scholarly journals Transcriptome Profiling of Antimicrobial Resistance in Pseudomonas aeruginosa

2016 ◽  
Vol 60 (8) ◽  
pp. 4722-4733 ◽  
Author(s):  
Ariane Khaledi ◽  
Monika Schniederjans ◽  
Sarah Pohl ◽  
Roman Rainer ◽  
Ulrich Bodenhofer ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Association Studies ◽  
Control Measures ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Learning Approaches ◽  
Content Type ◽  
Antibiotic Drug ◽  
The Future

ABSTRACTEmerging resistance to antimicrobials and the lack of new antibiotic drug candidates underscore the need for optimization of current diagnostics and therapies to diminish the evolution and spread of multidrug resistance. As the antibiotic resistance status of a bacterial pathogen is defined by its genome, resistance profiling by applying next-generation sequencing (NGS) technologies may in the future accomplish pathogen identification, prompt initiation of targeted individualized treatment, and the implementation of optimized infection control measures. In this study, qualitative RNA sequencing was used to identify key genetic determinants of antibiotic resistance in 135 clinicalPseudomonas aeruginosaisolates from diverse geographic and infection site origins. By applying transcriptome-wide association studies, adaptive variations associated with resistance to the antibiotic classes fluoroquinolones, aminoglycosides, and β-lactams were identified. Besides potential novel biomarkers with a direct correlation to resistance, global patterns of phenotype-associated gene expression and sequence variations were identified by predictive machine learning approaches. Our research serves to establish genotype-based molecular diagnostic tools for the identification of the current resistance profiles of bacterial pathogens and paves the way for faster diagnostics for more efficient, targeted treatment strategies to also mitigate the future potential for resistance evolution.

scholarly journals Fis Contributes to Resistance of Pseudomonas aeruginosa to Ciprofloxacin by Regulating Pyocin Synthesis

2020 ◽  
Vol 202 (11) ◽  
Author(s):  
Yuqing Long ◽  
Weixin Fu ◽  
Su Wang ◽  
Xuan Deng ◽  
Yongxin Jin ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Bacterial Resistance ◽  
Global Gene Expression ◽  
Chronic Infections ◽  
Mobility Shift ◽  
Content Type ◽  
Regulatory Pathways ◽  
Opportunistic Pathogenic

ABSTRACT Factor for inversion stimulation (Fis) is a versatile DNA binding protein that plays an important role in coordinating bacterial global gene expression in response to growth phases and environmental stresses. Previously, we demonstrated that Fis regulates the type III secretion system (T3SS) in Pseudomonas aeruginosa. In this study, we explored the role of Fis in the antibiotic resistance of P. aeruginosa and found that mutation of the fis gene increases the bacterial susceptibility to ciprofloxacin. We further demonstrated that genes related to pyocin biosynthesis are upregulated in the fis mutant. The pyocins are produced in response to genotoxic agents, including ciprofloxacin, and the release of pyocins results in lysis of the producer cell. Thus, pyocin biosynthesis genes sensitize P. aeruginosa to ciprofloxacin. We found that PrtN, the positive regulator of the pyocin biosynthesis genes, is upregulated in the fis mutant. Genetic experiments and electrophoretic mobility shift assays revealed that Fis directly binds to the promoter region of prtN and represses its expression. Therefore, our results revealed novel Fis-mediated regulation on pyocin production and bacterial resistance to ciprofloxacin in P. aeruginosa. IMPORTANCE Pseudomonas aeruginosa is an important opportunistic pathogenic bacterium that causes various acute and chronic infections in human, especially in patients with compromised immunity, cystic fibrosis (CF), and/or severe burn wounds. About 60% of cystic fibrosis patients have a chronic respiratory infection caused by P. aeruginosa. The bacterium is intrinsically highly resistant to antibiotics, which greatly increases difficulties in clinical treatment. Therefore, it is critical to understand the mechanisms and the regulatory pathways that are involved in antibiotic resistance. In this study, we elucidated a novel regulatory pathway that controls the bacterial resistance to fluoroquinolone antibiotics, which enhances our understanding of how P. aeruginosa responds to ciprofloxacin.

