scholarly journals Phylogenetic Distribution of CRISPR-Cas Systems in Staphylococcus lugdunensis

2021 ◽  
Author(s):  
Cheng-Yen Kao ◽  
Jang-Jih Lu ◽  
Lee-Chung Lin ◽  
Hsiao-Chi Lin ◽  
Shih-Cheng Chang
Keyword(s):  
Pathogenic Bacteria ◽  
Phylogenetic Distribution ◽  
Bacterial Genomes ◽  
Staphylococcus Lugdunensis ◽  
Evolutionary Studies

CRISPR-Cas systems have been characterized as playing several biological roles in many bacterial genomes. Moreover, CRISPR-Cas systems are useful for epidemiological, diagnostic, and evolutionary studies of pathogenic bacteria.

scholarly journals Is Staphylococcus lugdunensis Significant in Clinical Samples?

2017 ◽  
Vol 55 (11) ◽  
pp. 3167-3174 ◽  
Author(s):  
Xavier Argemi ◽  
Yves Hansmann ◽  
Philippe Riegel ◽  
Gilles Prévost
Keyword(s):  
Pathogenic Bacteria ◽  
Clinical Manifestations ◽  
Clinical Samples ◽  
Opportunistic Pathogens ◽  
Coagulase Negative Staphylococci ◽  
Staphylococcus Lugdunensis ◽  
Content Type ◽  
Severe Infections ◽  
Microbiological Data

ABSTRACTThe implication of coagulase-negative staphylococci in human diseases is a major issue, particularly in hospital settings wherein these species often act as opportunistic pathogens. In addition, some coagulase-negative staphylococci such asS. lugdunensishave emerged as pathogenic bacteria, implicated in severe infections, particularly, osteoarticular infections, foreign-body-associated infections, bacteremia, and endocarditis.In vitrostudies have shown the presence of several putative virulence factors such as adhesion factors, biofilm production, and proteolytic factors that might explain clinical manifestations. Taken together, the clinical and microbiological data might change the way clinicians and microbiologists look atS. lugdunensisin clinical samples.

Ectopic gene conversions in bacterial genomes

Genome ◽  
2007 ◽  
Vol 50 (11) ◽  
pp. 975-984 ◽  
Author(s):  
Robert T. Morris ◽  
Guy Drouin
Keyword(s):  
Pathogenic Bacteria ◽  
Sequence Similarity ◽  
Multigene Families ◽  
Pathogenic Species ◽  
Flanking Sequence ◽  
Bacterial Genomes ◽  
Divergent Gene ◽  
Species Comparisons ◽  
Species Groups ◽  
Gene Conversions

We characterized the gene conversions found between the duplicated genes of 75 bacterial genomes from five species groups (archaea, nonpathogenic and pathogenic firmicutes, and nonpathogenic and pathogenic proteobacteria). The number of gene conversions is positively correlated with the size of multigene families and the size of multigene families is not significantly different between pathogenic and nonpathogenic taxa. However, gene conversions occur twice as frequently in pathogenic species as in nonpathogenic species. Comparisons between closely related species also indicate a trend towards increased gene conversion in pathogenic species. Whereas the length of the conversions is positively correlated with flanking sequence similarity in all five groups, these correlations are smaller for pathogenic firmicutes and proteobacteria than for nonpathogenic firmicutes and proteobacteria. These results are consistent with our previous work on E. coli genomes and suggest that pathogenic bacteria allow recombination between more divergent gene sequences. This higher permissiveness is likely adaptive because it allows them to generate more genetic variability.

scholarly journals Modulating Pathogenesis with Mobile-CRISPRi

2019 ◽  
Vol 201 (22) ◽  
Author(s):  
Jiuxin Qu ◽  
Neha K. Prasad ◽  
Michelle A. Yu ◽  
Shuyan Chen ◽  
Amy Lyden ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pathogenic Bacteria ◽  
Bacterial Species ◽  
Effector Proteins ◽  
Infection Model ◽  
Secretion Systems ◽  
Bacterial Genomes ◽  
Gene Encoding ◽  
Content Type ◽  
Animal Infection

