%A Oh,Sujin %A Nam,Soo Kyung %A Chang,Ho Eun %A Park,Kyoung Un %D 2022 %J Frontiers in Cellular and Infection Microbiology %C %F %G English %K antimicrobial resistance,long-read next-generation sequencing,Molecular Epidemiology,Short-read next-generation sequencing,Strain typing,vancomycin-resistant enterococci %Q %R 10.3389/fcimb.2022.857801 %W %L %M %P %7 %8 2022-April-06 %9 Original Research %+ Kyoung Un Park,Department of Laboratory Medicine, Seoul National University College of Medicine,Republic of Korea,m91w95pf@snu.ac.kr %+ Kyoung Un Park,Department of Laboratory Medicine, Seoul National University Bundang Hospital,Republic of Korea,m91w95pf@snu.ac.kr %# %! Comparative Sequencing for Enterococci Epidemiology %* %< %T Comparative Analysis of Short- and Long-Read Sequencing of Vancomycin-Resistant Enterococci for Application to Molecular Epidemiology %U https://www.frontiersin.org/articles/10.3389/fcimb.2022.857801 %V 12 %0 JOURNAL ARTICLE %@ 2235-2988 %X Vancomycin-resistant enterococci (VRE) are nosocomial pathogens with genetic plasticity and widespread antimicrobial resistance (AMR). To prevent the spread of VRE in the hospital setting, molecular epidemiological approaches such as pulsed-field gel electrophoresis and multilocus sequence typing have been implemented for pathogen outbreak surveillance. However, due to the insufficient discriminatory power of these methods, whole-genome sequencing (WGS), which enables high-resolution analysis of entire genomic sequences, is being used increasingly. Herein, we performed WGS of VRE using both short-read next-generation sequencing (SR-NGS) and long-read next-generation sequencing (LR-NGS). Since standardized workflows and pipelines for WGS-based bacterial epidemiology are lacking, we established three-step pipelines for SR- and LR-NGS, as a standardized WGS-based approach for strain typing and AMR profiling. For strain typing, we analyzed single-nucleotide polymorphisms (SNPs) of VRE isolates and constructed SNP-based maximum-likelihood phylogenies. The phylogenetic trees constructed using short and long reads showed good correspondence. Still, SR-NGS exhibited higher sensitivity for detecting nucleotide substitutions of bacterial sequences. During AMR profiling, we examined AMR genes and resistance-conferring mutations. We also assessed the concordance between genotypic and phenotypic resistance, which was generally better for LR-NGS than SR-NGS. Further validation of our pipelines based on outbreak cases is necessary to ensure the overall performance of pipelines.