNecrotizing fasciitis, a life-threatening subcutaneous soft-tissue infection, principally caused by a Streptococcus pyogenes. At infection sites in hosts, bacterial pathogens are exposed to drastically changing environmental conditions and alter global gene expression patterns for survival and pathogenesis. However, there is no previous report about transcriptomic profiling of S. pyogenes in the necrotizing fasciitis. Here, we conducted comprehensive gene-expression analyses of S. pyogenes in the mouse model of necrotizing fasciitis at three distinct time points during infection. Our results indicated that S. pyogenes drastically upregulates the expression of virulence-associated genes and shifts metabolic-pathway usage during infection. The high-level expressions in particular of toxins, such as cytolysins, proteases, and nucleases, were observed at infection sites. In addition, the consistently enriched genes identified here included genes for metabolism of arginine and histidine, and carbohydrate uptake and utilization. Conversely, the genes associated with oxidative-stress response and cell division were consistently downregulated in the mouse model of necrotizing fasciitis. These data will provide useful information necessary for establishing novel treatment strategies (166 words).

scholarly journals PhyRepID: a comparative phylogenomics approach for large-scale quantification of protein repeat evolution

2020 ◽  
Author(s):  
I.A.E.M. van Belzen ◽  
E. S. Deutekom ◽  
B. Snel
Keyword(s):  
Neural Development ◽  
Protein Function ◽  
Large Scale ◽  
Repeat Unit ◽  
Protein Domain ◽  
Biological Processes ◽  
Vertebrate Species ◽  
Score Distribution ◽  
Structural Domains ◽  
Fast Evolution

AbstractProtein repeats consisting of domains or motifs are involved in key biological processes such as neural development, host-pathogen interactions, and speciation. Expansion and contraction of these repeats can strongly impact protein function as was shown for KNL1 and PRDM9. However, these known cases could only be identified manually and were previously incorrectly reported as conserved in large-scale analyses, because signatures of repeat evolution are difficult to resolve automatically.We developed PhyRepID to compare protein domain repeat evolution and analysed 4939 groups of orthologous proteins (OGs) from 14 vertebrate species. Our main contributions are 1) detecting a wide scope of repeats consisting of Pfam structural domains and motifs, 2) improving sensitivity and precision of repeat unit detection through optimization for the OGs, 3) using phylogenetic analysis to detect evolution within repeat regions. From these phylogenetic signals, we derived a “protein repeat duplication” (PRD) score that quantifies evolution in repeat regions and thereby enables large-scale comparison of protein families. Zinc finger repeats show remarkably fast evolution, comprising 25 of 100 fastest evolving proteins in our dataset, whilst cooperatively-folding domain repeats like beta-propellers are mostly conserved. Motif repeats have a similar PRD score distribution as domain repeats and also show a large diversity in evolutionary rates. A ranking based on the PRD score reflects previous manual observations of both highly conserved (CDC20) and rapidly evolving repeats (KNL1, PRDM9) and proposes novel candidates (e.g. AHNAK, PRX, SPATA31) showing previously undescribed rapid repeat evolution. PhyRepID is available on https://github.com/ivanbelzen/PhyRepID/.

scholarly journals Massive necrotizing fasciitis: a life threatening entity

2019 ◽  
Vol 2019 (11) ◽  
Author(s):  
Ramon Vilallonga ◽  
Alejandro Mazarro ◽  
María Rita Rodríguez-Luna ◽  
Enric Caubet ◽  
José Manuel Fort ◽  
...  
Keyword(s):  
Risk Factors ◽  
Necrotizing Fasciitis ◽  
Colorectal Resection ◽  
Clinical Suspicion ◽  
Skin Infections ◽  
Surgical Exploration ◽  
Life Threatening ◽  
Patient’S Outcome ◽  
Reconstructive Plastic Surgery ◽  
Reconstructive Plastic

Abstract Necrotizing fasciitis (NF) is a complicated soft tissue infection frequently associated with severe sepsis if an early medical and surgical treatment is not performed. We report two postoperative cases of severe NF after oophorectomy and colorectal resection. Because of the similarity with more benign skin infections at the early steps, clinical suspicion is crucial. Surgical exploration and resection will provide both the diagnosis confirming necrotizing infection of the fascia with vessels and treatment. Also, empirical broad-spectrum antibiotics must be initiated as soon as possible. Regardless of the presence of risk factors, NF is a condition with a high mortality rate and only an expeditious and undelayed treatment may improve the patient’s outcome. Surgical focus control requires wide and repeated resections, and planned reconstructive plastic surgery might be necessary.

scholarly journals JA signal-mediated immunity of Dendrobium catenatum to necrotrophic Southern Blight pathogen

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Cong Li ◽  
Qiuyi Shen ◽  
Xiang Cai ◽  
Danni Lai ◽  
Lingshang Wu ◽  
...  
Keyword(s):  
Large Scale ◽  
Plant Immunity ◽  
Expression Patterns ◽  
Protein Domain ◽  
Functional Identification ◽  
Necrotrophic Pathogen ◽  
Southern Blight ◽  
Meja Treatment ◽  
Sclerotium Delphinii ◽  
Large Scale Cultivation

