Division of Medical Microbiology and Virology, St. Paul's Hospital, Providence Health Care, 1081 Burrard St., Vancouver, BC V6Z 1Y6, Canada.
Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.
J Antimicrob Chemother. 2024 Jan 3;79(1):55-60. doi: 10.1093/jac/dkad346.
To utilize long-read nanopore sequencing (R10.4.1 flowcells) for WGS of a cluster of MDR Shigella sonnei, specifically characterizing genetic predictors of antimicrobial resistance (AMR).
WGS was performed on S. sonnei isolates identified from stool and blood between September 2021 and October 2022. Bacterial DNA from clinical isolates was extracted on the MagNA Pure 24 and sequenced on the GridION utilizing R10.4.1 flowcells. Phenotypic antimicrobial susceptibility testing was interpreted based on CLSI breakpoints. Sequencing data were processed with BugSeq, and AMR was assessed with BugSplit and ResFinder.
Fifty-six isolates were sequenced, including 53 related to the cluster of cases. All cluster isolates were identified as S. sonnei by sequencing, with global genotype 3.6.1.1.2 (CipR.MSM5), MLST 152 and PopPUNK cluster 3. Core genome MLST (cgMLST, examining 2513 loci) and reference-based MLST (refMLST, examining 4091 loci) both confirmed the clonality of the isolates. Cluster isolates were resistant to ampicillin (blaTEM-1), trimethoprim/sulfamethoxazole (dfA1, dfrA17; sul1, sul2), azithromycin (ermB, mphA) and ciprofloxacin (gyrA S83L, gyrA D87G, parC S80I). No genomic predictors of resistance to carbapenems were identified.
WGS with R10.4.1 enabled rapid sequencing and identification of an MDR S. sonnei community cluster. Genetic predictors of AMR were concordant with phenotypic antimicrobial susceptibility testing.
利用长读长纳米孔测序（R10.4.1 流池）对一组多重耐药志贺氏菌属 sonnei 进行 WGS，特别是对其抗生素耐药性（AMR）的遗传预测因子进行特征描述。
在 2021 年 9 月至 2022 年 10 月期间，从粪便和血液中分离出的志贺氏菌属 sonnei 分离株进行 WGS。从临床分离株中提取细菌 DNA，在 MagNA Pure 24 上提取并在 GridION 上利用 R10.4.1 流池进行测序。根据 CLSI 折点对表型抗生素药敏试验进行解释。对测序数据进行 BugSeq 处理，并用 BugSplit 和 ResFinder 评估 AMR。
共测序了 56 株分离株，其中 53 株与病例群有关。所有的群集分离株均通过测序鉴定为志贺氏菌属 sonnei，其全球基因型为 3.6.1.1.2（CipR.MSM5）、MLST 152 和 PopPUNK 集群 3。核心基因组 MLST（cgMLST，检测 2513 个基因座）和基于参考的 MLST（refMLST，检测 4091 个基因座）均证实了分离株的克隆性。群集分离株对氨苄西林（blaTEM-1）、复方磺胺甲噁唑（dfA1、dfrA17；sul1、sul2）、阿奇霉素（ermB、mphA）和环丙沙星（gyrA S83L、gyrA D87G、parC S80I）耐药。未发现碳青霉烯类抗生素耐药的基因组预测因子。
利用 R10.4.1 进行 WGS 能够快速测序并鉴定出一组多重耐药志贺氏菌属 sonnei 社区群集。AMR 的遗传预测因子与表型抗生素药敏试验一致。
