Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia.
Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia.
Microb Genom. 2020 Mar;6(3). doi: 10.1099/mgen.0.000339.
Multiply antibiotic-resistant infections are a global public health concern and accurate tracking of the spread of specific lineages is needed. Variation in the composition and structure of capsular polysaccharide (CPS), a critical determinant of virulence and phage susceptibility, makes it an attractive epidemiological marker. The outer core (OC) of lipooligosaccharide also exhibits variation. To take better advantage of the untapped information available in whole genome sequences, we have created a curated reference database of 92 publicly available gene clusters at the locus encoding proteins responsible for biosynthesis and export of CPS (K locus), and a second database for 12 gene clusters at the locus for outer core biosynthesis (OC locus). Each entry has been assigned a unique KL or OCL number, and is fully annotated using a simple, transparent and standardized nomenclature. These databases are compatible with , a tool for typing of bacterial surface polysaccharide loci, and their utility was validated using (a) >630 assembled draft genomes for which the KL and OCL regions had been previously typed manually, and (b) 3386 genome assemblies downloaded from NCBI. Among the previously typed genomes, was able to confidently assign KL and OCL types with 100 % accuracy. Among the genomes retrieved from NCBI, detected known KL and OCL in 87 and 90 % of genomes, respectively, indicating that the majority of common KL and OCL types are captured within the databases; 13 of the 92 KL in the database were not detected in any publicly available whole genome assembly. The failure to assign a KL or OCL type may indicate incomplete or poor-quality genomes. However, further novel variants may remain to be documented. Combining outputs with multilocus sequence typing (Institut Pasteur scheme) revealed multiple KL and OCL types in collections of a single sequence type (ST) representing each of the two predominant globally distributed clones, ST1 of GC1 and ST2 of GC2, and in collections of other clones comprising >20 isolates each (ST10, ST25, and ST140), indicating extensive within-clone replacement of these loci. The databases are available at https://github.com/katholt/Kaptive and will be updated as further locus types become available.
多药耐药感染是一个全球性的公共卫生关注点，需要准确跟踪特定谱系的传播情况。荚膜多糖 (Capsular Polysaccharide, CPS) 的组成和结构的变化是决定毒力和噬菌体敏感性的关键因素，使其成为有吸引力的流行病学标志物。脂寡糖 (Lipooligosaccharide, LOS) 的外核心 (Outer Core, OC) 也存在变化。为了更好地利用全基因组序列中尚未开发的信息，我们创建了一个经过精心整理的参考数据库，其中包含 92 个公开可用的基因簇，这些基因簇位于负责 CPS 生物合成和输出的蛋白质编码基因座 (K 基因座)，以及第二个位于 OC 生物合成基因座 (OC 基因座) 的 12 个基因簇数据库。每个条目都被分配了一个独特的 KL 或 OCL 编号，并使用简单、透明和标准化的命名法进行了全面注释。这些数据库与 兼容，这是一种用于细菌表面多糖基因座分型的工具，它们的实用性已通过以下方式得到验证：(a) >630 个已组装的草图基因组，这些基因组的 KL 和 OCL 区域之前已手动分型，以及 (b) 从 NCBI 下载的 3386 个基因组组装。在之前分型的基因组中， 能够以 100%的准确率自信地分配 KL 和 OCL 类型。在从 NCBI 检索到的基因组中， 分别在 87%和 90%的基因组中检测到已知的 KL 和 OCL，这表明数据库中捕获了大多数常见的 KL 和 OCL 类型；数据库中的 92 个 KL 中有 13 个在任何公开的全基因组组装中都未被检测到。未能分配 KL 或 OCL 类型可能表明基因组不完整或质量差。但是，可能还有更多新的变体有待记录。将输出与多位点序列分型 (巴斯德研究所方案) 相结合，揭示了每个两种主要全球分布克隆 (GC1 的 ST1 和 GC2 的 ST2) 的单个序列型 (ST) 代表的集合中的多个 KL 和 OCL 类型，以及包含 >20 个分离株的其他克隆集合 (ST10、ST25 和 ST140) 中的多个 KL 和 OCL 类型，表明这些基因座在克隆内的广泛替换。这些数据库可在 https://github.com/katholt/Kaptive 上获得，并将随着更多的基因座类型可用而进行更新。
