An Omics-Guided Investigation of a Hospital Outbreak Caused by blaNDM-1-Producing Pseudocitrobacter faecalis

Abstract

Carbapenemase-producing Enterobacterales (CPE) pose a major healthcare challenge. We report the first hospital outbreak of Pseudocitrobacter faecalis carrying blaNDM-1 using an omics-based approach. Short- and long-read sequencing enabled genomic epidemiological investigation to track its spread, characterize its resistome, and analyze the genomic context of blaNDM-1. Additionally, we developed and implemented a MALDI-TOF MS-based method for rapid outbreak isolate typing using protein biomarkers. Our investigation identified two independent blaNDM-1-producing clonal clusters of multi-drug and carbapenem-resistant P. faecalis circulating for over three years, carrying blaNDM-1 either chromosomally or on a plasmid. MALDI-TOF MS spectra analysis revealed candidate protein markers corresponding to genomic clusters, with one predicted biomarker applicable for rapid typing. P. faecalis is an emerging CPE taxon requiring hospital surveillance. Early whole genome sequencing (WGS) unexpectedly revealed two intertwined clones with independent carbapenemase acquisition routes. Cluster-specific markers enabled rapid typing, serving as proof-of-concept for validating proteomics in future surveillance.