淋病奈瑟菌耐药性序列分型（NG-STAR）克隆复合体与基因组系统发育一致，并提供简单的命名法、快速可视化和抗菌药物耐药（AMR）谱系预测。

Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR) clonal complexes are consistent with genomic phylogeny and provide simple nomenclature, rapid visualization and antimicrobial resistance (AMR) lineage predictions.

机构信息

WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.

Genomics and Health Area, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO-Public Health), Valencia, Spain.

出版信息

J Antimicrob Chemother. 2021 Mar 12;76(4):940-944. doi: 10.1093/jac/dkaa552.

DOI:10.1093/jac/dkaa552

PMID:33411920

Abstract

OBJECTIVES

Surveillance of antimicrobial resistance (AMR) in Neisseria gonorrhoeae, supported by molecular typing, ideally through genome sequencing, is imperative. We defined N. gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR) clonal complexes (CCs) and validated their usefulness in gonococcal AMR surveillance.

METHODS

All NG-STAR alleles and STs available in the public database (https://ngstar.canada.ca/) were analysed using PHYLOViZ 2.0 to define CCs according to the closest founder ST with ≥5 identical alleles and founding ST with the highest number of links. The published 2013 European gonococcal dataset (n = 1054), the 2016 WHO reference strain panel (n = 14) and N. gonorrhoeae isolates with ceftriaxone resistance determinant penA-60.001 (n = 7) from several countries were used for validation.

RESULTS

The majority of the isolates (n = 1063) were designated to 71 CCs. The most common CC was CC90 (n = 194), followed by CC63 (n = 166), CC139 (n = 73), CC158 (n = 73) and CC127 (n = 62). CC90 included isolates belonging to the internationally spread MDR clone N. gonorrhoeae Multi-Antigen Sequence Typing (NG-MAST) G1407 (predominantly MLST ST1901). The ceftriaxone-resistant isolates with penA-60.001 (n = 7) belonged to CC73 or STs linking between CC90 and CC73 (ST233 and ST1133). Phylogenomic analysis revealed that NG-STAR CCs more appropriately correlated to phylogenomic AMR clusters compared with MLST STs, NG-MAST STs, NG-MAST genogroups and NG-STAR STs.

CONCLUSIONS

NG-STAR CCs: are consistent with the gonococcal genome phylogeny; allow rapid visualizations with limited computational requirements; provide a simple, reproducible and portable nomenclature (for WGS and conventional Sanger sequencing data); and predict AMR lineages. Phenotypic AMR surveillance, supplemented with WGS, is imperative and NG-STAR CCs can effectively support this.

摘要

目的

通过分子分型（最好通过基因组测序）支持淋病奈瑟菌的抗生素耐药性（AMR）监测，这一点至关重要。我们定义了淋病奈瑟菌耐药性序列分型（NG-STAR）克隆复合体（CC），并验证了它们在淋病 AMR 监测中的有用性。

方法

使用 PHYLOViZ 2.0 分析公共数据库（https://ngstar.canada.ca/）中所有可用的 NG-STAR 等位基因和 ST，根据具有≥5 个相同等位基因的最接近的创始 ST 和具有最高链接数的创始 ST 来定义 CC。使用已发表的 2013 年欧洲淋球菌数据集（n=1054）、2016 年世界卫生组织参考菌株组（n=14）和来自多个国家的具有头孢曲松耐药决定因子 penA-60.001 的淋病奈瑟菌分离株（n=7）进行验证。

结果

大多数分离株（n=1063）被指定为 71 个 CC。最常见的 CC 是 CC90（n=194），其次是 CC63（n=166）、CC139（n=73）、CC158（n=73）和 CC127（n=62）。CC90 包括属于国际传播的多药耐药克隆淋病奈瑟菌多抗原序列分型（NG-MAST）G1407（主要为 MLST ST1901）的分离株。具有 penA-60.001 的头孢曲松耐药分离株（n=7）属于 CC73 或介于 CC90 和 CC73 之间的 ST（ST233 和 ST1133）。系统基因组分析表明，与 MLST ST、NG-MAST ST、NG-MAST 基因群和 NG-STAR ST 相比，NG-STAR CC 更能与系统基因组 AMR 簇相关。