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Abstract：
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.
摘要：
基于序列的分型(SBT)，类似于多位点序列分型（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。作为常见的序列类型（STs）引起许多感染，一些调查仍未解决。在这项研究中,各种基于全基因组测序（WGS）的方法根据公布的指南进行了评估，包括(I)基于单核苷酸多态性(SNP)的方法，（ii）使用不同数量的基因扩展MLST，（iii）确定基因的存在或不存在，和(Iv)基于kmer的方法。来自标准分型小组的肺炎杆菌血清群1分离株(n=106)，“先前由欧洲军团菌感染临床微生物学研究小组（ESGLI）使用，与另外229个分离株一起测试。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。具有完整延伸的MLST谱的分离株的百分比范围从99.1％（50个基因）到86.8％（1,455个基因），而只有41.5%的人使用基因存在/缺失方案产生了完整的图谱。重复证明所有方法提供100%的再现性。区分指数范围从0.972（核糖体MLST）到0.999（基于SNP），所有值均高于SBT（0.940）。流行病学的一致性通常与歧视力成反比。我们建议，具有〜50个基因的扩展MLST方案提供了最佳的流行病学一致性，同时大大改善了SBT提供的歧视，并且可以用作分层分型方案的一部分，该方案应保持向后兼容性并在必要时增加歧视。该分析将有助于ESGLI设计一个有可能成为嗜肺乳杆菌新的黄金标准分型方法的方案。
