Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy.
BMC Microbiol. 2011 Feb 1;11:25. doi: 10.1186/1471-2180-11-25.
Streptococcus pneumoniae is an important human pathogen representing a major cause of morbidity and mortality worldwide. We sequenced the genome of a serotype 11A, ST62 S. pneumoniae invasive isolate (AP200), that was erythromycin-resistant due to the presence of the erm(TR) determinant, and carried out analysis of the genome organization and comparison with other pneumococcal genomes.
The genome sequence of S. pneumoniae AP200 is 2,130,580 base pair in length. The genome carries 2216 coding sequences (CDS), 56 tRNA, and 12 rRNA genes. Of the CDSs, 72.9% have a predicted biological known function. AP200 contains the pilus islet 2 and, although its phenotype corresponds to serotype 11A, it contains an 11D capsular locus. Chromosomal rearrangements resulting from a large inversion across the replication axis, and horizontal gene transfer events were observed. The chromosomal inversion is likely implicated in the rebalance of the chromosomal architecture affected by the insertions of two large exogenous elements, the erm(TR)-carrying Tn1806 and a functional prophage designated φSpn_200. Tn1806 is 52,457 bp in size and comprises 49 ORFs. Comparative analysis of Tn1806 revealed the presence of a similar genetic element or part of it in related species such as Streptococcus pyogenes and also in the anaerobic species Finegoldia magna, Anaerococcus prevotii and Clostridium difficile. The genome of φSpn_200 is 35,989 bp in size and is organized in 47 ORFs grouped into five functional modules. Prophages similar to φSpn_200 were found in pneumococci and in other streptococcal species, showing a high degree of exchange of functional modules. φSpn_200 viral particles have morphologic characteristics typical of the Siphoviridae family and are capable of infecting a pneumococcal recipient strain.
The sequence of S. pneumoniae AP200 chromosome revealed a dynamic genome, characterized by chromosomal rearrangements and horizontal gene transfers. The overall diversity of AP200 is driven mainly by the presence of the exogenous elements Tn1806 and φSpn_200 that show large gene exchanges with other genetic elements of different bacterial species. These genetic elements likely provide AP200 with additional genes, such as those conferring antibiotic-resistance, promoting its adaptation to the environment.
肺炎链球菌是一种重要的人类病原体，是全球发病率和死亡率的主要原因。我们对血清型 11A、ST62 肺炎链球菌侵袭性分离株（AP200）进行了基因组测序，该分离株因存在 erm(TR)决定簇而对红霉素具有耐药性，并对基因组结构进行了分析，并与其他肺炎链球菌基因组进行了比较。
肺炎链球菌 AP200 的基因组序列长 2130580 个碱基对。基因组携带 2216 个编码序列（CDS）、56 个 tRNA 和 12 个 rRNA 基因。在这些 CDS 中，72.9%具有预测的生物学已知功能。AP200 包含菌毛岛 2，尽管其表型对应于血清型 11A，但它包含 11D 荚膜基因座。观察到由于复制轴上的大型倒位而导致的染色体重排和水平基因转移事件。染色体倒位可能与插入两个大型外源元件（携带 erm(TR)的Tn1806 和功能性噬菌体指定为φSpn_200）所影响的染色体结构的再平衡有关。Tn1806 大小为 52457bp，包含 49 个 ORF。Tn1806 的比较分析显示，在相关物种（如化脓性链球菌）以及厌氧物种金氏无乳链球菌、厌氧消化链球菌和艰难梭菌中存在类似的遗传元件或其一部分。φSpn_200 的基因组大小为 35989bp，由 47 个 ORF 组成，分为五个功能模块。在肺炎球菌和其他链球菌物种中发现了与 φSpn_200 相似的噬菌体，显示出功能模块的高度交换。φSpn_200 病毒粒子具有典型的 Siphoviridae 家族的形态特征，能够感染肺炎球菌受体菌株。
肺炎链球菌 AP200 染色体的序列揭示了一个动态的基因组，其特征是染色体重排和水平基因转移。AP200 的总体多样性主要由外源性元件 Tn1806 和 φSpn_200 驱动，它们与不同细菌物种的其他遗传元件进行了大量的基因交换。这些遗传元件可能为 AP200 提供了额外的基因，例如那些赋予抗生素耐药性的基因，促进了它对环境的适应。
