Project Four

Microbial Genomics Biomedical Core (MGBC)

PI: Anne-Catrin Uhlemann, MD, PhD

The MGBC will enable Columbia O’Brien Center investigators to have access to specialized genomic technologies and coordinated expert consultations for improved rigor and reproducibility in genomics and precision medicine. In recognition of the increasing impact of antimicrobial resistance in urinary tract infections, the MGBC has established a biorepository of multi-drug resistant UTI isolates. The services and biorepository are specifically designed to meet the needs of two of the Research Projects of the Columbia O’Brien Center and Opportunity Pool Awardees and will be available to the wider Urology research community. 

The MGBC will accomplish these goals through the following aims: 

1. Expand a biorepository of multi-drug resistant UTI isolate to multiple sites across New York City, establish a urine biorepository from clinically well-defined patients with different UTI symptoms and perform extended urine culture for organism identification

2. Provide Microbiome and metagenome analyses and Hi-C/MetaPore-C sequencing

3. Facilitate whole genome sequencing of dominant UTI pathogenic clones to elucidate bacterial determinants of UTI symptomatology

4. Generate bacterial mutants in multi-drug resistant clinical UTI isolates leveraging a highly efficient CRISPR-Cas system

5. Provide consultations and support of study design for the Research Projects

Importantly, the MGBC will serve as a national resource for members of other George M. O'Brien Cooperative Research Centers and other NIDDK Urologic Research Programs.

The Latest “Hot Stuff”

Microbiota analysis of urine from participants the RIVUR and CUTIE cohort (unpublished)

Collaboration: Ali Gharavi and Anne Catrin Uhlemann

The Randomized Intervention for Children with Vesicoureteral Reflux (RIVUR) study is a NIDDK-sponsored multicenter double-blind, randomized, placebo-controlled trial, where 607 children with VCUG documented VUR were recruited after a first or second UTI. Careful Urinary Tract Infection Evaluation (CUTIE) is a companion study to RIVUR, composed of 195 children with UTI but without any structural defects. We have obtained urine samples at baseline stored at -80 C from 276 RIVUR and 101 CUTIE participants, from the NIDDK biorepository. We have also received access to DNA and clinical data for these cohorts and have genome-wide microarray data generated in the past year on the Illumina MEGA chip. Our O’Brien microbiome core, led by Dr. Uhlemann, performed a pilot study of microbiota composition in 91 randomly selected samples from the RIVUR and CUTIE. We performed 16S rRNA V3-V4 2x300bp sequencing on an Illumina MiSeq. Data were analyzed using the DADA2 pipeline. We detected a wide range of bacterial taxa, including Klebsiella spp, Eschericia-Shigella, Pseudomonas, and Enterococci (Figure 2A). In preliminary analysis, we compared the association of microbiota composition with baseline characteristics. We did not detect any major differences in microbiota composition based on age, gender, severity of VUR, or evidence of kidney scarring, likely due to moest sample size. However, we detected a significant difference in alpha and beta diversity based on toilet training, with an excess enrichment in enterococcal species in participants without toilet training in differential abundance testing (Figure 2A-D). These findings motivate additional investigation of microbial composition to study the influence of patient characteristics on microbiota composition.