Knowledge of the epidemiology of plasmids is essential for understanding the evolution and spread of antimicrobial resistance. PlasmidSPAdes attempts to reconstruct plasmids using short-read sequence data. Accurate detection of extended-spectrum beta-lactamase (ESBL) genes and plasmid replicon genes is a prerequisite for the use of plasmid assembly tools to investigate the role of plasmids in the spread and evolution of ESBL production in Enterobacteriaceae . This study evaluated the performance of PlasmidSPAdes plasmid assembly for Enterobacteriaceae in terms of detection of ESBL-encoding genes, plasmid replicons and chromosomal wgMLST genes, and assessed the effect of k-mer size. Short-read sequence data for 59 ESBL-producing Enterobacteriaceae were assembled with PlasmidSPAdes using different k-mer sizes (21, 33, 55, 77, 99 and 127). For every k-mer size, the presence of ESBL genes, plasmid replicons and a selection of chromosomal wgMLST genes in the plasmid assembly was determined. Out of 241 plasmid replicons and 66 ESBL genes detected by whole-genome assembly, 213 plasmid replicons [88 %; 95 % confidence interval (CI): 83.9–91.9] and 43 ESBL genes (65 %; 95 % CI: 53.1–75.6) were detected in the plasmid assemblies obtained by PlasmidSPAdes. For most ESBL genes (83.3 %) and plasmid replicons (72.0 %), detection results did not differ between the k-mer sizes used in the plasmid assembly. No optimal k-mer size could be defined for the number of ESBL genes and plasmid replicons detected. For most isolates, the number of chromosomal wgMLST genes detected in the plasmid assemblies decreased with increasing k-mer size. Based on our findings, PlasmidSPAdes is not a suitable plasmid assembly tool for short-read sequence data for ESBL-encoding plasmids of Enterobacteriaceae .

中文翻译：

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使用短读长序列数据的 PlasmidSPAdes 组装检测肠杆菌科中的超广谱 β-内酰胺酶 (ESBL) 基因和质粒复制子。


了解质粒的流行病学对于了解抗菌素耐药性的演变和传播至关重要。 PlasmidSPAdes 尝试使用短读序列数据重建质粒。准确检测超广谱β-内酰胺酶（ESBL）基因和质粒复制子基因是利用质粒组装工具研究质粒在肠杆菌科细菌中ESBL产生的传播和进化中的作用的先决条件。本研究评估了肠杆菌科细菌PlasmidSPAdes 质粒组装在检测 ESBL 编码基因、质粒复制子和染色体 wgMLST 基因方面的性能，并评估了 k-mer 大小的影响。使用不同 k 聚体大小（21、33、55、77、99 和 127）使用 PlasmidSPAdes 组装 59 种产 ESBL肠杆菌科细菌的短读序列数据。对于每个 k 聚体大小，确定了质粒组装中是否存在 ESBL 基因、质粒复制子和染色体 wgMLST 基因的选择。通过全基因组组装检测到 241 个质粒复制子和 66 个 ESBL 基因，其中有 213 个质粒复制子 [88%；在 PlasmidSPAdes 获得的质粒组装体中检测到 95% 置信区间 (CI)：83.9–91.9] 和 43 个 ESBL 基因（65%；95% CI：53.1–75.6）。对于大多数 ESBL 基因 (83.3 %) 和质粒复制子 (72.0 %)，质粒组装中使用的 k 聚体大小之间的检测结果没有差异。对于检测到的 ESBL 基因和质粒复制子的数量，无法定义最佳的 k 聚体大小。对于大多数分离株，在质粒组装体中检测到的染色体 wgMLST 基因的数量随着 k-mer 大小的增加而减少。 根据我们的研究结果，PlasmidSPAdes 不是适合肠杆菌科ESBL 编码质粒的短读长序列数据的质粒组装工具。