scholarly journals Comparative Pathogenomics of Bacteria Causing Infectious Diseases in Fish

2012 ◽  
Vol 2012 ◽  
pp. 1-16 ◽  
Author(s):  
Ponnerassery S. Sudheesh ◽  
Aliya Al-Ghabshi ◽  
Nashwa Al-Mazrooei ◽  
Saoud Al-Habsi
Keyword(s):  
Infectious Diseases ◽  
Genome Sequencing ◽  
Virulence Factors ◽  
Pathogenic Bacteria ◽  
Bacterial Pathogens ◽  
Evolutionary Strategies ◽  
Ecological Niches ◽  
Specific Gene ◽  
Sequence Information ◽  
Fish Pathogens

Fish living in the wild as well as reared in the aquaculture facilities are susceptible to infectious diseases caused by a phylogenetically diverse collection of bacterial pathogens. Control and treatment options using vaccines and drugs are either inadequate, inefficient, or impracticable. The classical approach in studying fish bacterial pathogens has been looking at individual or few virulence factors. Recently, genome sequencing of a number of bacterial fish pathogens has tremendously increased our understanding of the biology, host adaptation, and virulence factors of these important pathogens. This paper attempts to compile the scattered literature on genome sequence information of fish pathogenic bacteria published and available to date. The genome sequencing has uncovered several complex adaptive evolutionary strategies mediated by horizontal gene transfer, insertion sequence elements, mutations and prophage sequences operating in fish pathogens, and how their genomes evolved from generalist environmental strains to highly virulent obligatory pathogens. In addition, the comparative genomics has allowed the identification of unique pathogen-specific gene clusters. The paper focuses on the comparative analysis of the virulogenomes of important fish bacterial pathogens, and the genes involved in their evolutionary adaptation to different ecological niches. The paper also proposes some new directions on finding novel vaccine and chemotherapeutic targets in the genomes of bacterial pathogens of fish.

scholarly journals Complete genome sequencing of Staphylococcus aureus: insights into virulence and antimicrobial resistance

2008 ◽  
Vol 29 (3) ◽  
pp. 115
Author(s):  
Benjamin Howden ◽  
Tim Stinear ◽  
John K Davies
Keyword(s):  
Staphylococcus Aureus ◽  
Antimicrobial Resistance ◽  
Genome Sequencing ◽  
Virulence Factors ◽  
Complete Genome ◽  
Bacterial Pathogens ◽  
Complete Genome Sequencing

Staphylococcus aureus remains one of the most important opportunistic bacterial pathogens of humans. It is characterised by the presence of many virulence factors, as well as an ability to rapidly develop or acquire antimicrobial resistance.

scholarly journals Anti-Bacterial Activity of Natural Plants on Fish Pathogens Isolated from Different Ponds of Dhaka City

2016 ◽  
pp. 9-12 ◽  
Author(s):  
Kamal Kanta Das ◽  
Ayesha Abedin ◽  
Rashed Noor
Keyword(s):  
Plant Extracts ◽  
Water Samples ◽  
Pathogenic Bacteria ◽  
Bacterial Resistance ◽  
Heterotrophic Bacteria ◽  
Bacterial Pathogens ◽  
Bacterial Activity ◽  
Diffusion Method ◽  
Fish Pathogens ◽  
Natural Plants

In aquaculture, the incidence of bacterial resistance towards synthetic antibiotics has become a serious problem. Therefore, current research has been focused on detecting the presence of pathogenic bacteria in water bodies and finding a novel therapy against pathogens imparted by the natural products replacing the use of synthetic antibiotics. A total of 10 pond water samples were analysed to determine the pathogenic load employing conventional cultural and biochemical tests. Anti-bacterial activities of natural plants on fish pathogens were determined using the agar-well-diffusion method. All the water samples studied high heterotrophic bacteria counts, which were upto 109 cfu/ml. Among bacterial pathogens, Pseudomonas spp. and Vibrio spp. were found to be present in 6 samples and Aeromonas spp. in 2 samples. The in vitro anti-bacterial activity of the herbal plant extracts against the bacterial pathogens revealed that most of the plant extracts are effective against the pathogenic bacterial isolates.Bangladesh J Microbiol, Volume 31, Number 1-2,June-Dec 2014, pp 9-12

scholarly journals Fabrication of Zinc Oxide-Xanthan Gum Nanocomposite via Green Route: Attenuation of Quorum Sensing Regulated Virulence Functions and Mitigation of Biofilm in Gram-Negative Bacterial Pathogens

Coatings ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1190
Author(s):  
Fohad Mabood Husain ◽  
Imran Hasan ◽  
Faizan Abul Qais ◽  
Rais Ahmad Khan ◽  
Pravej Alam ◽  
...  
Keyword(s):  
Zinc Oxide ◽  
Quorum Sensing ◽  
Virulence Factors ◽  
Xanthan Gum ◽  
Pathogenic Bacteria ◽  
Bacterial Pathogens ◽  
Cell Surface Hydrophobicity ◽  
Health Concern ◽  
Gram Negative ◽  
Slow Development

