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Additional file 1: Table S1. Histopathological characteristics according to the Banff 2019 criteria of AMR cases. Table S2. Comparison of relative abundance of gut microbiota between AMR and control groups at the species level. Table S3. Comparison of relative abundance of gut microbiota between AMR and control groups at the phylum level. Table S4. Comparison of relative abundance of gut microbiota between AMR and control groups at the genus level. Table S5. Comparison of relative abundance of KOs between AMR and control groups. Table S6. Interrelationship between AMR-associated gut microbial species, functions and metabolites. Table S7. Spearman correlation between species and clinical indicators. Table S8. Spearman correlation between metabolites and clinical indicators. Table S9. Area under the ROC curves of microbial biomarkers. Table S10. Antibiotic resistance and virulence genes of key species associated with AMR after kidney transplantation. Table S11. Area under the ROC curves of metabolic biomarkers

Xiangyong Tian,1,* Nan Jing,2,* Wenjing Duan,3 Xiaoqiang Wu,1 Chan Zhang,1 Shanmei Wang,2 Tianzhong Yan1 1Department of Urology, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Henan University People’s Hospital, Zhengzhou, People’s Republic of China; 2Department of Clinical Microbiology, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Henan University People’s Hospital, Zhengzhou, People’s Republic of China; 3Department of the Clinical Research Center, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Henan University People’s Hospital, Zhengzhou, People’s Republic of China*These authors contributed equally to this workCorrespondence: Tianzhong Yan, Department of Urology, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, Henan Province, 450003, People’s Republic of China, Email ytz460@hotmail.com Wenjing Duan, Department of the Clinical Research Center, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, Henan Province, 450003, People’s Republic of China, Email duanwenjingzzu@zzu.edu.cnBackground: Ralstonia mannitolilytica, an emerging opportunistic pathogen, can infect immunocompromised patients but is a rare cause of severe sepsis and septic shock in kidney transplant recipients (KTRs).Case Presentation: We present a case of septic shock after renal transplant in a 41-year-old male, which was finally proven to be caused by Ralstonia mannitolilytica through blood cultures and mass spectrometric analysis following the negative result of metagenomic next-generation sequencing (mNGS). He was finally cured after the application of sensitive antibiotics (sulfamethoxazole-trimethoprim, amikacin and piperacillin-tazobactam) based on the drug sensitivity test results. The patient had a satisfactory recovery with no complications during a 6-month follow-up period.Conclusion: This study highlights that Ralstonia mannitolilytica is an easily overlooked cause of septic shock in KTRs requiring a detailed inquiry of medical history with inflammatory markers monitored closely. Traditional blood cultures still should be taken seriously. It also provides a cautionary tale that negative results of mNGS have to be interpreted with caution.Keywords: Ralstonia mannitolilytica, kidney transplant, sepsis, metagenomic next-generation sequencing, mNGS, blood cultures

Junpeng Wang,1,2,* Xin Li,3,4,* Xiaoqiang Wu,1 Zhiwei Wang,1 Xuan Wu,1 Shanmei Wang,5 Gaopeng Jing,1 Tianzhong Yan1 1Department of Urology, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Henan University People’s Hospital, Zhengzhou, People’s Republic of China; 2Department of Organ Transplantation, Zhujiang Hospital, Southern Medical University, Guangzhou, People’s Republic of China; 3Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, People’s Republic of China; 4Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou, People’s Republic of China; 5Department of Clinical Microbiology, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China*These authors contributed equally to this workCorrespondence: Tianzhong YanDepartment of Urology, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, Henan Province, 450003, People’s Republic of ChinaEmail ytz460@hotmail.comBackground: In renal transplant recipients, carbapenem-resistant Klebsiella pneumoniae (CRKP) infection is a common complication, and usually associated with severe clinical outcomes due to a lack of effective treatment.Case Presentation: A 37-year-old woman with CRKP infection one month after kidney transplantation was involved in this study. Microbial characteristics of fecal samples from the patient were analyzed. Fecal microbiota transplantation (FMT) was performed for treating the CRKP infection. One week after FMT, the patient’s urine and anal swab cultures returned negative for CRKP, and 17 days after FMT, the incision showed complete healing. Moreover, the patient had no symptoms of infection two months after FMT. Alpha diversity analyses showed that before FMT, the patient was associated with obviously lower species richness and diversity than the donor, which significantly increased at one week, three weeks and two months after FMT. Beta diversity analyses showed that though the patient’s microbial community post-FMT still differed from the donor composition, their distances decreased visibly, especially at one week and three weeks after FMT. Obvious shift in microbial composition could be observed before and after FMT. The microbial composition of the patient post FMT resembled the donor composition. Relative abundance of genera such as Phascolarctobacterium and Lachnoclostridium increased after FMT, while the relative abundance of Klebsiella significantly decreased.Conclusion: This study demonstrated the therapeutic effect of FMT on infections caused by CRKP for a renal transplant patient. Further studies are required to confirm the findings of this study.Keywords: carbapenem-resistant Klebsiella pneumoniae, infection, fecal microbiota transplantation, gut microbiota

Objective To investigate the clinicopathological features of collecting duct carcinoma (CDC) and improve its diagnosis and treatment. Methods A retrospective analysis was performed with clinical data including follow-up results of five patients with CDC. Results A total of 5 cases, including 4 males and 1 female, were included in this analysis with the average age 54 years (range 42 to 65). Patients mainly suffered from lumbar pain, hematuria, abdominal mass and low grade fever. Four patients underwent radical nephrectomy while another received palliative nephrectomy. Lymph node metastasis occurred in 3 cases and renal hilum fat metastasis happened to 2 other cases. Tumors was located in the renal medulla and presented invasive growth. They had a tubulopapillary architecture with the hobnail-shaped cells protruding into the glandular lumen, and were accompanied by interstitial fibrosis and dysplasia of epithelial cells in collecting ducts adjacent to the tumors. One tumor was staged at AJCC II, two at AJCC III and two at AJCC IV. Postoperative interferon immunotherapy was applied in 2 cases. Patients were followed up for 5 to 18 months and the average survival time was 10 months. Conclusion The CDC exhibits special clinicopathological features, high degree of malignancy and poor prognosis. The diagnosis depends on the histopathological examination. Early detection and early surgical treatment are still the main methods to improve the prognosis of patients with CDC. Virtual Slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/3702794279387989