Abstract Background Dendrobium catenatum belongs to the Orchidaceae, and is a precious Chinese herbal medicine. In the past 20 years, D. catenatum industry has developed from an endangered medicinal plant to multi-billion dollar grade industry. The necrotrophic pathogen Sclerotium delphinii has a devastating effection on over 500 plant species, especially resulting in widespread infection and severe yield loss in the process of large-scale cultivation of D. catenatum. It has been widely reported that Jasmonate (JA) is involved in plant immunity to pathogens, but the mechanisms of JA-induced plant resistance to S. delphinii are unclear. Results In the present study, the role of JA in enhancing D. catenatum resistance to S. delphinii was investigated. We identified 2 COI1, 13 JAZ, and 12 MYC proteins in D. catenatum genome. Subsequently, systematic analyses containing phylogenetic relationship, gene structure, protein domain, and motif architecture of core JA pathway proteins were conducted in D. catenatum and the newly characterized homologs from its closely related orchid species Phalaenopsis equestris and Apostasia shenzhenica, along with the well-investigated homologs from Arabidopsis thaliana and Oryza sativa. Public RNA-seq data were investigated to analyze the expression patterns of D. catenatum core JA pathway genes in various tissues and organs. Transcriptome analysis of MeJA and S. delphinii treatment showed exogenous MeJA changed most of the expression of the above genes, and several key members, including DcJAZ1/2/5 and DcMYC2b, are involved in enhancing defense ability to S. delphinii in D. catenatum. Conclusions The findings indicate exogenous MeJA treatment affects the expression level of DcJAZ1/2/5 and DcMYC2b, thereby enhancing D. catenatum resistance to S. delphinii. This research would be helpful for future functional identification of core JA pathway genes involved in breeding for disease resistance in D. catenatum.

Necrotizing Fasciitis Occurred in the Lymphedematous leg

2021 ◽  
pp. 153473462110230
Author(s):  
Hisako Hara ◽  
Makoto Mihara ◽  
Takeshi Todokoro
Keyword(s):  
Case Report ◽  
Necrotizing Fasciitis ◽  
Lower Limb ◽  
Gynecologic Cancer ◽  
Vital Signs ◽  
Ethics Committee ◽  
Secondary Lymphedema ◽  
Delayed Treatment ◽  
Institutional Ethics ◽  
Life Threatening

Lymphedema is a chronic edema that sometimes occurs after treatment of gynecologic cancer, and cellulitis often occurs concomitantly with lymphedema. On the other hand, necrotizing fasciitis (NF) is a relatively rare, but life-threatening disease. The symptoms in cellulitis and NF are very similar. In this case report, we describe a case in which the diagnosis of NF in a lymphedematous limb was difficult. A 70-year-old woman had secondary lymphedema in bilateral legs and consulted our department. On the first day of lymphedema therapy, the patient complained of vomiting, diarrhea, and fever (37.7 °C) without local fever in the legs. She was diagnosed with acute gastroenteritis. On the next day, swelling and pain in her left leg occurred and her blood pressure was 59/44 mmHg. She was diagnosed with cellulitis accompanied by lower limb lymphedema and septic shock. On the second day, blisters appeared on the left leg, and computed tomography showed NF. We performed debridement under general anesthesia and her vital signs improved postoperatively. Streptococcus agalactiae (B) was detected in blood culture, and we administered bixillin and clindamycin. Postoperatively, necrosis in the skin and fat around the left ankle gradually spread, and it took 5 months to complete epithelialization. The diagnosis was more difficult than usual NF because patients with lymphedema often experience cellulitis. Clinicians should always think of NF to avoid mortality due to delayed treatment. This case report was approved by the institutional ethics committee.

Large scale gene regulatory network inference with a multi-level strategy

2016 ◽  
Vol 12 (2) ◽  
pp. 588-597 ◽  
Author(s):  
Jun Wu ◽  
Xiaodong Zhao ◽  
Zongli Lin ◽  
Zhifeng Shao
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Large Scale ◽  
Network Inference ◽  
Biological Processes ◽  
Molecular Processes ◽  
Gene Regulatory Network Inference ◽  
Cell Functions ◽  
Multi Level ◽  
Gene Regulatory

Transcriptional regulation is a basis of many crucial molecular processes and an accurate inference of the gene regulatory network is a helpful and essential task to understand cell functions and gain insights into biological processes of interest in systems biology.

scholarly journals Ehrlichia chaffeensis and Its Invasin EtpE Block Reactive Oxygen Species Generation by Macrophages in a DNase X-Dependent Manner

mBio ◽  
2017 ◽  
Vol 8 (6) ◽  
Author(s):  
Omid Teymournejad ◽  
Mingqun Lin ◽  
Yasuko Rikihisa
Keyword(s):  
Host Cell ◽  
Cell Receptor ◽  
Ros Generation ◽  
Ehrlichia Chaffeensis ◽  
Biological Processes ◽  
Wild Type ◽  
New Approach ◽  
Host Cell Receptor ◽  
Life Threatening ◽  
Human Monocytic Ehrlichiosis