The unabated abuse of antibiotics has created a selection pressure that has resulted in the development of antimicrobial resistance (AMR) among pathogenic bacteria. AMR has become a global health concern in recent times and is responsible for a high number of mortalities occurring across the globe. Owing to the slow development of antibiotics, new chemotherapeutic antimicrobials with a novel mode of action is required urgently. Therefore, in the current investigation, we green synthesized a nanocomposite comprising zinc oxide nanoparticles functionalized with extracellular polysaccharide xanthan gum (ZnO@XG). Synthesized nanomaterial was characterized by structurally and morphologically using UV-visible spectroscopy, XRD, FTIR, BET, SEM and TEM. Subinhibitory concentrations of ZnO@XG were used to determine quorum sensing inhibitory activity against Gram-negative pathogens, Chromobacterium violaceum, and Serratia marcescens. ZnO@XG reduced quorum sensing (QS) regulated virulence factors such as violacein (61%), chitinase (70%) in C. violaceum and prodigiosin (71%) and protease (72%) in S. marcescens at 128 µg/mL concentration. Significant (p ≤ 0.05) inhibition of biofilm formation as well as preformed mature biofilms was also recorded along with the impaired production of EPS, swarming motility and cell surface hydrophobicity in both the test pathogens. The findings of this study clearly highlight the potency of ZnO@XG against the QS controlled virulence factors of drug-resistant pathogens that may be developed as effective inhibitors of QS and biofilms to mitigate the threat of multidrug resistance (MDR). ZnO@XG may be used alone or in combination with antimicrobial drugs against MDR bacterial pathogens. Further, it can be utilized in the food industry to counter the menace of contamination and spoilage caused by the formation of biofilms.

Direct Detection of Enteropathogenic Bacteria in Estuarine Water Using Nucleic Acid Probes

1991 ◽  
Vol 24 (2) ◽  
pp. 261-266 ◽  
Author(s):  
Ivor T. Knight ◽  
Jocelyne DiRuggiero ◽  
Rita R. Colwell
Keyword(s):  
Water Samples ◽  
Pathogenic Bacteria ◽  
Direct Detection ◽  
Specific Gene ◽  
Estuarine Water ◽  
Indicator Organisms ◽  
Salmonella Spp ◽  
Dna And Rna ◽  
Enteropathogenic Bacteria ◽  
Highly Sensitive Detection

Direct detection and enumeration of pathogenic bacteria, rather than indicator organisms, in aquatic environments is desirable but hindered by the difficulties of culturing and identifying specific pathogens from these environments. We have developed a method for concentrating bacteria from water samples and extracting their DNA and RNA for use as targets for pathogen-specific gene probes. The method has been used to detect and enumerate Salmonella spp. in estuarine water samples. The probe binds Salmonella DNA quantitatively, making it possible to estimate relative amounts of target in each sample. Salmonella spp. were detected in samples which yielded no Salmonella spp. using culturing. Since the probe method does not require culturing the target organism, both culturable and non-culturable forms are detected. We have also used polymerase chain reaction to amplify a region of the enterotoxin gene in enterotoxigenic Escherichiacoli and Vibriocholerae (ltx and ctx, respectively). The amplified products are then identified with ctx and ltx probes, making specific, highly sensitive detection possible.

scholarly journals Cattle connection: molecular epidemiology of BVDV outbreaks via rapid nanopore whole-genome sequencing of clinical samples

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Jacqueline King ◽  
Anne Pohlmann ◽  
Kamila Dziadek ◽  
Martin Beer ◽  
Kerstin Wernike
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Economic Losses ◽  
Clinical Samples ◽  
Bovine Viral Diarrhea ◽  
Sequence Information ◽  
Whole Genome ◽  
Diarrhea Virus ◽  
Viral Diarrhea ◽  
Viral Loads

Abstract Background As a global ruminant pathogen, bovine viral diarrhea virus (BVDV) is responsible for the disease Bovine Viral Diarrhea with a variety of clinical presentations and severe economic losses worldwide. Classified within the Pestivirus genus, the species Pestivirus A and B (syn. BVDV-1, BVDV-2) are genetically differentiated into 21 BVDV-1 and four BVDV-2 subtypes. Commonly, the 5’ untranslated region and the Npro protein are utilized for subtyping. However, the genetic variability of BVDV leads to limitations in former studies analyzing genome fragments in comparison to a full-genome evaluation. Results To enable rapid and accessible whole-genome sequencing of both BVDV-1 and BVDV-2 strains, nanopore sequencing of twelve representative BVDV samples was performed on amplicons derived through a tiling PCR procedure. Covering a multitude of subtypes (1b, 1d, 1f, 2a, 2c), sample matrices (plasma, EDTA blood and ear notch), viral loads (Cq-values 19–32) and species (cattle and sheep), ten of the twelve samples produced whole genomes, with two low titre samples presenting 96 % genome coverage. Conclusions Further phylogenetic analysis of the novel sequences emphasizes the necessity of whole-genome sequencing to identify novel strains and supplement lacking sequence information in public repositories. The proposed amplicon-based sequencing protocol allows rapid, inexpensive and accessible obtainment of complete BVDV genomes.

