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Presentation Type:
Poster Presentation - Poster Presentation
Subject Category: MDR GNR
Whole-genome sequencing of carbapenem-resistant Enterobacterales
isolates and evaluation of hospital-acquired infections
Leama Ajaka; Shandra Day; Christina Liscynesky; Nora Colburn;
Christine Sun; Michael Sovic; Preeti Pancholi; Joan-Miquel Balada-
Llasat; Heather Smith and Shashanka Murthy
Background: Multidrug-resistant organisms (MDROs) are increasingly
implicated in nosocomial outbreaks worldwide. We evaluated whole-
genome sequencing (WGS) as an adjunctive epidemiological tool to iden-
tify infection clusters and MDRO transmission in the healthcare setting.
Methods: Clinical isolates of carbapenem-resistant Enterobacterales
(CRE) from July 1, 2021, to June 30, 2022, underwent Illumina WGS.
Assembled genomes were taxonomically classified with GTDB-Tk soft-
ware and were typed using multilocus sequence typing (MLST).
Average nucleotide identity (ANI) was calculated between genomes.
Numbers of differences among core single-nucleotide polymorphisms
(SNPs) were calculated for pairs within taxonomic groups, and the data
were evaluated in the context of patient dates and locations of care obtained
from the electronic medical record. Results: In total, 39 CRE isolates
underwent WGS (Fig. 1). Klebsiella pneumoniae represented the largest
number of isolates (n =18). Using MLST, 2 distinct groups of K. pneumo-
niae were identified (ST307 and ST258) with 5 and 4 isolates, respectively
(Fig. 2). Within ST307, SNP differences ranged between 8 and 115. 3 iso-
lates (CRE8, CRE10, and CRE12) were collected within 4 weeks of each
other and had ≤26 pairwise SNP differences. Notably, CRE8 and
CRE10 were located on the same unit at the same time and used the same
MRI scanner on the same day. CRE35 had >95 SNP differences and was
admitted 8 months prior to others in ST307 but had surgery in the same OR
as CRE8. Within ST258, pairwise comparison of samples revealed 139–588
SNP differences. CRE21, CRE31, and CRE33 had SNP differences of ≤150.
These patients were in the same hospital room (CRE33 and CRE21) and
unit (CRE31 and CRE33), but they did not overlap temporally. CRE37 had
>580 SNP differences, with no overlap in hospitalization dates or locations
with other patients. Conclusions: Two closely related K. pneumoniae iso-
late populations were identified using WGS. Strong temporal and spatial
commonalities were identified among isolates with few SNP differences.
Isolate pairs with intermediate SNP differences shared spatial commonal-
ities, suggesting possible indirect transmission between patients. No
common exposures were identified for pairs with large numbers of SNP
differences. WGS is an evolving tool to detect outbreak clonal populations
of MDRO not identified through traditional epidemiologic techniques.
WGS can provide insight into transmission patterns and the role of envi-
ronmental contamination in propagating these nosocomial infections.
More studies are needed to define the role and clinical significance of iso-
lates with intermediate SNP differences in transmission of these pathogens
between hosts and the healthcare environment.
Disclosures: None
Antimicrobial Stewardship & Healthcare Epidemiology 2023;3(Suppl. S2):s80
doi:10.1017/ash.2023.335
APSIC 2023 Abstracts
S80 2023;3 Suppl 2
https://doi.org/10.1017/ash.2023.335 Published online by Cambridge University Press