Top-Down Genomic Surveillance Approach to Investigate the Genomic Epidemiology and Antibiotic Resistance Patterns ofEnterococcus faeciumDetected in Cancer Patients in Arkansas

Abstract

Control of hospital-associated Enterococcus faecium infection is a strenuous task due to the difficulty of identifying transmission routes and the persistence of this nosocomial pathogen despite the implementation of infection control measures that have been successful with other important nosocomial pathogens. This study provides a comprehensive analysis of over one hundred E. faecium isolates collected from 66 cancer patients at the University of Arkansas for Medical Sciences (UAMS) between June, 2018 and May, 2019. In the top-down approach used in this study we employed, in addition to the 106 E. faecium UAMS isolates, a filtered set of 2167 E. faecium strains from the GenBank database to assess the current population structure of E. faecium species and, consequently, to identify the lineages associated with our clinical isolates. We then evaluated the antibiotic resistance and virulence profiles of hospital-associated strains from the species pool, focusing on antibiotics of last resort, in order to establish an updated classification of high-risk and multidrug-resistant nosocomial clones. Further investigation of the clinical isolates collected from UAMS patients using whole genome sequencing analytical methodologies (cgMLST, coreSNP and phylogenomics), with the addition of patient epidemiological data, revealed a polyclonal outbreak of three sequences types occurring simultaneously in different patient wards. The integration of genomic and epidemiological data collected from the patients increased our understanding of the relationships and transmission dynamics of the E. faecium isolates. Our study provides new insights into genomic surveillance of E. faecium to assist in monitoring and further limiting the spread of multidrug-resistant E. faecium.

Genomic Distance-based Rapid Uncovering of Microbial Population Structures (GRUMPS): a reference free genomic data cleaning methodology

“…abscessus) that was observed in the results produced by mlstverse 31 . The higher resolution of whole genome sequence methods in comparison with typing methodologies that leverages only a set of genes has been demonstrated in other studies 10,15,27 . In this case, GRUMPS produced a seamless classification of M. abscessus genomes in their three recognized subspecies (Figure 5).…”

“…The population structure E. faecium is typically divided into three clades: A1, A2, and B. A recently published study 27 by Udaondo et al . investigated the population structure of E. faecium using FastANI and a set of 2,273 genomes downloaded from GenBank, to classify genomes to their respective clade.…”

“…To further validate GRUMPS’ ability to accurately identify and remove low-quality genomes from species level datasets, we also compared the results obtained by GRUMPS for both E. faecium and M. abscessus to recent studies 27,31 related to the population structure of these two species. For M. abscessus , the results obtained by both the “regular” and “strict” cleaning modes of GRUMPS revealed the known population structure of this species with each of the known subspecies groups visible and distinctly separate from each other.…”

“…The population structure E. faecium is typically divided into three clades: A1, A2, and B. A recently published study 27 4b and 4c. The removal of the genomes belonging to clade B when using the "strict" cleaning mode of GRUMPS is due to the effect of the heavy sequencing bias towards genomes belonging to clades A1 and A2 which are in turn more genetically similar, illustrated by the color differences of the heatmap in Figure 4b.…”

“…The population structure E. faecium is typically divided into three clades: A1, A2, and B. A recently published study27 by Udaondo et al investigated the population structure of E. faecium using FastANI and a set of 2,273 genomes downloaded from GenBank, to classify genomes to their respective clade. Leveraging the clade classifications from this study, the described population structure of E. faecium was compared to the results obtained by GRUMPS.…”