Whole genome sequencing reveals the emergence of a Pseudomonas aeruginosa shared strain sub-lineage among patients treated within a single cystic fibrosis centre

Wee, Bryan A.; Tai, Anna; Sherrard, L.; Zakour, Nouri L. Ben; Hanks, Kirt R; Kidd, Timothy J.; Ramsay, Kay A.; Lamont, Iain L.; Whiley, David M.; Bell, Scott C.; Beatson, Scott A.

doi:10.1186/s12864-018-5018-x

Cited by 19 publications

(23 citation statements)

References 65 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It was previously hypothesized that virulence factors are selected against in CF infections, and in agreement with this, we found that 34 of the 52 highly variable genes were lost as part of a genomic region encoding the virulence factors hydrogen cyanide synthase ( hcnABC ) and type III secreted protein ExoY ( exoY ). It was also shown previously by Wee et al (2018) ( 26 ) that selective pressures associated with loss of hcnA , hcnB , hcnC , and exoY genes exist, and Wee et al also observed deletions of various sizes around the respective genes. Furthermore, the selective pressure associated with loss of hcnABC locus virulence genes was recently shown to possibly be related to the increased antibiotic resistance in multidrug-resistant strains ( 36 ).…”

Section: Discussionsupporting

confidence: 71%

See 1 more Smart Citation

Gene Loss and Acquisition in Lineages of Pseudomonas aeruginosa Evolving in Cystic Fibrosis Patient Airways

Gabrielaitė

Johansen

Molin

et al. 2020

mBio

View full text Add to dashboard Cite

Genome analyses have documented that there are differences in gene repertoire between evolutionary distant lineages of the same bacterial species; however, less is known about microevolutionary dynamics of gene loss and acquisition within bacterial lineages as they evolve over years. Here, we analyzed the genomes of 45 Pseudomonas aeruginosa lineages evolving in the lungs of cystic fibrosis (CF) patients to identify genes that are lost or acquired during the first years of infection. On average, lineage genome content changed by 88 genes (range, 0 to 473). Genes were more often lost than acquired, and prophage genes were more variable than bacterial genes. We identified convergent loss or acquisition of the same genes across lineages, suggesting selection for loss and acquisition of certain genes in the host environment. We found that a notable proportion of such genes are associated with virulence; a trait previously shown to be important for adaptation. Furthermore, we also compared the genomes across lineages to show that the within-lineage variable genes (i.e., genes that had been lost or acquired during the infection) often belonged to genomic content not shared across all lineages. In sum, our analysis adds to the knowledge on the pace and drivers of gene loss and acquisition in bacteria evolving over years in a human host environment and provides a basis to further understand how gene loss and acquisition play roles in lineage differentiation and host adaptation. IMPORTANCE Bacterial airway infections, predominantly caused by P. aeruginosa, are a major cause of mortality and morbidity of CF patients. While short insertions and deletions as well as point mutations occurring during infection are well studied, there is a lack of understanding of how gene loss and acquisition play roles in bacterial adaptation to the human airways. Here, we investigated P. aeruginosa within-host evolution with regard to gene loss and acquisition. We show that during long-term infection P. aeruginosa genomes tend to lose genes, in particular, genes related to virulence. This adaptive strategy allows reduction of the genome size and evasion of the host’s immune response. This knowledge is crucial to understand the basic mutational steps that, on the timescale of years, diversify lineages and adds to the identification of bacterial genetic determinants that have implications for CF disease.

show abstract

Section: Discussionsupporting

confidence: 71%

“…Some of these proteins had more than one function assigned by PseudoCAP. A literature search indicated that four of the genes ( hcnABC and exoY encoding hydrogen cyanide synthase and type III secreted protein, respectively) are known to play a role in the virulence and pathogenesis of P. aeruginosa ( 25 , 26 ).…”

Section: Resultsmentioning

confidence: 99%

Gene Loss and Acquisition in Lineages of Pseudomonas aeruginosa Evolving in Cystic Fibrosis Patient Airways

