Role of adherent-invasive Escherichia coli in inflammatory bowel disease

Ph.D.Background & Aims: Adherent invasive Escherichia coli (AIEC) invades gut epithelium and colonizes mucosa of patients with Crohn’s disease (CD). Fecal microbiota transplantation (FMT) has been reported to be effective in treating CD but the response rates are variable. We investigated the prevalence of AIEC in Chinese population, its impact on mucosal microbiota and how it affects FMT efficacy in a mouse model of colitis.Methods: The prevalence of AIEC was assessed in ileal tissues of Chinese CD patients (n=56) and healthy subjects (n=53). AIEC strains were isolated ex vivo from inflamed specimens by selection culture and gentamicin protection assay in Intesine- 407 cell lines. Mucosal microbiota was analysed by 16s rRNA sequencing. Whole genome sequencing, genome assembly and gene function annotation were conducted. AIEC strain 62d was cultured in LB broth supplemented with sterile fecal filtrate of a CD patient or a healthy subject. Bacterial RNAs were isolated for transcriptome sequencing. The effect of AIEC on FMT was assessed in C57BL/6 wild type DSS-colitis model. Level of AIEC colonization was assessed by selective culture and fluorescence in situ hybridization (FISH). Severity of colitis was determined by assessment of colon length, histological scoring and fecal lipocalin-2 (Lcn-2) level. Feces were collected before and after FMT for 16S rRNA sequencing to assess alterations in the gut microbiota in relation to AIEC colonisation.Results: AIEC was significantly associated with CD. The prevalence of AIEC was significantly higher in mucosa of CD subjects than healthy controls (p<0.05). Increased microbial dysbiosis was observed in AIEC-positive ileal tissues, compared with AIEC-negative and healthy tissues. Strains isolated from HK are genetically disparate from strains reported in western populations. The majority of Chinese AIEC isolates were multi-antibiotic-resistant, and these antibiotics resistant strains possessed significantly greater invasion properties than non-resistant strains. When cultured with CD versus health fecal filtrate, AIEC 62d showed enrichment in pathways for aromatic amino acids biosynthesis under CD fecal filtrate conditions. In our DSS-induced colitis model, FMT could significantly increase microbial diversity and ameliorate colitis in K12 (a non-invasive E. coli strain)-colonized but not AIEC-infected mice. The proportion of donor-derived microbes in AIEC-infected mice was significantly lower than that in K12-colonised mice, with a lack of engraftment of the species Akkermansia muciniphila and the genus Allobaculum.Conclusion: AIEC is associated with CD in the Chinese population. AIEC could compromise the efficacy of FMT by hindering the engraftment of donor-derived bacteria, leading to incomplete recovery of intestinal inflammation and microbial dysbiosis. Future application of FMT in IBD care may incorporate patient selection based on the presence AIEC in a personalized approach.研究背景與目的：粘附侵襲性大腸桿菌（AIEC）可侵入腸上皮並定植于克羅恩病（Crohn’s disease, CD） 患者的粘膜。據報導腸道微生物移植(Fecalmicrobiota transplantation, FMT)在治療CD 方面有一定療效，但結果不完全一致。我們調查了中國人群中AIEC的流行情況，AIEC對粘膜微生物群的影響，並探討了AIEC 對結腸炎小鼠模型中FMT 療效的影響。方法：在中國克羅恩病患者（n = 56）和健康受試者（n = 53）的迴腸組織中評估AIEC 的存在。通過選擇培養基和慶大霉素保護測定（Intesine-407 細胞系）從末端迴腸標本分離AIEC 菌株。通過16s rRNA測序分析粘膜微生物群。對分離的菌株進行全基因組測序、基因組組裝和基因功能註釋。我們在C57BL/6 野生型小鼠DSS-結腸炎模型中評估AIEC 對FMT 的作用。通過選擇性培養和熒光原位雜交（FISH）評估AIEC 在小鼠中的定植水平。通過評估結腸長度，組織學評分和糞便脂質運載蛋白-2（Lcn-2）水平來確定結腸炎的嚴重程度。在FMT 之前和之後收集糞便用於16S rRNA 測序以評估與AIEC 定植相關的腸道微生物群的改變。結果：CD 受試者粘膜中AIEC 的存在率顯著高於健康對照組（p