The environmental bacterium Pseudomonas aeruginosa, particularly multidrug-resistant clones, is often associated with nosocomial infections and outbreaks. Today, core genome multilocus sequence typing (cgMLST) is frequently applied to delineate sporadic cases from nosocomial transmissions. However, until recently, no cgMLST scheme for a standardized typing of P. aeruginosa was available. To establish a novel cgMLST scheme for P. aeruginosa, we initially determined the breadth of the P. aeruginosa population based on MLST data with a Bayesian approach (BAPS). Using genomic data of representative isolates for the whole population and all 12 serogroups, we extracted target genes and further refined them using a random data set of 1,000 P. aeruginosa genomes. Subsequently, we investigated reproducibility and discriminatory ability with repeatedly sequenced isolates and isolates from well-defined outbreak scenarios, respectively, and compared clustering applying two recently published cgMLST schemes. BAPS generated seven P. aeruginosa groups. To cover these and all serogroups, 15 reference strains were used to determine genes common in all strains. After refinement with the data set of 1,000 genomes, the cgMLST scheme consisted of 3,867 target genes, which are representative of the P. aeruginosa population and highly reproducible using biological replicates. We finally evaluated the scheme by reanalyzing two published outbreaks where the authors used single-nucleotide polymorphism (SNP) typing. In both cases, cgMLST was concordant with the previous SNP results and the results of the two other cgMLST schemes. In conclusion, the highly reproducible novel P. aeruginosa cgMLST scheme facilitates outbreak investigations due to the publicly available cgMLST nomenclature.

中文翻译：

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铜绿假单胞菌全基因组序列分型的核心基因组多位点序列分型方案的建立与评价

环境细菌铜绿假单胞菌，特别是多重耐药克隆，通常与医院感染和爆发有关。今天，核心基因组多位点序列分型 (cgMLST) 经常用于描述院内传播的散发病例。然而，直到最近，还没有用于铜绿假单胞菌标准化分型的 cgMLST 方案。为了为铜绿假单胞菌建立新的 cgMLST 方案，我们最初使用贝叶斯方法 (BAPS) 基于 MLST 数据确定了铜绿假单胞菌种群的广度。使用整个人群和所有 12 个血清群的代表性分离株的基因组数据，我们提取了目标基因，并使用 1,000 个随机数据集进一步细化了它们铜绿假单胞菌基因组。随后，我们分别研究了重复测序的分离株和来自明确定义的爆发场景的分离株的可重复性和区分能力，并比较了应用两个最近发布的 cgMLST 方案的聚类。BAPS 产生了七个铜绿假单胞菌群。为了涵盖这些和所有血清群，使用了 15 个参考菌株来确定所有菌株中常见的基因。用 1,000 个基因组的数据集细化后，cgMLST 方案由 3,867 个目标基因组成，这些目标基因代表铜绿假单胞菌种群和高度可重复使用生物重复。我们最终通过重新分析作者使用单核苷酸多态性 (SNP) 分型的两个已发表的爆发来评估该方案。在这两种情况下，cgMLST 与之前的 SNP 结果和其他两个 cgMLST 方案的结果一致。总之，由于公开的 cgMLST 命名法，高度可重复的新型铜绿假单胞菌cgMLST 方案促进了暴发调查。