Intraclonal genome diversity of Pseudomonas aeruginosa clones CHA and TB

被引:18
作者
Bezuidt, Oliver K. I. [1 ,2 ]
Klockgether, Jens [1 ]
Elsen, Sylvie [3 ,4 ,5 ,6 ]
Attree, Ina [3 ,4 ,5 ,6 ]
Davenport, Colin F. [1 ]
Tuemmler, Burkhard [1 ,7 ]
机构
[1] Hannover Med Sch, Klin Padiatr Pneumol Allergol & Neonatol, Klin Forschergrp, D-30625 Hannover, Germany
[2] Univ Pretoria, Dept Biochem, Bioinformat & Computat Biol Unit, ZA-0002 Pretoria, South Africa
[3] INSERM, UMR S 1036, Grenoble, France
[4] CNRS, ERL 5261, Grenoble, France
[5] UJF Grenoble 1, F-38041 Grenoble, France
[6] 6CEA, DSV iRTSV, F-38054 Grenoble, France
[7] Biomed Res Endstage and Obstruct Lung Dis Hannove, Hannover, Germany
关键词
Pseudomonas aeruginosa; Microevolution; Habitat adaptation; Genome diversity; POPULATION-STRUCTURE; DATA VISUALIZATION; SECRETION SYSTEM; SEQUENCE; PROTEIN; FAMILY; IMPACT; GENES; PHAGE; ADAPTATION;
D O I
10.1186/1471-2164-14-416
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Background: Adaptation of Pseudomonas aeruginosa to different living conditions is accompanied by microevolution resulting in genomic diversity between strains of the same clonal lineage. In order to detect the impact of colonized habitats on P. aeruginosa microevolution we determined the genomic diversity between the highly virulent cystic fibrosis (CF) isolate CHA and two temporally and geographically unrelated clonal variants. The outcome was compared with the intraclonal genome diversity between three more closely related isolates of another clonal complex. Results: The three clone CHA isolates differed in their core genome in several dozen strain specific nucleotide exchanges and small deletions from each other. Loss of function mutations and non-conservative amino acid replacements affected several habitat-and lifestyle-associated traits, for example, the key regulator GacS of the switch between acute and chronic disease phenotypes was disrupted in strain CHA. Intraclonal genome diversity manifested in an individual composition of the respective accessory genome whereby the highest number of accessory DNA elements was observed for isolate PT22 from a polluted aquatic habitat. Little intraclonal diversity was observed between three spatiotemporally related outbreak isolates of clone TB. Although phenotypically different, only a few individual SNPs and deletions were detected in the clone TB isolates. Their accessory genome mainly differed in prophage-like DNA elements taken up by one of the strains. Conclusions: The higher geographical and temporal distance of the clone CHA isolates was associated with an increased intraclonal genome diversity compared to the more closely related clone TB isolates derived from a common source demonstrating the impact of habitat adaptation on the microevolution of P. aeruginosa. However, even short-term habitat differentiation can cause major phenotypic diversification driven by single genomic variation events and uptake of phage DNA.
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页数:15
相关论文
共 62 条
[1]  
[Anonymous], ENTW WASS RUHR
[2]  
[Anonymous], 1978, ALTAS PROTEIN SEQUEN
[3]  
Apweiler R, 2004, NUCLEIC ACIDS RES, V32, pD115, DOI [10.1093/nar/gkh131, 10.1093/nar/gkw1099]
[4]   Proteome analysis of intraclonal diversity of two Pseudomonas aeruginosa TB clone isolates [J].
Arevalo-Ferro, C ;
Buschmann, J ;
Reil, G ;
Görg, A ;
Wiehlmann, L ;
Tümmler, B ;
Eberl, L ;
Riedel, K .
PROTEOMICS, 2004, 4 (05) :1241-1246
[5]   Complete genomic sequence of bacteriophage B3, a Mu-like phage of Pseudomonas aeruginosa [J].
Braid, MD ;
Silhavy, JL ;
Kitts, CL ;
Cano, RJ ;
Howe, MM .
JOURNAL OF BACTERIOLOGY, 2004, 186 (19) :6560-6574
[6]   High-order oligomerization is required for the function of the H-NS family member MvaT in Pseudomonas aeruginosa [J].
Castang, Sandra ;
Dove, Simon L. .
MOLECULAR MICROBIOLOGY, 2010, 78 (04) :916-931
[7]   An intragenic deletion in pilQ leads to nonpiliation of a Pseudomonas aeruginosa strain isolated from cystic fibrosis lung [J].
Chang, Yu-Sing Tammy ;
Klockgether, Jens ;
Tuemmler, Burkhard .
FEMS MICROBIOLOGY LETTERS, 2007, 270 (02) :201-206
[8]   Genomic Variation among Contemporary Pseudomonas aeruginosa Isolates from Chronically Infected Cystic Fibrosis Patients [J].
Chung, Jade C. S. ;
Becq, Jennifer ;
Fraser, Louise ;
Schulz-Trieglaff, Ole ;
Bond, Nicholas J. ;
Foweraker, Juliet ;
Bruce, Kenneth D. ;
Smith, Geoffrey P. ;
Welch, Martin .
JOURNAL OF BACTERIOLOGY, 2012, 194 (18) :4857-4866
[9]   A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3 [J].
Cingolani, Pablo ;
Platts, Adrian ;
Wang, Le Lily ;
Coon, Melissa ;
Tung Nguyen ;
Wang, Luan ;
Land, Susan J. ;
Lu, Xiangyi ;
Ruden, Douglas M. .
FLY, 2012, 6 (02) :80-92
[10]   Surface association and the MreB cytoskeleton regulate pilus production, localization and function in Pseudomonas aeruginosa [J].
Cowles, Kimberly N. ;
Gitai, Zemer .
MOLECULAR MICROBIOLOGY, 2010, 76 (06) :1411-1426