ABSTRACT Conditionally essential (CE) genes are required by pathogenic bacteria to establish and maintain infections. CE genes encode virulence factors, such as secretion systems and effector proteins, as well as biosynthetic enzymes that produce metabolites not found in the host environment. Due to their outsized importance in pathogenesis, CE gene products are attractive targets for the next generation of antimicrobials. However, the precise manipulation of CE gene expression in the context of infection is technically challenging, limiting our ability to understand the roles of CE genes in pathogenesis and accordingly design effective inhibitors. We previously developed a suite of CRISPR interference-based gene knockdown tools that are transferred by conjugation and stably integrate into bacterial genomes that we call Mobile-CRISPRi. Here, we show the efficacy of Mobile-CRISPRi in controlling CE gene expression in an animal infection model. We optimize Mobile-CRISPRi in Pseudomonas aeruginosa for use in a murine model of pneumonia by tuning the expression of CRISPRi components to avoid nonspecific toxicity. As a proof of principle, we demonstrate that knock down of a CE gene encoding the type III secretion system (T3SS) activator ExsA blocks effector protein secretion in culture and attenuates virulence in mice. We anticipate that Mobile-CRISPRi will be a valuable tool to probe the function of CE genes across many bacterial species and pathogenesis models. IMPORTANCE Antibiotic resistance is a growing threat to global health. To optimize the use of our existing antibiotics and identify new targets for future inhibitors, understanding the fundamental drivers of bacterial growth in the context of the host immune response is paramount. Historically, these genetic drivers have been difficult to manipulate precisely, as they are requisite for pathogen survival. Here, we provide the first application of Mobile-CRISPRi to study conditionally essential virulence genes in mouse models of lung infection through partial gene perturbation. We envision the use of Mobile-CRISPRi in future pathogenesis models and antibiotic target discovery efforts.

scholarly journals Mycobacterium phage Butters-encoded proteins contribute to host defense against viral attack

2020 ◽  
Author(s):  
Catherine M. Mageeney ◽  
Hamidu T. Mohammed ◽  
Marta Dies ◽  
Samira Anbari ◽  
Netta Cudkevich ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Phage Therapy ◽  
Defense Mechanism ◽  
Resistant Bacteria ◽  
Two Component System ◽  
Bacterial Genomes ◽  
Bacterial Host ◽  
Bioinformatics Analyses ◽  
Defense Systems ◽  
Two Component

ABSTRACTA diverse set of prophage-mediated mechanisms protecting bacterial hosts from infection has been recently uncovered within Cluster N mycobacteriophages. In that context, we unveil a novel defense mechanism in Cluster N prophage Butters. By using bioinformatics analyses, phage plating efficiency experiments, microscopy, and immunoprecipitation assays, we show that Butters genes located in the central region of the genome play a key role in the defense against heterotypic viral attack. Our study suggests that a two component system articulated by interactions between protein products of genes 30 and 31 confers defense against heterotypic phage infection by PurpleHaze or Alma, but is insufficient to confer defense against attack by the heterotypic phage Island3. Therefore, based on heterotypic phage plating efficiencies on the Butters lysogen, additional prophage genes required for defense are implicated.IMPORTANCEMany sequenced bacterial genomes including pathogenic bacteria contain prophages. Some prophages encode defense systems that protect their bacterial host against heterotypic viral attack. Understanding the mechanisms undergirding these defense systems will be critical to development of phage therapy that circumvents these defenses. Additionally, such knowledge will help engineer phage-resistant bacteria of industrial importance.

scholarly journals Genomic Potential for Polysaccharide Deconstruction in Bacteria

2014 ◽  
Vol 81 (4) ◽  
pp. 1513-1519 ◽  
Author(s):  
Renaud Berlemont ◽  
Adam C. Martiny
Keyword(s):  
Microbial Communities ◽  
Bacterial Growth ◽  
Glycoside Hydrolase ◽  
Glycoside Hydrolases ◽  
Phylogenetic Distribution ◽  
Bacterial Genomes ◽  
Oligosaccharide Processing ◽  
Taxonomic Groups ◽  
Structural Polymers

