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Cottalorda A, Leoz M, Dahyot S, Gravey F, Grand M, Froidure T, Aujoulat F, Le Hello S, Jumas-Bilak E, Pestel-Caron M. Within-Host Microevolution of Pseudomonas aeruginosa Urinary Isolates: A Seven-Patient Longitudinal Genomic and Phenotypic Study. Front Microbiol 2021; 11:611246. [PMID: 33519766 PMCID: PMC7840598 DOI: 10.3389/fmicb.2020.611246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/14/2020] [Indexed: 11/25/2022] Open
Abstract
Background Pseudomonas aeruginosa is responsible for up to 10% of healthcare associated urinary tract infections (UTI), which can be difficult to treat and can lead to bacterial persistence. While numerous whole genome sequencing (WGS) analyses have explored within-host genomic adaptation and microevolution of P. aeruginosa during cystic fibrosis (CF) infections, little is known about P. aeruginosa adaptation to the urinary tract. Results Whole genome sequencing was performed on 108 P. aeruginosa urinary isolates, representing up to five isolates collected from 2 to 5 successive urine samples from seven patients hospitalized in a French hospital over 48–488 days. Clone type single nucleotide polymorphisms (ctSNPs) analysis revealed that each patient was colonized by a single clone type (<6000 SNPs between two isolates) at a given time and over time. However, 0–126 SNPs/genome/year were detected over time. Furthermore, large genomic deletions (1–5% of the genome) were identified in late isolates from three patients. For 2 of them, a convergent deletion of 70 genes was observed. Genomic adaptation (SNPs and deletion) occurred preferentially in genes encoding transcriptional regulators, two-component systems, and carbon compound catabolism. This genomic adaptation was significantly associated with a reduced fitness, particularly in artificial urine medium, but no strict correlation was identified between genomic adaptation and biofilm formation. Conclusion This study provides the first insight into P. aeruginosa within-host evolution in the urinary tract. It was driven by mutational mechanisms and genomic deletions and could lead to phenotypic changes in terms of fitness and biofilm production. Further metabolomic and phenotypic analyses are needed to describe in-depth genotype-phenotype associations in this complex and dynamic host-environment.
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Affiliation(s)
- Agnès Cottalorda
- Normandie Université, UNIROUEN, Groupe de Recherche sur l'Adapatation Microbienne (GRAM 2.0 EA2656), Rouen, France
| | - Marie Leoz
- Normandie Université, UNIROUEN, Groupe de Recherche sur l'Adapatation Microbienne (GRAM 2.0 EA2656), Rouen, France
| | - Sandrine Dahyot
- Normandie Université, UNIROUEN, Groupe de Recherche sur l'Adapatation Microbienne (GRAM 2.0 EA2656), Rouen, France.,Department of Bacteriology, Rouen University Hospital, Normandie Université, UNIROUEN, Groupe de Recherche sur l'Adapatation Microbienne (GRAM 2.0 EA2656), Rouen, France
| | - François Gravey
- Normandie Université, UNICAEN, Groupe de Recherche sur l'Adapatation Microbienne (GRAM 2.0 EA2656), Caen, France
| | - Maxime Grand
- Normandie Université, UNIROUEN, Groupe de Recherche sur l'Adapatation Microbienne (GRAM 2.0 EA2656), Rouen, France
| | - Thomas Froidure
- Normandie Université, UNIROUEN, Groupe de Recherche sur l'Adapatation Microbienne (GRAM 2.0 EA2656), Rouen, France
| | - Fabien Aujoulat
- Team Pathogènes Hydriques Santé Environnement, UMR 5569 HydroSciences Montpellier, Unité de Bactériologie, UFR Pharmacie, University of Montpellier, Montpellier, France
| | - Simon Le Hello
- Normandie Université, UNICAEN, Groupe de Recherche sur l'Adapatation Microbienne (GRAM 2.0 EA2656), Caen, France
| | - Estelle Jumas-Bilak
- Team Pathogènes Hydriques Santé Environnement, UMR 5569 HydroSciences Montpellier, Unité de Bactériologie, UFR Pharmacie, University of Montpellier, Montpellier, France
| | - Martine Pestel-Caron
- Normandie Université, UNIROUEN, Groupe de Recherche sur l'Adapatation Microbienne (GRAM 2.0 EA2656), Rouen, France.,Department of Bacteriology, Rouen University Hospital, Normandie Université, UNIROUEN, Groupe de Recherche sur l'Adapatation Microbienne (GRAM 2.0 EA2656), Rouen, France
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Complete Genome Sequence of Pseudomonas aeruginosa PA1, Isolated from a Patient with a Respiratory Tract Infection. GENOME ANNOUNCEMENTS 2015; 3:3/6/e01453-15. [PMID: 26659688 PMCID: PMC4675953 DOI: 10.1128/genomea.01453-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We report the 6,498,072-bp complete genome sequence of Pseudomonas aeruginosa PA1, which was isolated from a patient with a respiratory tract infection in Chongqing, People's Republic of China. Whole-genome sequencing was performed using single-molecule real-time (SMRT) technology, and de novo assembly revealed a single contig with 396-fold sequence coverage.
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