ABSTRACT The obligatory intracellular pathogen Ehrlichia chaffeensis lacks most genes that confer resistance to oxidative stress but can block reactive oxygen species (ROS) generation by host monocytes-macrophages. Bacterial and host molecules responsible for this inhibition have not been identified. To infect host cells, Ehrlichia uses the C terminus of its surface invasin, entry-triggering protein of Ehrlichia (EtpE; EtpE-C), which directly binds the mammalian cell surface receptor glycosylphosphatidylinositol-anchored protein DNase X. We investigated whether EtpE-C binding to DNase X blocks ROS production by mouse bone marrow-derived macrophages (BMDMs). On the basis of a luminol-dependent chemiluminescence assay, E. chaffeensis inhibited phorbol myristate acetate (PMA)-induced ROS generation by BMDMs from wild-type, but not DNase X−/−, mice. EtpE-C is critical for inhibition, as recombinant EtpE-C (rEtpE-C)-coated latex beads, but not recombinant N-terminal EtpE-coated or uncoated beads, inhibited PMA-induced ROS generation by BMDMs from wild-type mice. DNase X is required for this inhibition, as none of these beads inhibited PMA-induced ROS generation by BMDMs from DNase X−/− mice. Previous studies showed that E. chaffeensis does not block ROS generation in neutrophils, a cell type that is a potent ROS generator but is not infected by E. chaffeensis. Human and mouse peripheral blood neutrophils did not express DNase X. Our findings point to a unique survival mechanism of ROS-sensitive obligate intramonocytic bacteria that involves invasin EtpE binding to DNase X on the host cell surface. This is the first report of bacterial invasin having such a subversive activity on ROS generation. IMPORTANCE Ehrlichia chaffeensis preferentially infects monocytes-macrophages and causes a life-threatening emerging tick-transmitted infectious disease called human monocytic ehrlichiosis. Ehrlichial infection, and hence the disease, depends on the ability of this bacterium to avoid or overcome powerful microbicidal mechanisms of host monocytes-macrophages, one of which is the generation of ROS. Our findings reveal that an ehrlichial surface invasin, EtpE, not only triggers bacterial entry but also blocks ROS generation by host macrophages through its host cell receptor, DNase X. As ROS sensitivity is an Achilles’ heel of this group of pathogens, understanding the mechanism by which E. chaffeensis rapidly blocks ROS generation suggests a new approach for developing effective anti-infective measures. The discovery of a ROS-blocking pathway is also important, as modulation of ROS generation is important in a variety of ailments and biological processes. IMPORTANCE Ehrlichia chaffeensis preferentially infects monocytes-macrophages and causes a life-threatening emerging tick-transmitted infectious disease called human monocytic ehrlichiosis. Ehrlichial infection, and hence the disease, depends on the ability of this bacterium to avoid or overcome powerful microbicidal mechanisms of host monocytes-macrophages, one of which is the generation of ROS. Our findings reveal that an ehrlichial surface invasin, EtpE, not only triggers bacterial entry but also blocks ROS generation by host macrophages through its host cell receptor, DNase X. As ROS sensitivity is an Achilles’ heel of this group of pathogens, understanding the mechanism by which E. chaffeensis rapidly blocks ROS generation suggests a new approach for developing effective anti-infective measures. The discovery of a ROS-blocking pathway is also important, as modulation of ROS generation is important in a variety of ailments and biological processes.

Dehydration-induced proteomic landscape of mitochondria in chickpea reveals large-scale coordination of key biological processes

2019 ◽  
Vol 192 ◽  
pp. 267-279 ◽  
Author(s):  
Dipak Gayen ◽  
Saurabh Gayali ◽  
Pragya Barua ◽  
Nilesh Vikram Lande ◽  
Swati Varshney ◽  
...  
Keyword(s):  
Large Scale ◽  
Biological Processes

scholarly journals Pyelonephritis can be a source of a life threatening necrotizing myofasciitis

2014 ◽  
Vol 8 (5-6) ◽  
pp. 462
Author(s):  
Haytham Kamel ◽  
Mohamed Soliman Edris Awed ◽  
Ahmed Fouad Kotb
Keyword(s):  
Necrotizing Fasciitis ◽  
Adult Male ◽  
Soft Tissues ◽  
Subcutaneous Tissue ◽  
Relevant Literature ◽  
Deep Fascia ◽  
Necrotizing Myositis ◽  
Life Threatening

Necrotizing fasciitis is a progressive, rapidly spreading, inflammatory infection located in deep fascia. It may cause necrosis of skin and subcutaneous tissue and can even result in involvement of adjacent soft tissues such as muscles resulting in necrotizing myositis. We report the case of an adult male presenting with necrotizing myofasciitis secondary to left pyelonephritis. We also review the relevant literature.

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