scholarly journals Cutibacterium acnes as an Opportunistic Pathogen: An Update of Its Virulence-Associated Factors

2021 ◽  
Vol 9 (2) ◽  
pp. 303 ◽  
Author(s):  
Constance Mayslich ◽  
Philippe Alain Grange ◽  
Nicolas Dupin
Keyword(s):  
Virulence Factors ◽  
Current Knowledge ◽  
Opportunistic Pathogen ◽  
Bacterial Attachment ◽  
Molecular Structures ◽  
Ecological Niches ◽  
Target Cells ◽  
Skin Microbiota ◽  
Host Immune Responses ◽  
Cutibacterium Acnes

Cutibacterium acnes is a member of the skin microbiota found predominantly in regions rich in sebaceous glands. It is involved in maintaining healthy skin and has long been considered a commensal bacterium. Its involvement in various infections has led to its emergence as an opportunist pathogen. Interactions between C. acnes and the human host, including the human skin microbiota, promote the selection of C. acnes strains capable of producing several virulence factors that increase inflammatory capability. This pathogenic property may be related to many infectious mechanisms, such as an ability to form biofilms and the expression of putative virulence factors capable of triggering host immune responses or enabling C. acnes to adapt to its environment. During the past decade, many studies have identified and characterized several putative virulence factors potentially involved in the pathogenicity of this bacterium. These virulence factors are involved in bacterial attachment to target cells, polysaccharide-based biofilm synthesis, molecular structures mediating inflammation, and the enzymatic degradation of host tissues. C. acnes, like other skin-associated bacteria, can colonize various ecological niches other than skin. It produces several proteins or glycoproteins that could be considered to be active virulence factors, enabling the bacterium to adapt to the lipophilic environment of the pilosebaceous unit of the skin, but also to the various organs it colonizes. In this review, we summarize current knowledge concerning characterized C. acnes virulence factors and their possible implication in the pathogenicity of C. acnes.

scholarly journals Whole-Genome Sequencing and Comparative Genomics of Three Helicobacter pylori Strains Isolated from the Stomach of a Patient with Adenocarcinoma

Pathogens ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 331
Author(s):  
Montserrat Palau ◽  
Núria Piqué ◽  
M. José Ramírez-Lázaro ◽  
Sergio Lario ◽  
Xavier Calvet ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Virulence Factors ◽  
Outer Membrane Proteins ◽  
Whole Genome ◽  
Flagellar Biosynthesis ◽  
H Pylori ◽  
Restriction Modification

Helicobacter pylori is a common pathogen associated with several severe digestive diseases. Although multiple virulence factors have been described, it is still unclear the role of virulence factors on H. pylori pathogenesis and disease progression. Whole genome sequencing could help to find genetic markers of virulence strains. In this work, we analyzed three complete genomes from isolates obtained at the same point in time from a stomach of a patient with adenocarcinoma, using multiple available bioinformatics tools. The genome analysis of the strains B508A-S1, B508A-T2A and B508A-T4 revealed that they were cagA, babA and sabB/hopO negative. The differences among the three genomes were mainly related to outer membrane proteins, methylases, restriction modification systems and flagellar biosynthesis proteins. The strain B508A-T2A was the only one presenting the genotype vacA s1, and had the most distinct genome as it exhibited fewer shared genes, higher number of unique genes, and more polymorphisms were found in this genome. With all the accumulated information, no significant differences were found among the isolates regarding virulence and origin of the isolates. Nevertheless, some B508A-T2A genome characteristics could be linked to the pathogenicity of H. pylori.

scholarly journals Advanced strategies for development of vaccines against human bacterial pathogens

2021 ◽  
Vol 37 (4) ◽  
Author(s):  
Abhinay Sharma ◽  
Pooja Sanduja ◽  
Aparna Anand ◽  
Pooja Mahajan ◽  
Carlos A. Guzman ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Infectious Diseases ◽  
Effective Treatment ◽  
Bacterial Pathogens ◽  
Vaccine Design ◽  
Human Beings ◽  
Rational Vaccine Design ◽  
New Vaccines