ABSTRACTGlycoside hydrolases are important enzymes that support bacterial growth by enabling the degradation of polysaccharides (e.g., starch, cellulose, xylan, and chitin) in the environment. Presently, little is known about the overall phylogenetic distribution of the genomic potential to degrade these polysaccharides in bacteria. However, knowing the phylogenetic breadth of these traits may help us predict the overall polysaccharide processing in environmental microbial communities. In order to address this, we identified and analyzed the distribution of 392,166 enzyme genes derived from 53 glycoside hydrolase families in 8,133 sequenced bacterial genomes. Enzymes for oligosaccharides and starch/glycogen were observed in most taxonomic groups, whereas glycoside hydrolases for structural polymers (i.e., cellulose, xylan, and chitin) were observed in clusters of relatives at taxonomic levels ranging from species to genus as determined by consenTRAIT. The potential for starch and glycogen processing, as well as oligosaccharide processing, was observed in 85% of the strains, whereas 65% possessed enzymes to degrade some structural polysaccharides (i.e., cellulose, xylan, or chitin). Potential degraders targeting one, two, and three structural polysaccharides accounted for 22.6, 32.9, and 9.3% of genomes analyzed, respectively. Finally, potential degraders targeting multiple structural polysaccharides displayed increased potential for oligosaccharide deconstruction. This study provides a framework for linking the potential for polymer deconstruction with phylogeny in complex microbial assemblages.

scholarly journals Phylogenetic Distribution of Potential Cellulases in Bacteria

2012 ◽  
Vol 79 (5) ◽  
pp. 1545-1554 ◽  
Author(s):  
Renaud Berlemont ◽  
Adam C. Martiny
Keyword(s):  
Plant Cell Wall ◽  
Cellulose Degradation ◽  
Microbial Community Composition ◽  
Glycoside Hydrolases ◽  
Phylogenetic Distribution ◽  
Soil Ecosystem ◽  
Bacterial Genomes ◽  
Genes Encoding ◽  
Plant Cell Wall Degradation ◽  
Mechanistic Basis

ABSTRACTMany microorganisms contain cellulases that are important for plant cell wall degradation and overall soil ecosystem functioning. At present, we have extensive biochemical knowledge of cellulases but little is known about the phylogenetic distribution of these enzymes. To address this, we analyzed the distribution of 21,985 genes encoding proteins related to cellulose utilization in 5,123 sequenced bacterial genomes. First, we identified the distribution of glycoside hydrolases involved in cellulose utilization and synthesis at different taxonomic levels, from the phylum to the strain. Cellulose degradation/utilization capabilities appeared in nearly all major groups and resulted in strains displaying various enzyme gene combinations. Potential cellulose degraders, having both cellulases and β-glucosidases, constituted 24% of all genomes whereas potential opportunistic strains, having β-glucosidases only, accounted for 56%. Finally, 20% of the bacteria have no relevant enzymes and do not rely on cellulose utilization. The latter group was primarily connected to specific bacterial lifestyles like autotrophy and parasitism. Cellulose degraders, as well as opportunists, have multiple enzymes with similar functions. However, the potential degraders systematically harbor about twice more β-glucosidases than their potential opportunistic relatives. Although scattered, the distribution of functional types, in bacterial lineages, is not random but mostly follows a Brownian motion evolution model. Degraders form clusters of relatives at the species level, whereas opportunists are clustered at the genus level. This information can form a mechanistic basis for the linking of changes in microbial community composition to soil ecosystem processes.

scholarly journals A case of aggressive aortic prosthetic valve endocarditis aggressive caused by Staphylococcus lugdunensis

