Genomic And Transcriptomic Analysis Of Enterococci Colonized In The Intestine And Isolated From The Infection Site

Enterococcus is a ubiquitous Gram-positive bacterium that is a major pathogen associated with healthcare-related infections and is closely related to human health.Enterococcus are adapted to grow in harsh environments and can use a variety of metabolic substrates.Two main species of Enterococcus,Enterococcus faecalis and Enterococcus faecium,are responsible for causing nosocomial infections,and both exhibit intrinsic resistance to commonly used antibiotics.The use of antibiotics can disrupt the gut microbiota,and if Enterococcus becomes dominant in the gut,it may lead to infection in the host.Therefore,it is hypothesized that Enterococcus with certain biological characteristics,and after metabolic adaptation,can cause urinary tract infections,bloodstream infections,and peritoneal cavity infections.Objective This study aims to investigate whether the intestinal colonization of Enterococcus leads to infections in patients.It compares the adaptive transcriptional changes in genes associated with Enterococcus colonization in the intestines and the affected infection sites.The findings will provide valuable insights into the clinical mechanisms underlying Enterococcus infections.Methods This retrospective study collected Enterococcus strains isolated from the gut colonization and paired them with Enterococcus strains isolated from infection sites in the same patients.The antibiotic susceptibility of isolated strains was detected using the agar dilution method and broth dilution method.Pulsed-field gel electrophoresis(PFGE)was used to analyze the homology of gut-colonizing and infecting Enterococcus strains with similar drug resistance characteristics.Whole-genome sequencing was performed on all isolated Enterococcus strains,and bioinformatics analysis was used to analyze the genome.Enterococcus faecium strains isolated from gut colonization were exposed to urine in vitro for 3 hours,and differentially expressed genes were studied using transcriptomics.Results A total of 92 Enterococcus strains were isolated from 24 patients with paired gut colonization and infection.E.faecium was the predominant strain causing infections,accounting for 79.2% of all cases.35 gut-colonizing Enterococcus strains were collected,including 27 E.faecium strains and 8 E.faecalis strains.Drug susceptibility testing showed that E.faecium was highly resistant to beta-lactams and tetracyclines,while E.faecalis was highly resistant to erythromycin,tetracyclines,and fluoroquinolones.The drug resistance profiles of paired gut-colonizing and infecting Enterococcus strains from the same patients were similar.Analysis of PFGE showed that gut-colonizing and infecting Enterococcus strains from 16 patients had similar band patterns.Whole-genome sequencing and bioinformatics analysis showed that the E.faecium strains isolated from gut colonization and infection sites of 11 patients were similar on the evolutionary tree.E.faecium causing infection was mainly ST78 type and carried more drug-resistant genes,while E.faecalis carried multiple virulence factors.Based on RNAseq,genes involved in carbohydrate metabolism,energy metabolism,and transport were differentially expressed in E.faecium exposed to urine.Conclusion This study showed that gut-colonizing Enterococcus strains have similar drug resistance and genetic characteristics to Enterococcus strains causing clinical infections.Enterococcus faecium is mainly of ST78 type,while the ST types of Enterococcus faecalis are diverse.Based on transcriptome analysis,colonized E.faecium was found to adapt to the nutritional environment of urine by switching substrate metabolism,including upregulation of lactose metabolism,amino acid metabolism,and de novo nucleotide synthesis genes to maintain basic metabolic needs.