PathoSPOT genomic epidemiology reveals under-the-radar nosocomial outbreaks

Abstract

Background Whole-genome sequencing (WGS) is increasingly used to map the spread of bacterial and viral pathogens in nosocomial settings. A limiting factor for more widespread adoption of WGS for hospital infection prevention practices is the availability of standardized tools for genomic epidemiology. Methods We developed the Pathogen Sequencing Phylogenomic Outbreak Toolkit (PathoSPOT) to automate integration of genomic and medical record data for rapid detection and tracing of nosocomial outbreaks. To demonstrate its capabilities, we applied PathoSPOT to complete genome surveillance data of 197 MRSA bacteremia cases from two hospitals during a 2-year period. Results PathoSPOT identified 8 clonal clusters encompassing 33 patients (16.8% of cases), none of which had been recognized by standard practices. The largest cluster corresponded to a prolonged outbreak of a hospital-associated MRSA clone among 16 adults, spanning 9 wards over a period of 21 months. Analysis of precise timeline and location data with our toolkit suggested that an initial exposure event in a single ward led to infection and long-term colonization of multiple patients, followed by transmissions to other patients during recurrent hospitalizations. Conclusions We demonstrate that PathoSPOT genomic surveillance enables the detection of complex transmission chains that are not readily apparent from epidemiological data and that contribute significantly to morbidity and mortality, enabling more effective intervention strategies.

Everybody nose: molecular and clinical characteristics of nasal colonization during active methicillin-resistant Staphylococcus aureus bloodstream infection

“…In a multicenter study, 82% of patients with MRSA bacteremia had identical clones in the anterior nares, and 86% of patients with MRSA colonization in anterior nares had clonally identical isolates later obtained from blood [ 10 ]. Colonization is also key to subtle transmission events and has been a central feature of outbreaks [ 11 , 12 ]. In the United States, most S. aureus infections are caused by two dominant clonal complexes (CC), CC5 and CC8 [ 2 ].…”

Unsuspected clonal spread of Methicillin-resistant Staphylococcus aureus causing bloodstream infections in hospitalized adults detected using whole genome sequencing

“…Most US hospitals have not yet implemented a WGS surveillance system for infection control. Hospitals may choose to approach bioinformatic surveillance using commercial workflows with integrated processes [35], available open source options [38], or create robust in-house surveillance methods [39]. In this analysis we demonstrated that different methods of DNA sequence alignment can readily detect similar variation in SNP differences.…”

The impact of genomics on precision public health: beyond the pandemic

“…Two articles in this special issue illustrate the important role of genomics in understanding and controlling the burden of antimicrobial resistant infections in hospitals. Berbel Caban et al [19] present a method to facilitate the detection of inhospital spread of methicillin resistant Staphylococcus aureus (MRSA or "golden Staph") by combining genomic and epidemiological data. The genetics of antimicrobial resistance can be incredibly complex, and for most pathogens, the overall burden of resistant infections is the combined result of the spread of resistance genes and plasmids between bacterial strains and the transmission of bacterial strains between patients.…”