Doctoral Thesis
Molecular epidemiology of non-faecium non-faecalis enterococcal bloodstream infections in Australia, 2014-2023
Doctor of Philosophy (PhD), Murdoch University
2026
DOI:
https://doi.org/10.60867/00000184
Abstract
The thesis investigated the epidemiology, antimicrobial resistance (AMR), virulence determinants, and genomic characteristics of 869 non-faecium non-faecalis (NFF) enterococci, which had caused bacteraemia in Australia from 2014 to 2023, inclusive. Wholegenome sequencing (WGS) was used to confirm species identity and describe the molecular epidemiology and population structure of NFF enterococci, including E. casseliflavus, E. gallinarum and E. lactis. In addition, proteomic and molecular identification assays were developed to accurately identify E. lactis, a species which is currently misidentified as E. faecium by current routine diagnostic laboratory techniques.
NFF enterococcal bacteraemia episodes were predominantly associated with elderly patients and patients with community-onset biliary tract infections. The 30-day all-cause mortality of NFF enterococcal bacteraemia was similar to that of E. faecalis and E. faecium. A custom matrix-assisted laser desorption ionisation-time of flight mass spectrometry (MALDI-TOF MS) database and multiplex qPCR assay achieved 100% sensitivity and specificity for identifying E. lactis. For E. gallinarum, a core-genome multilocus sequence typing scheme comprising 1,719 loci was developed, successfully characterising 98.9% of E. gallinarum genomes. Using WGS, 26.1% of isolates initially reported as E. casseliflavus by MALDI-TOF MS were identified as E. entomosocium, E. innesii, or Candidatus E. testudinis. Phenotypic resistance to different antibiotic classes was associated with known antimicrobial resistance genetic determinants and putative novel ones. Tetracycline and erythromycin resistance determinants were identified on mobile genetic elements (MGEs) previously identified in Clostridioides difficile, E. faecalis, E. faecium, Staphylococcus aureus, and Staphylococcus intermedius. Virulenceassociated genes related to adhesion and biofilm formation were also detected in several NFF enterococcal species.
Overall, the thesis demonstrates that NFF enterococci are clinically relevant opportunistic pathogens with a disease burden comparable to that of E. faecalis and E. faecium. NFF enterococci are frequently misidentified by routine diagnostic methods, including MALDI-TOF MS. Furthermore, NFF enterococci harbour multiple AMR genetic determinants located on MGEs, suggesting the species may contribute to horizontal AMR gene transfer. The thesis highlights the importance of WGS for improving species identification, surveillance, and detection of AMR and virulence determinants in NFF enterococci.
Details
- Title
- Molecular epidemiology of non-faecium non-faecalis enterococcal bloodstream infections in Australia, 2014-2023
- Authors/Creators
- Marhami Fahriani
- Contributors
- Geoffrey Coombs (Supervisor) - Murdoch University, Centre for Biosecurity and One HealthShakeel Mowlaboccus (Supervisor) - Murdoch University, School of Medical, Molecular and Forensic SciencesChristopher Mullally (Supervisor) - Murdoch University, School of Medical, Molecular and Forensic Sciences
- Awarding Institution
- Murdoch University; Doctor of Philosophy (PhD)
- Identifiers
- 991005928117507891
- Murdoch Affiliation
- School of Medical, Molecular and Forensic Sciences
- Resource Type
- Doctoral Thesis
UN Sustainable Development Goals (SDGs)
This output has contributed to the advancement of the following goals:
Source: SDGs in the Output
Metrics
6 File views/ downloads
4 Record Views