Abstract

Objectives

WGS-based antimicrobial susceptibility testing (AST) is as reliable as phenotypic AST for several antimicrobial/bacterial species combinations. However, routine use of WGS-based AST is hindered by the need for bioinformatics skills and knowledge of antimicrobial resistance (AMR) determinants to operate the vast majority of tools developed to date. By leveraging on ResFinder and PointFinder, two freely accessible tools that can also assist users without bioinformatics skills, we aimed at increasing their speed and providing an easily interpretable antibiogram as output.

Methods

The ResFinder code was re-written to process raw reads and use Kmer-based alignment. The existing ResFinder and PointFinder databases were revised and expanded. Additional databases were developed including a genotype-to-phenotype key associating each AMR determinant with a phenotype at the antimicrobial compound level, and species-specific panels for in silico antibiograms. ResFinder 4.0 was validated using Escherichia coli (n = 584), Salmonella spp. (n = 1081), Campylobacter jejuni (n = 239), Enterococcus faecium (n = 106), Enterococcus faecalis (n = 50) and Staphylococcus aureus (n = 163) exhibiting different AST profiles, and from different human and animal sources and geographical origins.

Results

Genotype–phenotype concordance was ≥95% for 46/51 and 25/32 of the antimicrobial/species combinations evaluated for Gram-negative and Gram-positive bacteria, respectively. When genotype–phenotype concordance was <95%, discrepancies were mainly linked to criteria for interpretation of phenotypic tests and suboptimal sequence quality, and not to ResFinder 4.0 performance.

Conclusions

WGS-based AST using ResFinder 4.0 provides in silico antibiograms as reliable as those obtained by phenotypic AST at least for the bacterial species/antimicrobial agents of major public health relevance considered.

中文翻译：

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ResFinder 4.0用于根据基因型预测表型。

摘要

目标

基于WGS的抗微生物药敏试验（AST）对于几种抗微生物/细菌物种组合，与表型AST一样可靠。但是，基于WGS的AST的常规使用受到生物信息学技能和抗菌素耐药性（AMR）决定因素知识的需求的困扰，以操作迄今为止开发的绝大多数工具。通过利用ResFinder和PointFinder这两个可自由访问的工具，它们也可以帮助没有生物信息学技能的用户，我们旨在提高他们的速度并提供易于理解的抗菌谱图作为输出。

方法

重新编写了ResFinder代码，以处理原始读取并使用基于Kmer的对齐方式。现有的ResFinder和PointFinder数据库已得到修改和扩展。开发了其他数据库，包括将每个AMR决定簇与抗微生物化合物水平的表型相关联的基因型到表型的键，以及用于计算机抗菌谱的物种特异性面板。ResFinder 4.0已使用大肠杆菌（n  =  584），沙门氏菌（Salmonella spp ）进行了验证。（n  =  1081），空肠弯曲菌（n  =  239），粪肠球菌（n  =  106），粪肠球菌（n  =  50）和金黄色葡萄球菌（n  =  163）表现出不同的AST谱，并且来自不同的人类和动物来源以及地理来源。

结果

在革兰氏阴性菌和革兰氏阳性菌评估的抗菌/物种组合中，分别有46/51和25/32的基因型与表型一致性≥95％。当基因型-表型一致性低于95％时，差异主要与表型测试的解释标准和次优序列质量相关，而与ResFinder 4.0性能无关。

结论

使用ResFinder 4.0的基于WGS的AST，至少对于所考虑的具有重大公共卫生意义的细菌物种/抗菌剂，提供的计算机电子抗菌图谱与表型AST一样可靠。