Evaluation of a Combined Multilocus Sequence Typing and Whole-Genome Sequencing Two-Step Algorithm for Routine Typing of .

TitleEvaluation of a Combined Multilocus Sequence Typing and Whole-Genome Sequencing Two-Step Algorithm for Routine Typing of .
Publication TypeJournal Article
Year of Publication2021
AuthorsKamboj M, McMillen T, Syed M, Chow HYan, Jani K, Aslam A, Brite J, Fanelli B, Hasan NA, Dadlani M, Westblade L, Zehir A, Simon M, N Babady E
JournalJ Clin Microbiol
Date Published2021 01 21
KeywordsAlgorithms, Clostridioides, Clostridioides difficile, Humans, Multilocus Sequence Typing, New York City

Multilocus sequence typing (MLST) is a low-resolution but rapid genotyping method for Whole-genome sequencing (WGS) has emerged as the new gold standard for 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 typing. 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 isolates typed, 91% ( = 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 followed by WGS for MLST concordant strains is a less technically demanding, cost-saving approach for performing typing than WGS alone without loss of discriminatory power.

Alternate JournalJ Clin Microbiol
PubMed ID33177119
PubMed Central IDPMC8111118
Grant ListP30 CA008748 / CA / NCI NIH HHS / United States
UL1 TR000457 / TR / NCATS NIH HHS / United States
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Lars Westblade, Ph.D.

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