Genomic comparison of unrelated serotype 3 pneumococcal isolates

In this study, the genomes of three unrelated serotype 3 isolates (ST180, ST458, ST378) have been compared. This serotype is regarded as an important OM pathogen and has low invasiveness but high mortality. The current licensed multivalent conjugate vaccines do not offer protection against this serotype and an increase in its prevalence was seen in the US following the introduction of the PCV-7. ST180 is the most prevalent ST within serotype 3 in Asia, the US and Europe. The genomes of two serotype 3 ST180 isolates are already publicly available (SP3-BS71, OXC141). In conrast, ST458 is the most prevalent serotype 3 isolate in Africa and Australian Aboriginal communties. The genome of a serotype 3 ST458 isolate from a remote Aboriginal community was sequenced using an Illumina Genome Analyser II, along with the genome of the strain WU2 (ST378), which has been used in numerous pneumococcal studies over a 30 year period. The sequence reads were assembled against the OXC141 genome, allowing genomic comparison of the three STs. In addition, large contigs which could not align with the reference genome were also analsed identifying accessory regions absent in the OXC141 genome.

本研究对3株无亲缘关系的3型血清型分离株进行了基因组比较分析，这3株分离株的序列型（Sequence Type，简称ST）分别为ST180、ST458、ST378。该血清型被视为重要的OM（中耳炎，Otitis Media）病原体，其侵袭性较低但致死率较高。目前获批上市的多价结合疫苗无法对该血清型提供保护，且自PCV-7（7价肺炎球菌结合疫苗）引入美国后，该血清型的流行率呈上升趋势。ST180是亚洲、美国及欧洲地区3型血清型中最为流行的序列型。目前已有2株3型血清型ST180分离株的基因组序列公开（SP3-BS71、OXC141）。与之相反，ST458是非洲及澳大利亚原住民社区中最流行的3型血清型分离株。本研究采用Illumina基因组分析仪II（Illumina Genome Analyser II）对1株来自偏远原住民社区的3型血清型ST458分离株的基因组进行了测序，同时还对菌株WU2（ST378）的基因组进行了测序；该菌株在过去30年间已被广泛应用于多项肺炎链球菌相关研究。本研究以OXC141的基因组作为参考序列进行测序读段的组装，从而实现3种序列型菌株的基因组比较分析。此外，本研究还对无法与参考基因组比对的大片段重叠群（contig）进行了分析，成功鉴定出OXC141基因组中缺失的附属基因区域。