Multilocus sequence typing (MLST) is a low-resolution but rapid genotyping method for Clostridioides difficile. Whole-genome sequencing (WGS) has emerged as the new gold standard for C. difficile typing, but cost and lack of standardization still limit broad utilization. In this study, we evaluated the potential to combine the portability of MLST with the increased resolution of WGS for a cost-saving approach to routine C. difficile typing. C. difficile strains from two New York City hospitals (hospital A and hospital B) were selected. WGS single-nucleotide polymorphism (wgSNP) was performed using established methods. Sequence types (ST) were determined using PubMLST, while wgSNP analysis was performed using the Bionumerics software. An additional analysis of a subset of data (hospital A) was made comparing the Bionumerics software to the CosmosID pipeline. Cost and turnaround time to results were compared for the algorithmic approach of MLST followed by wgSNP versus direct wgSNP. Among the 202 C. difficile isolates typed, 91% (n = 185/203) clustered within the representative ST, showing a high agreement between MLST and wgSNP. While clustering was similar between the Bionumerics and CosmosID pipelines, large differences in the overall number of SNPs were noted. A two-step algorithm for routine typing results in significantly lower cost than routine use of WGS. Our results suggest that using MLST as a first step in routine typing of C. difficile followed by WGS for MLST concordant strains is a less technically demanding, cost-saving approach for performing C. difficile typing than WGS alone without loss of discriminatory power.

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难辨梭菌常规分型的多基因座序列分型和全基因组测序两步算法相结合的评估

多基因座序列分型（MLST）是一种难辨梭菌的低分辨率但快速的基因分型方法。全基因组测序（WGS）已成为艰难梭菌分型的新金标准，但成本和缺乏标准化仍限制了其广泛应用。在这项研究中，我们评估了将MLST的便携性与提高的WGS分辨率相结合的潜力，从而可以节省成本地进行艰难梭菌分型。艰难梭菌选择了来自纽约市两家医院（医院A和医院B）的菌株。WGS单核苷酸多态性（wgSNP）使用已建立的方法进行。使用PubMLST确定序列类型（ST），而使用Bionumerics软件进行wgSNP分析。比较了生物数字软件和CosmosID管道，对数据的子集（医院A）进行了其他分析。比较了MLST，wgSNP与直接wgSNP的算法方法的成本和取得结果的时间。在202株艰难梭菌分离株中，有91％（n= 185/203）聚集在代表性ST内，表明MLST和wgSNP之间的一致性很高。虽然生物数字管线和CosmosID管线之间的聚类相似，但注意到SNP总数存在很大差异。与常规使用WGS相比，用于常规键入的两步算法可大大降低成本。我们的研究结果表明，使用MLST作为艰难梭菌常规分型的第一步，然后使用WGS处理MLST一致菌株，比单独使用WGS进行艰难梭菌分型的技术要求低，节省成本，并且不会损失鉴别力。