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首页> 外文期刊>Journal of Clinical Microbiology >Evaluation of an Optimal Epidemiological Typing Scheme for Legionella pneumophila with Whole-Genome Sequence Data Using Validation Guidelines
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Evaluation of an Optimal Epidemiological Typing Scheme for Legionella pneumophila with Whole-Genome Sequence Data Using Validation Guidelines

机译：使用验证指南评估全基因组序列数据的嗜肺军团菌最佳流行病学分型方案

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Sequence-based typing (SBT), analogous to multilocus sequence typing (MLST), is the current “gold standard” typing method for investigation of legionellosis outbreaks caused by Legionella pneumophila. However, as common sequence types (STs) cause many infections, some investigations remain unresolved. In this study, various whole-genome sequencing (WGS)-based methods were evaluated according to published guidelines, including (i) a single nucleotide polymorphism (SNP)-based method, (ii) extended MLST using different numbers of genes, (iii) determination of gene presence or absence, and (iv) a kmer-based method. L. pneumophila serogroup 1 isolates (n = 106) from the standard “typing panel,” previously used by the European Society for Clinical Microbiology Study Group on Legionella Infections (ESGLI), were tested together with another 229 isolates. Over 98% of isolates were considered typeable using the SNP- and kmer-based methods. Percentages of isolates with complete extended MLST profiles ranged from 99.1% (50 genes) to 86.8% (1,455 genes), while only 41.5% produced a full profile with the gene presence/absence scheme. Replicates demonstrated that all methods offer 100% reproducibility. Indices of discrimination range from 0.972 (ribosomal MLST) to 0.999 (SNP based), and all values were higher than that achieved with SBT (0.940). Epidemiological concordance is generally inversely related to discriminatory power. We propose that an extended MLST scheme with ～50 genes provides optimal epidemiological concordance while substantially improving the discrimination offered by SBT and can be used as part of a hierarchical typing scheme that should maintain backwards compatibility and increase discrimination where necessary. This analysis will be useful for the ESGLI to design a scheme that has the potential to become the new gold standard typing method for L. pneumophila.
机译：基于序列的分型（SBT）类似于多基因座序列分型（MLST），是目前调查由嗜肺军团菌引起的军团菌病暴发的“金标准”分型方法。但是，由于常见的序列类型（ST）会引起许多感染，因此一些研究仍未解决。在这项研究中，根据已发布的指南评估了各种基于全基因组测序（WGS）的方法，包括（i）基于单核苷酸多态性（SNP）的方法，（ii）使用不同数目的基因的扩展MLST，（iii ）确定是否存在基因，以及（iv）基于kmer的方法。来自先前由欧洲临床微生物学会军团菌感染研究小组（ESGLI）使用的标准“分型面板”的肺炎嗜血杆菌血清群1分离株（ n = 106）与另外229种一起进行了测试隔离株。使用基于SNP和kmer的方法，超过98％的分离株被认为是可分型的。具有完整扩展的MLST谱的分离株百分比范围从99.1％（50个基因）到86.8％（1,455个基因），而只有41.5％的人通过基因存在/不存在方案产生了完整谱。重复实验表明，所有方法均具有100％的重现性。辨别指数从0.972（核糖体MLST）到0.999（基于SNP）不等，所有值均高于SBT达到的值（0.940）。流行病学一致性通常与歧视能力成反比。我们提出，扩展的具有约50个基因的MLST方案可提供最佳的流行病学一致性，同时可显着改善SBT所提供的区分度，并且可以用作分层类型分类方案的一部分，该方案应保持向后兼容性并在必要时增加区分度。该分析将有助于ESGLI设计一种方案，该方案有可能成为嗜肺乳杆菌的新金标准分类方法。

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