scholarly journals Evolution of Cost-Free Resistance under Fluctuating Drug Selection in Pseudomonas aeruginosa

mSphere ◽  
2017 ◽  
Vol 2 (4) ◽  
Author(s):  
Anita H. Melnyk ◽  
Nicholas McCloskey ◽  
Aaron J. Hinz ◽  
Jeremy Dettman ◽  
Rees Kassen
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Antibiotic Treatment ◽  
Experimental Evolution ◽  
Public Health Problem ◽  
Content Type ◽  
Compensatory Evolution ◽  
High Fitness ◽  
Treatment Conditions ◽  
Resistant Strains

ABSTRACT Antibiotic resistance is a global problem that greatly impacts human health. How resistance persists, even in the absence of antibiotic treatment, is thus a public health problem of utmost importance. In this study, we explored the antibiotic treatment conditions under which cost-free resistance arises, using experimental evolution of the bacterium Pseudomonas aeruginosa and the quinolone antibiotic ciprofloxacin. We found that intermittent antibiotic treatment led to the evolution of cost-free resistance and demonstrate that compensatory evolution is the mechanism responsible for cost-free resistance. Our results suggest that discontinuous administration of antibiotic may be contributing to the high levels of antibiotic resistance currently found worldwide. Antibiotic resistance evolves rapidly in response to drug selection, but it can also persist at appreciable levels even after the removal of the antibiotic. This suggests that many resistant strains can both be resistant and have high fitness in the absence of antibiotics. To explore the conditions under which high-fitness, resistant strains evolve and the genetic changes responsible, we used a combination of experimental evolution and whole-genome sequencing to track the acquisition of ciprofloxacin resistance in the opportunistic pathogen Pseudomonas aeruginosa under conditions of constant and fluctuating antibiotic delivery patterns. We found that high-fitness, resistant strains evolved readily under fluctuating but not constant antibiotic conditions and that their evolution was underlain by a trade-off between resistance and fitness. Whole-genome sequencing of evolved isolates revealed that resistance was gained through mutations in known resistance genes and that second-site mutations generally compensated for costs associated with resistance in the fluctuating treatment, leading to the evolution of cost-free resistance. Our results suggest that current therapies involving intermittent administration of antibiotics are contributing to the maintenance of antibiotic resistance at high levels in clinical settings. IMPORTANCE Antibiotic resistance is a global problem that greatly impacts human health. How resistance persists, even in the absence of antibiotic treatment, is thus a public health problem of utmost importance. In this study, we explored the antibiotic treatment conditions under which cost-free resistance arises, using experimental evolution of the bacterium Pseudomonas aeruginosa and the quinolone antibiotic ciprofloxacin. We found that intermittent antibiotic treatment led to the evolution of cost-free resistance and demonstrate that compensatory evolution is the mechanism responsible for cost-free resistance. Our results suggest that discontinuous administration of antibiotic may be contributing to the high levels of antibiotic resistance currently found worldwide.

scholarly journals Multidrug Adaptive Resistance of Pseudomonas aeruginosa Swarming Cells

2019 ◽  
Vol 64 (3) ◽  
Author(s):  
Shannon R. Coleman ◽  
Travis Blimkie ◽  
Reza Falsafi ◽  
Robert E. W. Hancock
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Efflux Pump ◽  
Iron Acquisition ◽  
Polymyxin B ◽  
Rna Seq ◽  
Multidrug Efflux ◽  
Multidrug Efflux Pump ◽  
Content Type ◽  
Adaptive Resistance

ABSTRACT Swarming surface motility is a complex adaptation leading to multidrug antibiotic resistance and virulence factor production in Pseudomonas aeruginosa. Here, we expanded previous studies to demonstrate that under swarming conditions, P. aeruginosa PA14 is more resistant to multiple antibiotics, including aminoglycosides, β-lactams, chloramphenicol, ciprofloxacin, tetracycline, trimethoprim, and macrolides, than swimming cells, but is not more resistant to polymyxin B. We investigated the mechanism(s) of swarming-mediated antibiotic resistance by examining the transcriptomes of swarming cells and swarming cells treated with tobramycin by transcriptomics (RNA-Seq) and reverse transcriptase quantitative PCR (qRT-PCR). RNA-Seq of swarming cells (versus swimming) revealed 1,581 dysregulated genes, including 104 transcriptional regulators, two-component systems, and sigma factors, numerous upregulated virulence and iron acquisition factors, and downregulated ribosomal genes. Strain PA14 mutants in resistome genes that were dysregulated under swarming conditions were tested for their ability to swarm in the presence of tobramycin. In total, 41 mutants in genes dysregulated under swarming conditions were shown to be more resistant to tobramycin under swarming conditions, indicating that swarming-mediated tobramycin resistance was multideterminant. Focusing on two genes downregulated under swarming conditions, both prtN and wbpW mutants were more resistant to tobramycin, while the prtN mutant was additionally resistant to trimethoprim under swarming conditions; complementation of these mutants restored susceptibility. RNA-Seq of swarming cells treated with subinhibitory concentrations of tobramycin revealed the upregulation of the multidrug efflux pump MexXY and downregulation of virulence factors.

scholarly journals New Molecular Tool for a Quick and Easy Detection of Apple Scab in the Field

Agronomy ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 581 ◽  
Author(s):  
Sara Franco Ortega ◽  
Simona Prencipe ◽  
Maria Lodovica Gullino ◽  
Davide Spadaro
Keyword(s):  
Direct Detection ◽  
Venturia Inaequalis ◽  
Apple Scab ◽  
Elongation Factor ◽  
Lamp Assay ◽  
Control Measures ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Sensitivity Testing ◽  
User Friendly

Venturia inaequalis, an agent of apple scab, is the most important pathogen of Malus x domestica. Control measures against this pathogen rely on intensive phytosanitary programs based on predictive models to identify the meteorological conditions conducive to the primary infection. The detection of the pathogen in field, both in naturally infected symptomatic and asymptomatic leaves, is desirable. Loop-mediated isothermal amplification (LAMP) assays are profitable molecular diagnostic tools for the direct detection of pathogens in field. A LAMP assay for V. inaequalis has been designed on the elongation factor 1-alpha sequence. The validation of the LAMP assay was carried out following the international EPPO standard PM 7/98 in terms of specificity, sensitivity, repeatability and reproducibility. Specificity testing was performed using target and non-target species, such as phylogenetically related Venturia species and other pathogens commonly found in apple, resulting in positive amplification only for the target with a time to positive ranging from 20 to 30 min. Sensitivity testing was performed with serial dilutions of DNA of the target and by artificial inoculation of young apple leaves. The reliability of the LAMP assay as an early-detection tool and its user-friendly application make it suitable for the diagnosis of apple scab in the field.

scholarly journals TpiA is a Key Metabolic Enzyme That Affects Virulence and Resistance to Aminoglycoside Antibiotics through CrcZ in Pseudomonas aeruginosa

mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Yushan Xia ◽  
Dan Wang ◽  
Xiaolei Pan ◽  
Bin Xia ◽  
Yuding Weng ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Carbon Metabolism ◽  
Essential Role ◽  
Bacterial Resistance ◽  
Triosephosphate Isomerase ◽  
Aminoglycoside Antibiotics ◽  
Metabolic Enzyme ◽  
Dihydroxyacetone Phosphate ◽  
Content Type

ABSTRACT Carbon metabolism plays an essential role in bacterial pathogenesis and susceptibility to antibiotics. In Pseudomonas aeruginosa, Crc, Hfq, and a small RNA, CrcZ, are central regulators of carbon metabolism. By screening mutants of genes involved in carbon metabolism, we found that mutation of the tpiA gene reduces the expression of the type III secretion system (T3SS) and bacterial resistance to aminoglycoside antibiotics. TpiA is a triosephosphate isomerase that reversibly converts glyceraldehyde 3-phosphate to dihydroxyacetone phosphate, a key step connecting glucose metabolism with glycerol and phospholipid metabolisms. We found that mutation of the tpiA gene enhances the bacterial carbon metabolism, respiration, and oxidative phosphorylation, which increases the membrane potential and promotes the uptake of aminoglycoside antibiotics. Further studies revealed that the level of CrcZ is increased in the tpiA mutant due to enhanced stability. Mutation of the crcZ gene in the tpiA mutant background restored the expression of the T3SS genes and the bacterial resistance to aminoglycoside antibiotics. Overall, this study reveals an essential role of TpiA in the metabolism, virulence, and antibiotic resistance in P. aeruginosa. IMPORTANCE The increase in bacterial resistance against antibiotics imposes a severe threat to public health. It is urgent to identify new drug targets and develop novel antimicrobials. Metabolic homeostasis of bacteria plays an essential role in their virulence and resistance to antibiotics. Recent studies demonstrated that antibiotic efficacies can be improved by modulating the bacterial metabolism. Pseudomonas aeruginosa is an important opportunistic human pathogen that causes various infections. The bacterium is intrinsically resistant to antibiotics. In this study, we provide clear evidence that TpiA (triosephosphate isomerase) plays an essential role in the metabolism of P. aeruginosa and influences bacterial virulence and antibiotic resistance. The significance of this work is in identifying a key enzyme in the metabolic network, which will provide clues as to the development of novel treatment strategies against infections caused by P. aeruginosa.

Pandemic designs for the future: perspectives of technology education teachers during COVID-19

2020 ◽  
Vol 121 (5/6) ◽  
pp. 419-431
Author(s):  
Jillianne Code ◽  
Rachel Ralph ◽  
Kieran Forde
Keyword(s):  
Blended Learning ◽  
Technology Education ◽  
Research Question ◽  
Substantial Effect ◽  
Professional Organization ◽  
Learning Approaches ◽  
Blended Instruction ◽  
Content Type ◽  
The Future ◽  
Specialist Teachers

Purpose The disruption caused by the pandemic declaration and subsequent public health measures put in place have had a substantial effect on teachers’ abilities to support student engagement in technology education (TE). The purpose of this paper is to explore the following research question: How do TE teachers see emergency remote teaching (ERT) transitions to blended learning into the next academic year affecting their profession? Design/methodology/approach A snowball and convenience sampling design was used to recruit specialist teachers in TE through their professional organization and were asked to respond to the question: What are your concerns about the future of teaching TE remotely? The qualitative data collected from the participants (N = 42) was analyzed thematically (Braun and Clarke, 2006). Findings The analysis revealed that the switch to ERT impacted the teachers’ ability to support hands-on competency development owing to inequitable student access to tools, materials and resources, all of which affected student motivation and engagement. As a result, teachers raised questions about the overall effectiveness of online learning approaches and TE’s future and sustainability if offered completely online. Originality/value This research is the first of its kind exploring the experiences of TE teachers during the COVID-19 pandemic. In answer to the challenges identified by teachers, the authors offer a blended learning design framework informed by pandemic transformed pedagogy that can serve as a model for educators to use when designing blended instruction.

scholarly journals Aggressive Emerging Pathovars of Xanthomonas arboricola Represent Widespread Epidemic Clones Distinct from Poorly Pathogenic Strains, as Revealed by Multilocus Sequence Typing

