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Scientific Reports Jun 2020To assess the role of core metabolism genes in bacterial virulence - independently of their effect on growth - we correlated the genome, the transcriptome and the...
To assess the role of core metabolism genes in bacterial virulence - independently of their effect on growth - we correlated the genome, the transcriptome and the pathogenicity in flies and mice of 30 fully sequenced Pseudomonas strains. Gene presence correlates robustly with pathogenicity differences among all Pseudomonas species, but not among the P. aeruginosa strains. However, gene expression differences are evident between highly and lowly pathogenic P. aeruginosa strains in multiple virulence factors and a few metabolism genes. Moreover, 16.5%, a noticeable fraction of the core metabolism genes of P. aeruginosa strain PA14 (compared to 8.5% of the non-metabolic genes tested), appear necessary for full virulence when mutated. Most of these virulence-defective core metabolism mutants are compromised in at least one key virulence mechanism independently of auxotrophy. A pathway level analysis of PA14 core metabolism, uncovers beta-oxidation and the biosynthesis of amino-acids, succinate, citramalate, and chorismate to be important for full virulence. Strikingly, the relative expression among P. aeruginosa strains of genes belonging in these metabolic pathways is indicative of their pathogenicity. Thus, P. aeruginosa strain-to-strain virulence variation, remains largely obscure at the genome level, but can be dissected at the pathway level via functional transcriptomics of core metabolism.
Topics: Animals; Gene Expression Regulation, Bacterial; Genes, Bacterial; Host-Pathogen Interactions; Male; Mutation; Pseudomonas aeruginosa; Virulence
PubMed: 32528034
DOI: 10.1038/s41598-020-66194-4 -
The ISME Journal Mar 2009Mature Pseudomonas aeruginosa biofilms undergo specific developmental events. Using a bacteriophage mutant, generated by deletion of the entire filamentous Pf4 prophage,...
Mature Pseudomonas aeruginosa biofilms undergo specific developmental events. Using a bacteriophage mutant, generated by deletion of the entire filamentous Pf4 prophage, we show that the phage is essential for several stages of the biofilm life cycle and that it significantly contributes to the virulence of P. aeruginosa in vivo. Here, we show for the first time that biofilms of the Pf4 phage-deficient mutant did not develop hollow centres or undergo cell death, typical of the differentiation process of wild-type (WT) P. aeruginosa PAO1 biofilms. Furthermore, microcolonies of the Pf4 mutant were significantly smaller in size and less stable compared with the WT biofilm. Small colony variants (SCVs) were detectable in the dispersal population of the WT biofilm at the time of dispersal and cell death, whereas no SCVs were detected in the effluent of the Pf4 mutant biofilm. This study shows that at the time when cell death occurs in biofilms of the WT, the Pf4 phage converts into a superinfective form, which correlates with the appearance of variants in the dispersal population. Unexpectedly, mice infected with the Pf4 mutant survived significantly longer than those infected with its isogenic WT strain, showing that Pf4 contributes to the virulence of P. aeruginosa. Hence, a filamentous prophage is a major contributor to the life cycle and adaptive behaviour of P. aeruginosa and offers an explanation for the prevalence of phage in this organism.
Topics: Animals; Biofilms; Gene Order; Mice; Mice, Inbred BALB C; Prophages; Pseudomonas Infections; Pseudomonas Phages; Pseudomonas aeruginosa; Sequence Deletion; Survival Analysis; Viral Plaque Assay; Virulence
PubMed: 19005496
DOI: 10.1038/ismej.2008.109 -
Environmental Microbiology Reports Apr 2016Bacterial populations differentiate at the subspecies level into clonal complexes. Intraclonal genome diversity was studied in 100 isolates of the two dominant...
Bacterial populations differentiate at the subspecies level into clonal complexes. Intraclonal genome diversity was studied in 100 isolates of the two dominant Pseudomonas aeruginosa clones C and PA14 collected from the inanimate environment, acute and chronic infections. The core genome was highly conserved among clone members with a median pairwise within-clone single nucleotide sequence diversity of 8 × 10(-6) for clone C and 2 × 10(-5) for clone PA14. The composition of the accessory genome was, on the other hand, as variable within the clone as between unrelated clones. Each strain carried a large cargo of unique genes. The two dominant worldwide distributed P. aeruginosa clones combine an almost invariant core with the flexible gain and loss of genetic elements that spread by horizontal transfer.
Topics: Conserved Sequence; Environmental Microbiology; Gene Transfer, Horizontal; Genetic Variation; Genome, Bacterial; Genotype; Humans; Pseudomonas Infections; Pseudomonas aeruginosa
PubMed: 26711897
DOI: 10.1111/1758-2229.12372 -
Journal of Bacteriology Jul 2004Pseudomonas aeruginosa has a wide ecological distribution that includes natural habitats and clinical settings. To analyze the population structure and distribution of...
Pseudomonas aeruginosa has a wide ecological distribution that includes natural habitats and clinical settings. To analyze the population structure and distribution of P. aeruginosa, a collection of 111 isolates of diverse habitats and geographical origin, most of which contained a genome with a different SpeI macrorestriction profile, was typed by restriction fragment length polymorphism based on 14 single nucleotide polymorphisms (SNPs) located at seven conserved loci of the core genome (oriC, oprL, fliC, alkB2, citS, oprI, and ampC). The combination of these SNPs plus the type of fliC present (a or b) allowed the assignment of a genetic fingerprint to each strain, thus providing a simple tool for the discrimination of P. aeruginosa strains. Thirteen of the 91 identified SNP genotypes were found in two or more strains. In several cases, strains sharing their SNP genotype had different SpeI macrorestriction profiles. The highly virulent CHA strain shared its SNP genotype with other strains that had different SpeI genotypes and which had been isolated from nonclinical habitats. The reference strain PAO1 also shared its SNP genotype with other strains that had different SpeI genotypes. The P. aeruginosa chromosome contains a conserved core genome and variable amounts of accessory DNA segments (genomic islands and islets) that can be horizontally transferred among strains. The fact that some SNP genotypes were overrepresented in the P. aeruginosa population studied and that several strains sharing an SNP genotype had different SpeI macrorestriction profiles supports the idea that changes occur at a higher rate in the accessory DNA segments than in the conserved core genome.
Topics: Electrophoresis, Gel, Pulsed-Field; Genetic Linkage; Genotype; Polymorphism, Single Nucleotide; Pseudomonas aeruginosa
PubMed: 15205425
DOI: 10.1128/JB.186.13.4228-4237.2004 -
ELife Jan 2017Bacteria often live in biofilms, which are microbial communities surrounded by a secreted extracellular matrix. Here, we demonstrate that hydrodynamic flow and matrix...
Bacteria often live in biofilms, which are microbial communities surrounded by a secreted extracellular matrix. Here, we demonstrate that hydrodynamic flow and matrix organization interact to shape competitive dynamics in biofilms. Irrespective of initial frequency, in competition with matrix mutants, wild-type cells always increase in relative abundance in planar microfluidic devices under simple flow regimes. By contrast, in microenvironments with complex, irregular flow profiles - which are common in natural environments - wild-type matrix-producing and isogenic non-producing strains can coexist. This result stems from local obstruction of flow by wild-type matrix producers, which generates regions of near-zero shear that allow matrix mutants to locally accumulate. Our findings connect the evolutionary stability of matrix production with the hydrodynamics and spatial structure of the surrounding environment, providing a potential explanation for the variation in biofilm matrix secretion observed among bacteria in natural environments.
Topics: Biofilms; Environment; Microbial Interactions; Microfluidics; Pseudomonas aeruginosa
PubMed: 28084994
DOI: 10.7554/eLife.21855 -
The American Naturalist Sep 2019Predicting the evolution of expanding populations is critical to controlling biological threats such as invasive species and cancer metastasis. Expansion is primarily...
Predicting the evolution of expanding populations is critical to controlling biological threats such as invasive species and cancer metastasis. Expansion is primarily driven by reproduction and dispersal, but nature abounds with examples of evolution where organisms pay a reproductive cost to disperse faster. When does selection favor this "survival of the fastest"? We searched for a simple rule, motivated by evolution experiments where swarming bacteria evolved into a hyperswarmer mutant that disperses ∼100% faster but pays a growth cost of ∼10% to make many copies of its flagellum. We analyzed a two-species model based on the Fisher equation to explain this observation: the population expansion rate () results from an interplay of growth () and dispersal () and is independent of the carrying capacity: . A mutant can take over the edge only if its expansion rate () exceeds the expansion rate of the established species (); this simple condition ( ) determines the maximum cost in slower growth that a faster mutant can pay and still be able to take over. Numerical simulations and time-course experiments where we tracked evolution by imaging bacteria suggest that our findings are general: less favorable conditions delay but do not entirely prevent the success of the fastest. Thus, the expansion rate defines a traveling wave fitness, which could be combined with trade-offs to predict evolution of expanding populations.
Topics: Biological Evolution; Green Fluorescent Proteins; Models, Theoretical; Mutation; Pseudomonas aeruginosa; Selection, Genetic
PubMed: 31553215
DOI: 10.1086/704594 -
Molecular Microbiology May 2013Pseudomonas aeruginosa causes serious acute and chronic infections in humans. Major differences exist in disease pathogenesis, clinical treatment and outcomes between...
