Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin-resistant Enterococcus faecium

Martin P McHugh, Kerry Andrea Pettigrew, Surabhi Taori, Thomas J. Evans, Alistair Leanord, Stephen H. Gillespie, Kate E. Templeton, Matthew T. G. Holden

Research output: Contribution to journalArticlepeer-review

13 Downloads (Pure)

Abstract

Background
WGS is increasingly being applied to healthcare-associated vancomycin-resistant Enterococcus faecium (VREfm) outbreaks. Within-patient diversity could complicate transmission resolution if single colonies are sequenced from identified cases.

Objectives
Determine the impact of within-patient diversity on transmission resolution of VREfm.

Materials and methods
Fourteen colonies were collected from VREfm positive rectal screens, single colonies were collected from clinical samples and Illumina WGS was performed. Two isolates were selected for Oxford Nanopore sequencing and hybrid genome assembly to generate lineage-specific reference genomes. Mapping to closely related references was used to identify genetic variations and closely related genomes. A transmission network was inferred for the entire genome set using Phyloscanner.

Results and discussion
In total, 229 isolates from 11 patients were sequenced. Carriage of two or three sequence types was detected in 27% of patients. Presence of antimicrobial resistance genes and plasmids was variable within genomes from the same patient and sequence type. We identified two dominant sequence types (ST80 and ST1424), with two putative transmission clusters of two patients within ST80, and a single cluster of six patients within ST1424. We found transmission resolution was impaired using fewer than 14 colonies.

Conclusions
Patients can carry multiple sequence types of VREfm, and even within related lineages the presence of mobile genetic elements and antimicrobial resistance genes can vary. VREfm within-patient diversity could be considered in future to aid accurate resolution of transmission networks.
Original languageEnglish
JournalJournal of Antimicrobial Chemotherapy
DOIs
Publication statusPublished - 7 Feb 2024

Fingerprint

Dive into the research topics of 'Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin-resistant Enterococcus faecium'. Together they form a unique fingerprint.

Cite this