Phenotypic and Genomic Variability of Serial Peri-Lung Transplantation Pseudomonas aeruginosa Isolates From Cystic Fibrosis Patients

Datar, Rucha; Pelegrin, Andreu Coello; Orenga, Sylvain; Chalansonnet, Valérie; Mirande, Caroline; Dombrecht, Jill; Perry, John D.; Perry, Audrey; Goossens, Herman; Belkum, Alex van

doi:10.3389/fmicb.2021.604555

Cited by 11 publications

(12 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, the genetic mediators of persister formation for P. aeruginosa are poorly understood [ 4 ]. In the current study, genome sequencing of persister-forming isolates revealed that they had smaller genomes (4.66–4.9 Mbp), compared to PAO1-genome (6.3 Mbp) sequenced previously [ 55 ], and the genome of Pseudomonas CF-isolates (6.36 Mbp) recently sequenced [ 50 ]. The smaller genome size for our isolates could be due to the short-reads-based sequencing and assembly used in our study.…”

Section: Discussionmentioning

confidence: 77%

“…Further investigation is required to explore the validity and features of this clade. Similarly, the phylogenetic analysis of P. aeruginosa CF isolates performed by Datar et al [ 50 ] revealed their unique clustering and indicate their location in different clades. To the best of our knowledge, our study is the first to study the genome sequence of persister isolates from local hospitals in Egypt.…”

Section: Discussionmentioning

confidence: 94%

“…Similarly, a recent study of Pseudomonas CF isolates revealed that more than 75% of the CF isolates were resistant to at least half of the antibiotics. Additionally, 25% of their isolates were found to be resistant to all the tested antibiotics, and only 36% of CF-isolates were resistant to tobramycin [ 50 ]. Furthermore, it was reported that persister (Hip) isolates were resistant to ciprofloxacin by 72.4% [ 45 ].…”

Section: Discussionmentioning

confidence: 99%

“…Resistome profiling indicated the presence of a broad collection of antibiotic-resistance genes in our persisters’ genome, with 25 resistance genes distributed in persister-isolates, most of which confer resistance to β-lactams (11 genes), aminoglycoside resistance (6 genes), and chloramphenicol resistance (3 genes), while resistance to other antibiotic classes is mediated by one gene each. CARD analysis revealed that the CF-isolates genome contains a high number of resistance genes, including beta-lactam resistance genes ( n = 6), efflux pumps ( n = 37), antibiotic inactivation enzymes ( n = 8), and only one aminoglycoside resistance gene [ 50 ].…”

Section: Discussionmentioning

confidence: 99%

See 3 more Smart Citations

Genome Analysis of Pseudomonas aeruginosa Strains from Chronically Infected Patients with High Levels of Persister Formation

et al. 2023

View full text Add to dashboard Cite

The appearance of persister cells with low metabolic rates are key factors leading to antibiotic treatment failure. Such persisters are multidrug tolerant and play a key role in the recalcitrance of biofilm-based chronic infections. Here, we present the genomic analyses of three distinct Pseudomonas aeruginosa Egyptian persister-isolates recovered from chronic human infections. To calculate the persister frequencies, viable counts were determined before and after treatment with levofloxacin. The susceptibilities of isolates to different antibiotics were determined using the agar-dilution method. To determine their recalcitrance, the levofloxacin persisters were further challenged with lethal concentrations of meropenem, tobramycin, or colistin. Furthermore, the biofilm formation of the persister strains was estimated phenotypically, and they were reported to be strong biofilm-forming strains. The genotypic characterization of the persisters was performed using whole genome sequencing (WGS) followed by phylogenetic analysis and resistome profiling. Interestingly, out of the thirty-eight clinical isolates, three isolates (8%) demonstrated a persister phenotype. The three levofloxacin-persister isolates were tested for their susceptibility to selected antibiotics; all of the tested isolates were multidrug resistant (MDR). Additionally, the P. aeruginosa persisters were capable of surviving over 24 h and were not eradicated after exposure to 100X-MIC of levofloxacin. WGS for the three persisters revealed a smaller genome size compared to PAO1-genome. Resistome profiling indicated the presence of a broad collection of antibiotic-resistance genes, including genes encoding for antibiotic-modifying enzymes and efflux pump. Phylogenetic analysis indicated that the persister isolates belong to a distinct clade rather than the deposited P. aeruginosa strains in the GenBank. Conclusively, the persister isolates in our study are MDR and form a highly strong biofilm. WGS revealed a smaller genome that belongs to a distinct clade.

show abstract

Section: Discussionmentioning

confidence: 77%

Section: Discussionmentioning

confidence: 94%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Genome Analysis of Pseudomonas aeruginosa Strains from Chronically Infected Patients with High Levels of Persister Formation

et al. 2023

View full text Add to dashboard Cite

show abstract

“…Microbial and host factors furthermore impact the ongoing adaptive response exhibited by mutating strains within the airways of immunocompromised CF patients. This results in the acquisition of advantageous attributes such as virulence factor assembly, motility, antibiotic resistance, and metabolic adaptation [ 14 ]. Prior studies have shown that hypermutator strains may constitute up to 60% of all P .…”

Section: Introductionmentioning

confidence: 99%

Genomic heterogeneity underlies multidrug resistance in Pseudomonas aeruginosa: A population-level analysis beyond susceptibility testing

et al. 2022

View full text Add to dashboard Cite

Background Pseudomonas aeruginosa is a persistent and difficult-to-treat pathogen in many patients, especially those with Cystic Fibrosis (CF). Herein, we describe a longitudinal analysis of a series of multidrug resistant (MDR) P. aeruginosa isolates recovered in a 17-month period, from a young female CF patient who underwent double lung transplantation. Our goal was to understand the genetic basis of the observed resistance phenotypes, establish the genomic population diversity, and define the nature of sequence evolution over time. Methods Twenty-two sequential P. aeruginosa isolates were obtained within a 17-month period, before and after a double-lung transplant. At the end of the study period, antimicrobial susceptibility testing, whole genome sequencing (WGS), phylogenetic analyses and RNAseq were performed in order to understand the genetic basis of the observed resistance phenotypes, establish the genomic population diversity, and define the nature of sequence changes over time. Results The majority of isolates were resistant to almost all tested antibiotics. A phylogenetic reconstruction revealed 3 major clades representing a genotypically and phenotypically heterogeneous population. The pattern of mutation accumulation and variation of gene expression suggested that a group of closely related strains was present in the patient prior to transplantation and continued to change throughout the course of treatment. A trend toward accumulation of mutations over time was observed. Different mutations in the DNA mismatch repair gene mutL consistent with a hypermutator phenotype were observed in two clades. RNAseq performed on 12 representative isolates revealed substantial differences in the expression of genes associated with antibiotic resistance and virulence traits. Conclusions The overwhelming current practice in the clinical laboratories setting relies on obtaining a pure culture and reporting the antibiogram from a few isolated colonies to inform therapy decisions. Our analyses revealed significant underlying genomic heterogeneity and unpredictable evolutionary patterns that were independent of prior antibiotic treatment, highlighting the need for comprehensive sampling and population-level analysis when gathering microbiological data in the context of CF P. aeruginosa chronic infection. Our findings challenge the applicability of antimicrobial stewardship programs based on single-isolate resistance profiles for the selection of antibiotic regimens in chronic infections such as CF.

show abstract

Investigating genotype‐phenotype correlations in primary ciliary dyskinesia: a sibling cohort study

Hazan,

Aviram,

Levanon

et al. 2024

Pediatric Pulmonology

View full text Add to dashboard Cite

IntroductionPrimary Ciliary Dyskinesia (PCD) is a complex mostly autosomal recessive disorder characterized by dysfunction of primary motor cilia, leading to multisystemic manifestations, primarily affecting the rhino‐sinopulmonary system. Despite advancements in understanding its pathogenesis, genotype‐phenotype correlations are not fully elucidated. Utilizing sibling cohorts offers a promising approach to investigate these genotype‐phenotype correlations in PCD.Materials and MethodsThis retrospective cohort study, conducted from 2010 to 2023 at Soroka University Medical Center in Be'er‐Sheva, Israel, included patients with a confirmed diagnosis of PCD. Variables and outcomes compared include typical presenting symptoms, lung function, structural changes in chest tomography (CT), and anthropometric data.ResultsSeventeen sibling patients from eight families met the inclusion criteria. At the last follow‐up visit, the median age was 16 years. Genetic diagnosis revealed homozygous pathogenic variants including DNAH11, DNAAF3, DNAL1, and ZMYND10. Full concordance rates were observed for unexplained neonatal respiratory distress, chronic cough, and rhinosinusitis in patients with DNAH11 mutations. The family with the DNAAF3 mutation exhibited the lowest difference in Forced Expiratory Volume in 1 s (FEV1) Z‐scores (0.48), but the highest differences in Forced Vital Capacity (FVC) Z‐scores (3.39). High differences in FEV1 Z‐scores were identified in the family with the DNAL1 mutation (2.06), while the lowest differences in FVC Z‐scores (0.39) were observed in the same family.DiscussionHigh concordance rates for certain mutations in clinical features suggest potential genotype‐phenotype correlations, in contrast to weak concordance in lung function. Challenges remain in establishing direct correlations between genetic mutations and clinical outcomes.

show abstract

Phenotypic and Genomic Variability of Serial Peri-Lung Transplantation Pseudomonas aeruginosa Isolates From Cystic Fibrosis Patients

Cited by 11 publications

References 49 publications

Genome Analysis of Pseudomonas aeruginosa Strains from Chronically Infected Patients with High Levels of Persister Formation

Genome Analysis of Pseudomonas aeruginosa Strains from Chronically Infected Patients with High Levels of Persister Formation

Genomic heterogeneity underlies multidrug resistance in Pseudomonas aeruginosa: A population-level analysis beyond susceptibility testing

Investigating genotype‐phenotype correlations in primary ciliary dyskinesia: a sibling cohort study

Contact Info

Product

Resources

About