869. Outbreak of Vancomycin Resistant Enterococcus faecium (VREfm) in a Hematology Unit Identified Through Whole Genome Sequencing
Authors: Krishnan Gayathri , Udaondo Zulema , Jun Se-Ran , Kothari Atul 
Published: January 2021

Background

VREfm is a major cause of Hospital Acquired Infection in the United States. We analyzed all the VREfm infections that occurred in our institution between 2018 and 2019 using Whole Genome Sequencing (WGS) to understand epidemiological relationship between previously unidentified clusters. In this study we describe a cluster in our hematology oncology unit.

Methods

A total of 109 discrete VREfm isolates from 66 patients were analyzed. VREfm isolates used in this study were identified from positive blood and urine cultures. Genomic deoxyribonucleic acid (DNA) was extracted from pure cultures. The purity and integrity of extracted DNA were determined using appropriate assays. Library construction and sequencing were conducted and Multi Locust Sequence Typing (MLST) obtained (image 1). Phylogenomic tree was plotted using the Interactive Tree of Life (image 2).

Image 1 - methods

Image 2 - Tree of Life

Results

Total of 7 clusters were identified. Here we describe one cluster (image 3) with the highest genetic similarity which showed maximum difference of 5 Single Nucleotide Polymorphisms (zero between patient 1 and 2, image 4). The cluster is composed of 24 clinical strains of VREfm from 6 patients, over a 9 month time period (Image 5). All patients had hematologic malignancies; 4/6 patients had received recent chemotherapy and 5/6 patients were neutropenic. 4 patients were admitted in a single unit (labelled E7), 1 patient was on a sister unit (labelled F7); and 1 patient was in the cancer infusion center. All patients had central venous access placed by radiology at the time of diagnosis of infection and had visited our outpatient infusion center multiple times during this time frame.

Image 3 - Close look at cluster 1

Image 4 - Dendrogram of 106 isolates performed with coreSNP(Single Nucleotide Polymorphisms) pairwise distances. • Dendogram shows different patients (same color for isolates that belong to the same patient) and the patient numbers. • Besides the patient number, the number of largest number SNPS that separate those isolates is shown. • Branches represent the number of coreSNPs that differ strains from that branch. As you see isolates from cluster 1 differ in a maximum of 5 SNPs but isolates of patient 1 and patient 2 differ in 0 SNPs between them. Cluster 1 is represented by a green square.

Image 5 - Time period of infections

Conclusion

The prolonged period in our cluster argues in favor of an environmental niche in the hospital unit. We are unable to elucidate pattern of transmission in a cluster of infections without knowing patient colonization of VREfm; because we are likely looking at the tip of the iceberg when analyzing infected cases. It is difficult to ascribe causality to any one of these exposures without concomitant surveillance cultures of environment and personnel. Retrospective WGS is of limited value in infection control. We now have third generation sequencing with the MinION device to do real time sequencing with which we also validated some of our samples.

Disclosures

Atul Kothari, MD, Ansun Biopharma (Consultant)