Genome and transcriptome analysis of Enterococcus faecium from intestinal colonization and Enterococcus faecium from urinary tract infection
IntroductionEnterococcus faecium 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 E. faecium without UTI (only-colonization...
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Frontiers Media S.A.
2023-10-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1273949/full |
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| author | Ge Huang Ge Huang Yizheng Zhou Hai Cheng Tao Lv Lisi Zheng Chengbin Li Yunbo Chen Yunbo Chen |
| author_facet | Ge Huang Ge Huang Yizheng Zhou Hai Cheng Tao Lv Lisi Zheng Chengbin Li Yunbo Chen Yunbo Chen |
| author_sort | Ge Huang |
| collection | DOAJ |
| description | IntroductionEnterococcus faecium 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 E. faecium without UTI (only-colonization) and colonized E. faecium causing UTI (endogenous infections).MethodWe 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.ResultBased on PFGE and WGS, eight isolates of endogenously infected E. faecium and nine isolates of only-colonized E. faecium were characterized and carbon and nitrogen regulated metabolisms such as genes encoding the phosphotransferase (PTS) system were enriched in endogenously infected E. faecium. 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 E. faecium isolates, highlighting the important role of certain carbon regulatory genes in the colonization and survival of endogenously infected E. faecium.ConclusionIn 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. |
| first_indexed | 2024-03-11T14:30:16Z |
| format | Article |
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| language | English |
| last_indexed | 2024-03-11T14:30:16Z |
| publishDate | 2023-10-01 |
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| series | Frontiers in Microbiology |
| spelling | doaj.art-7d8827008e03433197ff60e320504f332023-10-31T09:53:44ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-10-011410.3389/fmicb.2023.12739491273949Genome and transcriptome analysis of Enterococcus faecium from intestinal colonization and Enterococcus faecium from urinary tract infectionGe Huang0Ge Huang1Yizheng Zhou2Hai Cheng3Tao Lv4Lisi Zheng5Chengbin Li6Yunbo Chen7Yunbo Chen8Department of Clinical Laboratory Center, Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, ChinaJingzhou Hospital Affiliated to Yangtze University, Jingzhou, ChinaJingzhou Hospital Affiliated to Yangtze University, Jingzhou, ChinaJingzhou Hospital Affiliated to Yangtze University, Jingzhou, ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, ChinaJingzhou Hospital Affiliated to Yangtze University, Jingzhou, ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, ChinaJinan Microecological Biomedicine Shandong Laboratory, Jinan, ChinaIntroductionEnterococcus faecium 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 E. faecium without UTI (only-colonization) and colonized E. faecium causing UTI (endogenous infections).MethodWe 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.ResultBased on PFGE and WGS, eight isolates of endogenously infected E. faecium and nine isolates of only-colonized E. faecium were characterized and carbon and nitrogen regulated metabolisms such as genes encoding the phosphotransferase (PTS) system were enriched in endogenously infected E. faecium. 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 E. faecium isolates, highlighting the important role of certain carbon regulatory genes in the colonization and survival of endogenously infected E. faecium.ConclusionIn 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.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1273949/fullE. faeciumurinary tract infectionendogenous infectionstranscriptomeGWAS |
| spellingShingle | Ge Huang Ge Huang Yizheng Zhou Hai Cheng Tao Lv Lisi Zheng Chengbin Li Yunbo Chen Yunbo Chen Genome and transcriptome analysis of Enterococcus faecium from intestinal colonization and Enterococcus faecium from urinary tract infection Frontiers in Microbiology E. faecium urinary tract infection endogenous infections transcriptome GWAS |
| title | Genome and transcriptome analysis of Enterococcus faecium from intestinal colonization and Enterococcus faecium from urinary tract infection |
| title_full | Genome and transcriptome analysis of Enterococcus faecium from intestinal colonization and Enterococcus faecium from urinary tract infection |
| title_fullStr | Genome and transcriptome analysis of Enterococcus faecium from intestinal colonization and Enterococcus faecium from urinary tract infection |
| title_full_unstemmed | Genome and transcriptome analysis of Enterococcus faecium from intestinal colonization and Enterococcus faecium from urinary tract infection |
| title_short | Genome and transcriptome analysis of Enterococcus faecium from intestinal colonization and Enterococcus faecium from urinary tract infection |
| title_sort | genome and transcriptome analysis of enterococcus faecium from intestinal colonization and enterococcus faecium from urinary tract infection |
| topic | E. faecium urinary tract infection endogenous infections transcriptome GWAS |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1273949/full |
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