Pseudomonas aeruginosa causes serious acute and chronic infections in humans. Major differences exist in disease pathogenesis, clinical treatment and outcomes between acute and chronic infections. P. aeruginosa acute infection characteristically involves the type III secretion systems (T3SS) while chronic infection is often associated with the formation of biofilms, a major cause of difficulties to eradicate chronic infections. The choice between acute and chronic infection or the switch between them by P. aeruginosa is controlled by regulatory pathways that control major virulence factors and genes associated with biofilm formation. In this study, we characterized a hybrid sensor kinase PA1611 that controls the expression of genes associated with acute and chronic infections in P. aeruginosa PAO1. Expression of PA1611 completely repressed T3SS and swarming motility while it promoted biofilm formation. The protein PA1611 regulates two small RNAs (sRNAs), rsmY and rsmZ which in turn control RsmA. Independent of phosphate relay, PA1611 interacts directly with RetS in vivo. The positive effect of RetS on factors associated with acute infection could presumably be restrained by PA1611 when chronic infection conditions are present. This RetS-PA1611 interaction, together with the known RetS-GacS interaction, may control disease progression and the lifestyle choice of P. aeruginosa.
Topics: Bacterial Proteins; Biofilms; Gene Expression Regulation, Bacterial; Histidine Kinase; Humans; Locomotion; Protein Binding; Protein Kinases; Pseudomonas Infections; Pseudomonas aeruginosa; Virulence Factors
PubMed: 23560772
DOI: 10.1111/mmi.12223 -
Microbes and Infection Nov 2003Resistance to antimicrobial agents is the most important feature of biofilm infections. As a result, infections caused by bacterial biofilms are persistent and very... (Review)
Review
Resistance to antimicrobial agents is the most important feature of biofilm infections. As a result, infections caused by bacterial biofilms are persistent and very difficult to eradicate. Although several mechanisms have been postulated to explain reduced susceptibility to antimicrobials in bacterial biofilms, it is becoming evident that biofilm resistance is multifactorial. The contribution of each of the different mechanisms involved in biofilm resistance is now beginning to emerge.
Topics: Anti-Bacterial Agents; Bacterial Adhesion; Biofilms; Drug Resistance, Bacterial; Pseudomonas aeruginosa
PubMed: 14623017
DOI: 10.1016/j.micinf.2003.08.009 -
Acta Medica Iranica 2012The aim of the study was to determine the resistance patterns of Pseudomonas aeruginosa isolates recovered from patients with surgical wounds in hospitals and also to...
The aim of the study was to determine the resistance patterns of Pseudomonas aeruginosa isolates recovered from patients with surgical wounds in hospitals and also to investigate their epidemiological relatedness using molecular typing techniques. Twenty Pseudomonas sp. isolated from surgical wounds were subjected to antibiotic susceptibility testing by disk diffusion, plasmid profile, SDS-PAGE and PCR using the parC, gyr A gene and RAPD using the 1254 primer. The isolates showed resistance to 12 different antibiotics with six being 100% resistant. Plasmids were detected in 16 (80%) of the isolates. The RAPD-PCR using the primer 1254, SDS-PAGE classified the 20 Pseudomonas spp. into 5 and 6 types respectively. Pseudomona aeruginosa strains isolated from surgical wounds were generally resistant to a broad range of antibiotics and this is rather worrisome. The typing techniques classified the 20 isolates into 5 and 6 groups.
Topics: Humans; Microbial Sensitivity Tests; Molecular Typing; Nigeria; Pseudomonas aeruginosa; Surgical Wound Infection
PubMed: 22837123
DOI: No ID Found -
Methods in Molecular Biology (Clifton,... 2014Bacterial persistence, which is observed in a broad range of microbial species, is the capacity of a bacterial cell subpopulation called "persisters" to tolerate...
Bacterial persistence, which is observed in a broad range of microbial species, is the capacity of a bacterial cell subpopulation called "persisters" to tolerate exposure to normally lethal concentrations of bactericidal antibiotics. This ability, which is not due to antibiotic-resistant mutants, has been implicated in antibiotic treatment failures and may account for latent, chronic, and relapsing infections. Antibiotic tolerant/Persister (AT/P) cells have been notoriously difficult to study due to their low frequency and transient nature. This chapter describes the main methods used to isolate and study Pseudomonas aeruginosa AT/P cells and discusses new technologies that may ease research of P. aeruginosa persisters in the near future.
Topics: Anti-Bacterial Agents; Colony Count, Microbial; Drug Resistance, Bacterial; Microbial Sensitivity Tests; Microbial Viability; Mutation; Pseudomonas aeruginosa; Reproducibility of Results
PubMed: 24818944
DOI: 10.1007/978-1-4939-0473-0_54