Department of Infection Control, Amphia Hospital, Breda, the Netherlands
Laboratory for Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, the Netherlands.
Antimicrob Agents Chemother. 2021 May 18;65(6). doi: 10.1128/AAC.00147-21.
Limited information is available on whether -containing plasmids from isolates in a hospital outbreak can be differentiated from epidemiologically unrelated -containing plasmids based on sequence data. This study aimed to evaluate the performance of three approaches to distinguish epidemiologically related from unrelated -containing pKpQiL-like IncFII(k2)-IncFIB(pQiL) plasmids. Epidemiologically related isolates were subjected to short- and long-read whole-genome sequencing. A hybrid assembly was performed, and plasmid sequences were extracted from the assembly graph. Epidemiologically unrelated plasmid sequences were extracted from GenBank. Pairwise comparisons of epidemiologically related and unrelated plasmids based on SNPs using snippy and of phylogenetic distance using Roary and using a similarity index that penalizes size differences between plasmids (Stoesser index) were performed. The percentage of pairwise comparisons misclassified as genetically related or as clonally unrelated was determined using different genetic thresholds for genetic relatedness. The ranges of number of SNPs, Roary phylogenetic distance, and Stoesser index overlapped between the epidemiologically related and unrelated plasmids. When a genetic similarity threshold that classified 100% of epidemiologically related plasmid pairs as genetically related was used, the percentages of plasmids misclassified as epidemiologically related ranged from 6.7% (Roary) to 20.8% (Stoesser index). Although epidemiologically related plasmids can be distinguished from unrelated plasmids based on genetic differences, -containing pKpQiL-like IncFII(k2)-IncFIB(pQiL) plasmids show a high degree of sequence similarity. The phylogenetic distance as determined using Roary showed the highest degree of discriminatory power between the epidemiologically related and unrelated plasmids.
关于是否可以根据序列数据将医院暴发分离株中的含质粒与流行病学上无关的含质粒区分开来，目前相关信息有限。本研究旨在评估三种方法在区分流行病学相关和无关含 pKpQiL 样 IncFII(k2)-IncFIB(pQiL)质粒中的表现。对流行病学相关分离株进行了短读长和长读长全基因组测序。进行了混合组装，并从组装图中提取了质粒序列。从 GenBank 中提取了流行病学上无关的质粒序列。使用 snippy 基于 SNP 进行了流行病学相关和无关质粒的成对比较，使用 Roary 进行了系统发育距离比较，并使用惩罚质粒大小差异的相似性指数（Stoesser 指数）进行了比较。使用不同的遗传相关度遗传阈值，确定了将成对比较错误分类为遗传相关或克隆无关的百分比。流行病学相关和无关质粒之间的 SNP 数量、Roary 系统发育距离和 Stoesser 指数的范围重叠。当使用将 100%的流行病学相关质粒对分类为遗传相关的遗传相似性阈值时，将质粒错误分类为流行病学相关的百分比范围为 6.7%（Roary）至 20.8%（Stoesser 指数）。尽管可以根据遗传差异将流行病学相关的质粒与无关的质粒区分开来，但含 pKpQiL 样 IncFII(k2)-IncFIB(pQiL)质粒显示出高度的序列相似性。使用 Roary 确定的系统发育距离在流行病学相关和无关质粒之间显示出最高的区分能力。