2015 ◽  
Vol 81 (14) ◽  
pp. 4651-4668 ◽  
Author(s):  
Marion Fischer-Le Saux ◽  
Sophie Bonneau ◽  
Salwa Essakhi ◽  
Charles Manceau ◽  
Marie-Agnès Jacques
Keyword(s):  
Genetic Structure ◽  
Xanthomonas Campestris ◽  
Plant Pathogens ◽  
Genetic Relationships ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Phylogenic Tree ◽  
Content Type ◽  
Epidemiological Surveys ◽  
Xanthomonas Arboricola

ABSTRACTDeep and comprehensive knowledge of the genetic structure of pathogenic species is the cornerstone on which the design of precise molecular diagnostic tools is built.Xanthomonas arboricolais divided into pathovars, some of which are classified as quarantine organisms in many countries and are responsible for diseases on nut and stone fruit trees that have emerged worldwide. Recent taxonomic studies of the genusXanthomonasshowed that strains isolated from other hosts should be classified inX. arboricola, extending the host range of the species. To investigate the genetic structure ofX. arboricolaand the genetic relationships between highly pathogenic strains and strains apparently not relevant to plant health, we conducted multilocus sequence analyses on a collection of strains representative of the known diversity of the species. Most of the pathovars were clustered in separate monophyletic groups. The pathovars pruni, corylina, and juglandis, responsible for pandemics in specific hosts, were highly phylogenetically related and clustered in three distinct clonal complexes. In contrast, strains with no or uncertain pathogenicity were represented by numerous unrelated singletons scattered in the phylogenic tree. Depending on the pathovar, intra- and interspecies recombination played contrasting roles in generating nucleotide polymorphism. This work provides a population genetics framework for molecular epidemiological surveys of emerging plant pathogens withinX. arboricola. Based on our results, we propose to reclassify three former pathovars ofXanthomonas campestrisasX. arboricolapv. arracaciae comb. nov.,X. arboricolapv. guizotiae comb. nov., andX. arboricolapv. zantedeschiae comb. nov. An emended description ofX. arboricolaVauterin et al. 1995 is provided.

scholarly journals The Widespread Multidrug-Resistant Serotype O12 Pseudomonas aeruginosa Clone Emerged through Concomitant Horizontal Transfer of Serotype Antigen and Antibiotic Resistance Gene Clusters

mBio ◽  
2015 ◽  
Vol 6 (5) ◽  
Author(s):  
Sandra Wingaard Thrane ◽  
Véronique L. Taylor ◽  
Luca Freschi ◽  
Irena Kukavica-Ibrulj ◽  
Brian Boyle ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Horizontal Transfer ◽  
Core Genome ◽  
Gene Clusters ◽  
Multidrug Resistant ◽  
Clinical Settings ◽  
Content Type ◽  
The Past ◽  
Antibiotic Resistance Determinant

ABSTRACTThe O-specific antigen (OSA) inPseudomonas aeruginosalipopolysaccharide is highly varied by sugar identity, side chains, and bond between O-repeats. These differences classifiedP. aeruginosainto 20 distinct serotypes. In the past few decades, O12 has emerged as the predominant serotype in clinical settings and outbreaks. These serotype O12 isolates exhibit high levels of resistance to various classes of antibiotics. Here, we explore how theP. aeruginosaOSA biosynthesis gene clusters evolve in the population by investigating the association between the phylogenetic relationships among 83P. aeruginosastrains and their serotypes. While most serotypes were closely linked to the core genome phylogeny, we observed horizontal exchange of OSA biosynthesis genes among phylogenetically distinctP. aeruginosastrains. Specifically, we identified a “serotype island” ranging from 62 kb to 185 kb containing theP. aeruginosaO12 OSA gene cluster, an antibiotic resistance determinant (gyrAC248T), and other genes that have been transferred betweenP. aeruginosastrains with distinct core genome architectures. We showed that these genes were likely acquired from an O12 serotype strain that is closely related toP. aeruginosaPA7. Acquisition and recombination of the “serotype island” resulted in displacement of the native OSA gene cluster and expression of the O12 serotype in the recipients. Serotype switching by recombination has apparently occurred multiple times involving bacteria of various genomic backgrounds. In conclusion, serotype switching in combination with acquisition of an antibiotic resistance determinant most likely contributed to the dissemination of the O12 serotype in clinical settings.IMPORTANCEInfection rates in hospital settings by multidrug-resistant (MDR)Pseudomonas aeruginosaclones have increased during the past decades, and serotype O12 is predominant among these epidemic strains. It is not known why the MDR phenotype is associated with serotype O12 and how this clone type has emerged. This study shows that evolution of MDR O12 strains involved a switch from an ancestral O4 serotype to O12. Serotype switching was the result of horizontal transfer and genetic recombination of lipopolysaccharide (LPS) biosynthesis genes originating from an MDR taxonomic outlierP. aeruginosastrain. Moreover, the recombination event also resulted in acquisition of antibiotic resistance genes. These results impact on our understanding of MDR outbreak strain and serotype evolution and can potentially assist in better monitoring and prevention.

