Threshold-free genomic cluster detection to track transmission pathways in health-care settings: a genomic epidemiology analysis.

ABSTRACT:

Background

A crucial barrier to the routine application of whole-genome sequencing (WGS) for infection prevention is the insufficient criteria for determining whether a genomic linkage is consistent with transmission within the facility. We evaluated the use of single-nucleotide variant (SNV) thresholds, as well as a novel threshold-free approach, for inferring transmission linkages in a high-transmission setting.

Methods

We did a retrospective genomic epidemiology analysis of samples previously collected in the context of an intervention study at a long-term acute care hospital in the USA. We performed WGS on 435 isolates of Klebsiella pneumoniae harbouring the bla_KPC carbapenemase (KPC-Kp) collected from 256 patients through admission and surveillance culturing

SUBMITTER: Hawken SE 

PROVIDER: S-EPMC9869340 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature