| Title: |
Whole-genome sequencing-based pathogen characterization for streptococcal infection directly from positive blood culture samples |
| Authors: |
Li, Yuan; Lin, Wuling; Li, Zhongya; Tran, Theresa; Metcalf, Benjamin J.; Velusamy, Srinivasan; Gross, Annastasia; Snippes Vagnone, Paula; Lynfield, Ruth; Beall, Bernard; McGee, Lesley; Chochua, Sopio |
| Contributors: |
Dien Bard, Jennifer; Centers for Disease Control and Prevention |
| Source: |
Journal of Clinical Microbiology ; volume 64, issue 1 ; ISSN 0095-1137 1098-660X |
| Publisher Information: |
American Society for Microbiology |
| Publication Year: |
2026 |
| Description: |
Clinical laboratories are increasingly using diagnostic tests directly on positive blood cultures, which may lead to fewer attempts to recover bacterial isolates. Consequently, public health laboratories can benefit from assays that directly process blood culture samples without requiring submission of clinical isolates to determine additional pathogen features not identified by clinical tests, such as vaccine serotype and bacterial genomic relatedness, for surveillance and outbreak response purposes. In partnership with the Minnesota Active Bacterial Core surveillance (ABCs) site, we identified blood culture samples positive for ABCs streptococcal pathogens and characterized them by a direct whole-genome sequencing from blood culture (dWGS) assay. The dWGS results were compared with the results of a reference method (WGS of isolates from the same cultures) to evaluate concordance in pathogen features and genome assemblies. Of the 97 eligible blood culture samples, 83 (86%) passed dWGS quality control criteria and were subjected to a total of 655 dWGS-based tests, which yielded 651 (99.3%) evaluable results. The percent agreement with reference results was 100% (83/83) for M protein gene ( emm )/capsular types and 100% (81/81) for multilocus sequencing types. For genotypic antimicrobial susceptibility testing prediction, the percent prediction agreement was 100% (487/487), false resistant prediction rate was 0% (0/417), and the false susceptible prediction rate was 0% (0/66). Assemblies of pathogen genomes from the same patient differed by 1.08 ± 1.68 (mean ± SD) sites per genome. The dWGS assay can extract high-quality, important streptococcal strain characteristics directly from positive blood culture samples to support evolving public health needs. IMPORTANCE Whole-genome sequencing (WGS) technologies have emerged as a transformative toolkit used by public health microbiology laboratories to detect and characterize pathogens. The surveillance of bacterial diseases often relies on clinical ... |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| DOI: |
10.1128/jcm.01126-25 |
| Availability: |
https://doi.org/10.1128/jcm.01126-25; https://journals.asm.org/doi/pdf/10.1128/jcm.01126-25 |
| Rights: |
https://creativecommons.org/licenses/by/4.0/ ; https://journals.asm.org/non-commercial-tdm-license |
| Accession Number: |
edsbas.8E5248BC |
| Database: |
BASE |