scholarly journals Anthranilate Acts as a Signal to Modulate Biofilm Formation, Virulence, and Antibiotic Tolerance of Pseudomonas aeruginosa and Surrounding Bacteria

2022 ◽  
Author(s):  
Hyeon-Ji Hwang ◽  
Xi-Hui Li ◽  
Soo-Kyoung Kim ◽  
Joon-Hee Lee
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Biofilm Formation ◽  
Chronic Infection ◽  
Antibiotic Tolerance ◽  
Content Type ◽  
Before And After

Pseudomonas aeruginosa is a notorious pathogen with high antibiotic resistance, strong virulence, and ability to cause biofilm-mediated chronic infection. We found that these characteristics change profoundly before and after the time when anthranilate is produced as an “anthranilate peak”.

scholarly journals The rise and the fall of a Pseudomonas aeruginosa endemic lineage in a hospital

2021 ◽  
Vol 7 (9) ◽  
Author(s):  
Marie Petitjean ◽  
Paulo Juarez ◽  
Alexandre Meunier ◽  
Etienne Daguindau ◽  
Hélène Puja ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Infection Control ◽  
Water Distribution ◽  
Efflux Pump ◽  
Hospital Setting ◽  
Metal Resistance ◽  
Control Measures ◽  
Hospital Environment ◽  
Content Type ◽  
Over Time

The biological features that allow a pathogen to survive in the hospital environment are mostly unknown. The extinction of bacterial epidemics in hospitals is mostly attributed to changes in medical practice, including infection control, but the role of bacterial adaptation has never been documented. We analysed a collection of Pseudomonas aeruginosa isolates belonging to the Besançon Epidemic Strain (BES), responsible for a 12year nosocomial outbreak, using a genotype-to-phenotype approach. Bayesian analysis estimated the emergence of the clone in the hospital 5 years before its opening, during the creation of its water distribution network made of copper. BES survived better than the reference strains PAO1 and PA14 in a copper solution due to a genomic island containing 13 metal-resistance genes and was specifically able to proliferate in the ubiquitous amoeba Vermamoeba vermiformis. Mutations affecting amino-acid metabolism, antibiotic resistance, lipopolysaccharide biosynthesis, and regulation were enriched during the spread of BES. Seven distinct regulatory mutations attenuated the overexpression of the genes encoding the efflux pump MexAB-OprM over time. The fitness of BES decreased over time in correlation with its genome size. Overall, the resistance to inhibitors and predators presumably aided the proliferation and propagation of BES in the plumbing system of the hospital. The pathogen further spread among patients via multiple routes of contamination. The decreased prevalence of patients infected by BES mirrored the parallel and convergent genomic evolution and reduction that affected bacterial fitness. Along with infection control measures, this may have participated in the extinction of BES in the hospital setting.

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