Spencer David H, Kas Arnold, Smith Eric E, Raymond Christopher K, Sims Elizabeth H, Hastings Michele, Burns Jane L, Kaul Rajinder, Olson Maynard V
The University of Washington Genome Center, Department of Medicine, University of Washington. Children's Hospital and Regional Medical Center, Seattle, Washington 98195, USA.
J Bacteriol. 2003 Feb;185(4):1316-25. doi: 10.1128/JB.185.4.1316-1325.2003.
Whole-genome shotgun sequencing was used to study the sequence variation of three Pseudomonas aeruginosa isolates, two from clonal infections of cystic fibrosis patients and one from an aquatic environment, relative to the genomic sequence of reference strain PAO1. The majority of the PAO1 genome is represented in these strains; however, at least three prominent islands of PAO1-specific sequence are apparent. Conversely, approximately 10% of the sequencing reads derived from each isolate fail to align with the PAO1 backbone. While average sequence variation among all strains is roughly 0.5%, regions of pronounced differences were evident in whole-genome scans of nucleotide diversity. We analyzed two such divergent loci, the pyoverdine and O-antigen biosynthesis regions, by complete resequencing. A thorough analysis of isolates collected over time from one of the cystic fibrosis patients revealed independent mutations resulting in the loss of O-antigen synthesis alternating with a mucoid phenotype. Overall, we conclude that most of the PAO1 genome represents a core P. aeruginosa backbone sequence while the strains addressed in this study possess additional genetic material that accounts for at least 10% of their genomes. Approximately half of these additional sequences are novel.
全基因组鸟枪法测序被用于研究三株铜绿假单胞菌分离株的序列变异，其中两株来自囊性纤维化患者的克隆感染，一株来自水生环境，相对于参考菌株PAO1的基因组序列。这些菌株中代表了大部分PAO1基因组；然而，至少有三个明显的PAO1特异性序列岛。相反，来自每个分离株的大约10%的测序读数未能与PAO1主链比对。虽然所有菌株之间的平均序列变异约为0.5%，但在核苷酸多样性的全基因组扫描中明显存在差异显著的区域。我们通过完全重测序分析了两个这样的差异位点，即铁载体和O抗原生物合成区域。对从一名囊性纤维化患者随时间收集的分离株进行的全面分析揭示了导致O抗原合成丧失的独立突变与黏液样表型交替出现。总体而言，我们得出结论，大多数PAO1基因组代表了铜绿假单胞菌的核心主链序列，而本研究中涉及的菌株拥有额外的遗传物质，占其基因组的至少10%。这些额外序列中约一半是新的。