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Kazuhiro Yamazaki ◽  
Kenji Minakata ◽  
Kazuhisa Sakamoto ◽  
Jiro Sakai ◽  
Yujiro Ide ◽  
...  
Keyword(s):  
Infective Endocarditis ◽  
Aortic Valve ◽  
Aortic Valve Replacement ◽  
Valve Replacement ◽  
Prosthetic Valve ◽  
Pathogenic Bacteria ◽  
Prosthetic Valve Endocarditis ◽  
Drug Susceptibility ◽  
Coagulase Negative Staphylococcus ◽  
Staphylococcus Lugdunensis

Abstract Background Staphylococcus lugdunensis is a coagulase-negative Staphylococcus species, which are weak pathogenic bacteria generally. However, the acute and severe pathogenicity of Staphylococcus lugdunensis infective endocarditis may be due to the rapid growth of large vegetation and consequent valve destruction. Case presentation The patient was an 81-year-old male who visited our hospital with chief complaints of low back pain and high fever. Four years before this visit, he had undergone aortic valve replacement for aortic regurgitation. He was found to be hypotensive. Although there is no heart murmur on auscultation and echocardiography revealed negative findings with aortic valve, a blood test showed increases in the white blood cell count and C-reactive protein concentration. On the next day, Gram-positive cocci were detected in a blood culture and echocardiography detected a large vegetation on the prosthetic valve with increased flow velocity. Therefore, he underwent redo aortic valve replacement emergently. Staphylococcus lugdunensis was identified in blood samples and vegetation culture. Consequently, the patient was treated with antibiotics for 5 weeks after the operation and discharged home. Conclusions We experienced rapidly progressive prosthetic valve endocarditis caused by Staphylococcus lugdunensis. Hence, Staphylococcus lugdunensis infective endocarditis requires aggressive treatment, and the pathogenicity of this coagulase-negative Staphylococcus with high drug susceptibility should not be underestimated.

scholarly journals The Bacterial Genomic Context of Highly Trimethoprim-Resistant DfrB Dihydrofolate Reductases Highlights an Emerging Threat to Public Health

Antibiotics ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 433
Author(s):  
Claudèle Lemay-St-Denis ◽  
Sarah-Slim Diwan ◽  
Joelle N. Pelletier
Keyword(s):  
Public Health ◽  
Pathogenic Bacteria ◽  
Antibiotic Resistance Genes ◽  
Genomic Context ◽  
Bacterial Genomes ◽  
New Members ◽  
The Family ◽  
Dihydrofolate Reductases ◽  
Systematic Biases ◽  
The 1960S

Type B dihydrofolate reductase (dfrb) genes were identified following the introduction of trimethoprim in the 1960s. Although they intrinsically confer resistance to trimethoprim (TMP) that is orders of magnitude greater than through other mechanisms, the distribution and prevalence of these short (237 bp) genes is unknown. Indeed, this knowledge has been hampered by systematic biases in search methodologies. Here, we investigate the genomic context of dfrbs to gain information on their current distribution in bacterial genomes. Upon searching publicly available databases, we identified 61 sequences containing dfrbs within an analyzable genomic context. The majority (70%) of those sequences also harbor virulence genes and 97% of the dfrbs are found near a mobile genetic element, representing a potential risk for antibiotic resistance genes. We further identified and confirmed the TMP-resistant phenotype of two new members of the family, dfrb10 and dfrb11. Dfrbs are found both in Betaproteobacteria and Gammaproteobacteria, a majority (59%) being in Pseudomonas aeruginosa. Previously labelled as strictly plasmid-borne, we found 69% of dfrbs in the chromosome of pathogenic bacteria. Our results demonstrate that the intrinsically TMP-resistant dfrbs are a potential emerging threat to public health and justify closer surveillance of these genes.

scholarly journals Structures of the CRISPR/Cas System in the Genome of the Staphylococcus aureus ST228 Strain and Phage Races Detected by Bioinformatics

2020 ◽  
Vol 31 ◽  
pp. 3-18
Author(s):  
A. Yu. Borisenko ◽  
◽  
Yu. P. Dzhioev ◽  
L. A. Stepanenko ◽  
Yu. M. Zemlyanskaya ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Bacterial Strain ◽  
Bacterial Infections ◽  
Pathogenic Bacteria ◽  
Multidrug Resistant ◽  
Aureus Strain ◽  
Modern World ◽  
Bacterial Genomes ◽  
Alternative Antibiotic

