Effect of the urine micro-environment on the genome, evolution and behaviour of strains of Enterococcus involved in treatment-resistant urinary tract infection

Abstract

Urinary tract infections (UTIs) are common. Despite antibiotic treatment, they often recur, and some infections persist, causing life-threatening complications. Consequently, UTI is a common reason for antibiotic prescription, worsening the antimicrobial resistance (AMR) crisis. Infections caused by Enterococcus spp. are common in certain settings, including in hospitals and amongst the elderly, but are little studied. Using a combination of genomics, microscopy and microbiology, I aimed to understand more about the biology of two Enterococcus species in the context of UTI. First, I performed a phylogenetic study to delineate the population structure of Enterococcus faecalis and Enterococcus faecium from public repositories alongside the lab’s clinical isolates. I also performed a pan-genome-wide association study of AMR genes. My results supported the presence of little genetic diversity among human-associated E. faecalis and E. faecium isolates. Second, I created urine-containing media to better mimic the complexity of the urinary tract, performed growth assays and tested the minimum inhibitory concentration (MIC) of different antibiotics on Enterococcus. While nitrofurantoin did not show MIC differences with urine, amoxicillin exhibited a strong urine effect. Consequently, I identified five putative β-lactamase-encoding genes in E. faecalis. Lastly, I used microscopy and RNAseq to determine how urine affects E. faecalis. Scanning electron microscopy did not show significant differences in morphology when bacteria were grown in urine. However, a pilot RNAseq experiment revealed differentially expressed metabolic genes, especially those involved in sugar transport. Additionally, I found differential expression levels of three putative β-lactamase genes. In conclusion, with the combination of omics and microbiology, I showed that E. faecalis exhibits unique adaptive features to the urinary tract, elucidating aspects that may inform the development of new diagnostic tools