AUTHOR=Huang Ge , Zhou Yizheng , Cheng Hai , Lv Tao , Zheng Lisi , Li Chengbin , Chen Yunbo 

TITLE=Genome and transcriptome analysis of Enterococcus faecium from intestinal colonization and Enterococcus faecium from urinary tract infection

JOURNAL=Frontiers in Microbiology

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1273949

DOI=10.3389/fmicb.2023.1273949

ISSN=1664-302X

ABSTRACT=<sec id="sec1"><title>Introduction</title><p><italic>Enterococcus faecium</italic> is a common pathogen responsible for urinary tract infections (UTIs) and often establishes extensive colonization within the intestinal tract. Our aim was to assess the genomic and transcriptomic differences between colonized <italic>E. faecium</italic> without UTI (only-colonization) and colonized <italic>E. faecium</italic> causing UTI (endogenous infections).</p></sec><sec id="sec2"><title>Method</title><p>We investigated the correlation between fecal isolates from the same patient and UTI-causing isolates using PFGE and WGS, and classified fecal isolates into two groups: those that solely colonized and those associated with endogenous urinary tract infections. We characterized the genomes of colonization-only and endogenously infected isolates by Scoary GWAS, and the transcriptomes of the isolates at 3 h urine exposure to assess pathogen-related changes.</p></sec><sec id="sec3"><title>Result</title><p>Based on PFGE and WGS, eight isolates of endogenously infected <italic>E. faecium</italic> and nine isolates of only-colonized <italic>E. faecium</italic> were characterized and carbon and nitrogen regulated metabolisms such as genes encoding the phosphotransferase (PTS) system were enriched in endogenously infected <italic>E. faecium</italic>. Transcriptome analysis revealed significant differences in gene expression in the PTS system, lysine synthesis, galactose metabolism and citrate import between endogenously infected and only-colonized <italic>E. faecium</italic> isolates, highlighting the important role of certain carbon regulatory genes in the colonization and survival of endogenously infected <italic>E. faecium</italic>.</p></sec><sec id="sec4"><title>Conclusion</title><p>In only-colonized and endogenously infected isolates, we observed differential expression patterns of genes related to carbon metabolism and amino acids, suggesting that metabolic diversity is a strategy for isolates leading to endogenous infection.</p></sec>