In the modern world, infections caused by multidrug-resistant (MDR) bacteria have become carriers of global threats to human health. Today these pathogenic bacteria have come to be referred to as "superbugs" and their number and aggressiveness is growing. This group of "superbugs" also includes Staphylococcus aureus. It is capable of infecting almost any tissue in the human body. Therefore, it became necessary to find alternative antibiotic methods of treating bacterial infections. The use of bacteriophages is again among them. We propose a new approach in the search for strain-specific (target) phages through the structures of the CRISPR/Cas-systems of bacteria. As is known, CRISPR/Cas systems are the most ancient system of "adaptive immunity" in bacteria. This system makes bacteria resistant to phages and plasmids. This approach is based on the use of methods of structural genomics and software bioinformatics modeling. Using them, an algorithm was developed to search for the structures of CRISPR/Cas systems in bacterial genomes presented in the NCBI databases and screening through their CRISPR cassettes of phages with which a particular strain could meet. The design of the developed algorithm was tested on the genome of methicillin-resistant S. aureus strain (ST228-MRSA-I) from the GenBank database. The results of the search for loci and structures of the CRISPR/Cas system in the genome of this strain showed that the identified system belongs to type III-A. It was found that the cas genes and the CRISPR cassette are located at a distance from each other and between them are located several genes that perform other functions in the genome of the S. aureus strain. It was shown that the structures of spacers in the detected CRISPR cassette are identical to protospacers of phages, the hosts of which are bacteria of the following genera – Staphylococcus, Mycobacterium, Streptococcus, Bacillus, Gordonia, Arthrobacter, Streptomyces. Thus, it can be stated that the developed algorithm of software methods for searching for loci of CRISPR/Cas systems and screening for phages makes it possible to type both the system itself and through its spacers to detect and identify phage races with which a particular bacterial strain could meet. The degree of resistance of a particular bacterial strain to specific phages is also determined, which in the long term should ensure the effectiveness of targeted phage therapy for infections caused by pathogenic bacteria, including "superbugs".

scholarly journals Prophage Genomics

2003 ◽  
Vol 67 (2) ◽  
pp. 238-276 ◽  
Author(s):  
Carlos Canchaya ◽  
Caroline Proux ◽  
Ghislain Fournous ◽  
Anne Bruttin ◽  
Harald Brüssow
Keyword(s):  
Pathogenic Bacteria ◽  
Plant Pathogens ◽  
Bacterial Genome ◽  
Ecological Niches ◽  
Host Bacterium ◽  
Mobile Dna ◽  
Genome Sequences ◽  
Bacterial Genomes ◽  
Gram Positive ◽  
Gram Positive Bacteria

SUMMARY The majority of the bacterial genome sequences deposited in the National Center for Biotechnology Information database contain prophage sequences. Analysis of the prophages suggested that after being integrated into bacterial genomes, they undergo a complex decay process consisting of inactivating point mutations, genome rearrangements, modular exchanges, invasion by further mobile DNA elements, and massive DNA deletion. We review the technical difficulties in defining such altered prophage sequences in bacterial genomes and discuss theoretical frameworks for the phage-bacterium interaction at the genomic level. The published genome sequences from three groups of eubacteria (low- and high-G+C gram-positive bacteria and γ-proteobacteria) were screened for prophage sequences. The prophages from Streptococcus pyogenes served as test case for theoretical predictions of the role of prophages in the evolution of pathogenic bacteria. The genomes from further human, animal, and plant pathogens, as well as commensal and free-living bacteria, were included in the analysis to see whether the same principles of prophage genomics apply for bacteria living in different ecological niches and coming from distinct phylogenetical affinities. The effect of selection pressure on the host bacterium is apparently an important force shaping the prophage genomes in low-G+C gram-positive bacteria and γ-proteobacteria.

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