AbstractInfectious diseases are one of the main grounds of death and disabilities in human beings globally. Lack of effective treatment and immunization for many deadly infectious diseases and emerging drug resistance in pathogens underlines the need to either develop new vaccines or sufficiently improve the effectiveness of currently available drugs and vaccines. In this review, we discuss the application of advanced tools like bioinformatics, genomics, proteomics and associated techniques for a rational vaccine design.

scholarly journals Metabolic Modeling of Pectobacterium parmentieri SCC3193 Provides Insights into Metabolic Pathways of Plant Pathogenic Bacteria

2019 ◽  
Vol 7 (4) ◽  
pp. 101 ◽  
Author(s):  
Sabina Zoledowska ◽  
Luana Presta ◽  
Marco Fondi ◽  
Francesca Decorosi ◽  
Luciana Giovannetti ◽  
...  
Keyword(s):  
In Silico ◽  
Pathogenic Bacteria ◽  
Metabolic Modeling ◽  
Metabolic Model ◽  
Metabolic Adaptation ◽  
Ecological Niches ◽  
Plant Colonization ◽  
Phenotypic Data ◽  
Plant Pathogenic Bacteria ◽  
Metabolic Versatility

Understanding plant–microbe interactions is crucial for improving plants’ productivity and protection. Constraint-based metabolic modeling is one of the possible ways to investigate the bacterial adaptation to different ecological niches and may give insights into the metabolic versatility of plant pathogenic bacteria. We reconstructed a raw metabolic model of the emerging plant pathogenic bacterium Pectobacterium parmentieri SCC3193 with the use of KBase. The model was curated by using inParanoind and phenotypic data generated with the use of the OmniLog system. Metabolic modeling was performed through COBRApy Toolbox v. 0.10.1. The curated metabolic model of P. parmentieri SCC3193 is highly reliable, as in silico obtained results overlapped up to 91% with experimental data on carbon utilization phenotypes. By mean of flux balance analysis (FBA), we predicted the metabolic adaptation of P. parmentieri SCC3193 to two different ecological niches, relevant for the persistence and plant colonization by this bacterium: soil and the rhizosphere. We performed in silico gene deletions to predict the set of essential core genes for this bacterium to grow in such environments. We anticipate that our metabolic model will be a valuable element for defining a set of metabolic targets to control infection and spreading of this plant pathogen.

scholarly journals E. coli NF73-1 Isolated From NASH Patients Aggravates NAFLD in Mice by Translocating Into the Liver and Stimulating M1 Polarization

2020 ◽  
Vol 10 ◽  
Author(s):  
Yifan Zhang ◽  
Weiwei Jiang ◽  
Jun Xu ◽  
Na Wu ◽  
Yang Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Comparative Genomics ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Normal Diet ◽  
Specific Gene ◽  
Whole Genome ◽  
Metabolic Switch ◽  
M1 Macrophages ◽  
E Coli

ObjectiveThe gut microbiota is associated with nonalcoholic fatty liver disease (NAFLD). We isolated the Escherichia coli strain NF73-1 from the intestines of a NASH patient and then investigated its effect and underlying mechanism.Methods16S ribosomal RNA (16S rRNA) amplicon sequencing was used to detect bacterial profiles in healthy controls, NAFLD patients and NASH patients. Highly enriched E. coli strains were cultured and isolated from NASH patients. Whole-genome sequencing and comparative genomics were performed to investigate gene expression. Depending on the diet, male C57BL/6J mice were further grouped in normal diet (ND) and high-fat diet (HFD) groups. To avoid disturbing the bacterial microbiota, some of the ND and HFD mice were grouped as “bacteria-depleted” mice and treated with a cocktail of broad-spectrum antibiotic complex (ABX) from the 8th to 10th week. Then, E. coli NF73-1, the bacterial strain isolated from NASH patients, was administered transgastrically for 6 weeks to investigate its effect and mechanism in the pathogenic progression of NAFLD.ResultsThe relative abundance of Escherichia increased significantly in the mucosa of NAFLD patients, especially NASH patients. The results from whole-genome sequencing and comparative genomics showed a specific gene expression profile in E. coli strain NF73-1, which was isolated from the intestinal mucosa of NASH patients. E. coli NF73-1 accelerates NAFLD independently. Only in the HFD-NF73-1 and HFD-ABX-NF73-1 groups were EGFP-labeled E. coli NF73-1 detected in the liver and intestine. Subsequently, translocation of E. coli NF73-1 into the liver led to an increase in hepatic M1 macrophages via the TLR2/NLRP3 pathway. Hepatic M1 macrophages induced by E. coli NF73-1 activated mTOR-S6K1-SREBP-1/PPAR-α signaling, causing a metabolic switch from triglyceride oxidation toward triglyceride synthesis in NAFLD mice.ConclusionsE. coli NF73-1 is a critical trigger in the progression of NAFLD. E. coli NF73-1 might be a specific strain for NAFLD patients.

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