Gabrielaitė

Johansen

Molin

et al. 2020

mBio

View full text Add to dashboard Cite

show abstract

“…Indeed, the P. aeruginosa genome was shown to accumulate a median of 3 SNPs per year, varying between 0.5 and 14 SNPs per year [6–9, 12, 14–18]. Small indels have also been reported at rates ranging from 0.4 to 2.7 indels per year (0.1 to 0.28 indels per SNP) [12, 14, 17].…”

Section: Genomic Adaptation Of P Aeruginosamentioning

confidence: 99%

“…aeruginosa strain isolates collected 7.5 years apart from the same patient [6]. Following studies were performed on a broader range of isolates from unique patients [7–12] or on transmissible lineages such as DK2 or AUST-02 [13–15]. Finally, Marvig et al .…”

Section: Introductionmentioning

confidence: 99%

From genotype to phenotype: adaptations of Pseudomonas aeruginosa to the cystic fibrosis environment

2021

View full text Add to dashboard Cite

Pseudomonas aeruginosa is one of the main microbial species colonizing the lungs of cystic fibrosis patients and is responsible for the decline in respiratory function. Despite the hostile pulmonary environment, P. aeruginosa is able to establish chronic infections thanks to its strong adaptive capacity. Various longitudinal studies have attempted to compare the strains of early infection with the adapted strains of chronic infection. Thanks to new ‘-omics’ techniques, convergent genetic mutations, as well as transcriptomic and proteomic dysregulations have been identified. As a consequence of this evolution, the adapted strains of P. aeruginosa have particular phenotypes that promote persistent infection.

show abstract

“…Therefore, genotypic analyses are required. Pulsed-field gel electrophoresis (PFGE) is the “gold standard” method for microbial typing 15,17–20…”

Section: Introductionmentioning

confidence: 99%

<p>Genotypic characterization of <em>Pseudomonas aeruginosa</em> isolates from Turkish children with cystic fibrosis</p>

Okur

Yürüyen

Güngör

et al. 2019

IDR

View full text Add to dashboard Cite

Objective: To identify epidemic and other transmissible Pseudomonas aeruginosa strains, genotypic analyses are required. The aim of this study was to assess the distribution of P. aeruginosa strains within the Turkish pediatric cystic fibrosis (CF) clinic population. Methods: Eighteen patients attending the pediatric CF clinic of Cerrahpasa Medical Faculty were investigated in the study. Throat swab and/or sputum samples were taken from each patient at 3-month intervals. The isolates of patients were analyzed by pulsed-field gel electrophoresis (PFGE). The intra- and interpatient genotypic heterogeneity of isolates was examined to determine the clonal isolates of P. aeruginosa within the cohort. Results: A total of 108 clinical isolates of P. aeruginosa were obtained from 18 patients between May 2013 and May 2014. The pulsotypes of the first patient’s isolates could not be obtained by PFGE. From the remaining 17 patients and 101 isolates, 55 distinct pulsotypes were detected. The number of pulsotypes observed in more than one patient (minor clonal strains, cluster strains) was 8 (14.5%), and one of them colonized three patients. However, none of them was detected in more than three patients. These pulsotypes were composed of 20 isolates. In addition, with the PFGE analysis of 81 isolates, we detected 47 (85.6%) pulsotypes, which belonged to only one patient. Over different periods of this study, only 2 (11.8%) patients were colonized with the same pulsotype. Conclusion: Our study indicates that there was considerable genomic diversity among the P. aeruginosa isolates in our clinic. The presence of shared pulsotypes supports cross-transmission between patients.

show abstract

Whole genome sequencing reveals the emergence of a Pseudomonas aeruginosa shared strain sub-lineage among patients treated within a single cystic fibrosis centre

Cited by 19 publications

References 65 publications

Gene Loss and Acquisition in Lineages of Pseudomonas aeruginosa Evolving in Cystic Fibrosis Patient Airways

Gene Loss and Acquisition in Lineages of Pseudomonas aeruginosa Evolving in Cystic Fibrosis Patient Airways

From genotype to phenotype: adaptations of Pseudomonas aeruginosa to the cystic fibrosis environment

<p>Genotypic characterization of <em>Pseudomonas aeruginosa</em> isolates from Turkish children with cystic fibrosis</p>

Contact Info

Product

Resources

About