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Not all Escherichia coli-associated urinary tract infections in females originate in the rectum

Friday, October 6, 2023

8:45 AM – 8:49 AM US PST

Location: B113-116

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Image Label: Females with E. coli UTI

Presenting Author(s)

Lauren C. Westbay, MD

Physician
NorthShore University HealthSystem
Chicago, Illinois, United States

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Co-Author(s)

AE

Adriana Ene, MS

Research Assistant
Loyola University Chicago
Chicago, Illinois, United States
BH

Baylie Hochstedler-Kramer, MS

PhD Candidate
Loyola University Chicago
Maywood, Illinois, United States
AW

Alan J. Wolfe, PhD (he/him/his)

Professor
Loyola University Chicago
Maywood, Illinois, United States
CP

Catherine Putonti, PhD

Professor
Loyola University Chicago
Chicago, Illinois, United States
EM

Elizabeth R. Mueller, MD, MSME, FACS

Professor and Division Director
Loyola University Chicago/Loyola University Medical Center
OAK PARK, Illinois, United States
NS

Natalie Stegman

Graduate Research Assistant
Loyola Univeristy Chicago
Chicago, Illinois, United States
OG

Olivia Gyssler, BS (she/her/hers)

Medical Student
Loyola University Chicago Stritch School of Medicine
Riverside, Illinois, United States
TP

Thythy Pham, MD, MA

Associate Professor; Fellowship Director
Loyola University Medical Center
Maywood, Illinois, United States
Marian Acevedo-Alvarez, MD, MPH

Assistant Professor
Loyola University Medical Center
Maywood, Illinois, United States

Disclosure(s):

Lauren C. Westbay, MD: No financial relationships to disclose

Adriana Ene, MS: No financial relationships to disclose

Baylie Hochstedler-Kramer, MS: No financial relationships to disclose

Alan J. Wolfe, PhD: Pathnostics: Advisory Board (Ongoing), Funding (Ongoing); VB Tech: Funding (Ongoing)

Catherine Putonti, PhD: No financial relationships to disclose

Elizabeth R. Mueller, MD, MSME, FACS: No relevant disclosure to display

Natalie Stegman: No financial relationships to disclose

Olivia Gyssler, BS: No financial relationships to disclose

Thythy Pham, MD, MA: No financial relationships to disclose

Marian Acevedo Alvarez, MD, MPH: No financial relationships to disclose

Objectives: Test the hypothesis that all E. coli-associated urinary tract infections (UTIs) originate in the gastrointestinal tract using metagenomic sequencing.

Methods: Females presenting with clinical symptoms of a UTI (dysuria, urgency, frequency) and leukocytes on urine dipstick were invited to participate. Demographics were collected with a catheterized urine sample and a rectal swab. A 10 ml aliquot of urine was sent to the clinical laboratory for analysis using standard culture techniques. The remaining catheterized urine and a rectal swab went to the research lab and were cultured to enrich for E. coli. Following enrichment, genomic DNA was extracted and stored at -80C. If the clinical lab found E. coli in the urine, then the extracted DNA was sequenced by SeqCenter, metagenomic sequencing reads examined using the bioinformatics tool STRONG, and metagenomic-assembled genomes (MAGs) constructed. Taxonomic classification used BLAST; MAGs analysis used Bowtie2, SPAdes, Mauve, and Mash.

Results: 38 females were enrolled. Twenty-two (57.8%) samples met clinical microbiology criteria for culture and were predominated by E. coli (10⁵ CFU/mL). The remaining samples did not meet the criteria (n=8, 21.1%) or had a different predominant bacterium (n=8, 21.1%). E. coli-predominated participants were predominantly White (72.8%) and post-menopausal (90.9%) with an average age of 63.5 years. Sixteen (72.7%) E. coli-predominated participants had recurrent UTI, 8 (36.4%) used vaginal estrogen and 2 (9.1%) reported recent intercourse (Table). Shotgun metagenomic sequencing identified E. coli in both urine and rectal samples for 19 (86.4%) of the 22 E. coli-predominated participants. All urine samples contained a single E. coli phylotype; 4 rectal samples contained more than 1. We compared each E. coli-predominated participant’s urinary E. coli MAG to her rectal MAG(s). Fourteen (74%) participants had nearly identical MAGs, suggesting a rectal strain had colonized the bladder. However, 5 (26%) participants had MAGs that shared little nucleotide sequence similarity; thus, these E. coli-predominated UTIs cannot be attributed to a recent acquisition from the rectum. In two cases, the predominant E. coli strain in the urine was from the same phylotype as an E. coli strain from the rectum. Thus, only through shotgun metagenomic sequencing could we examine the microbiota at the strain level.

Conclusions: In this study of 19 females with symptomatic E. coli UTIs, 26% were found to have a separate lineage of E. coli in their bladder and rectum. This provides evidence for an exception to the current hypothesis and would suggest that some E. coli-associated UTIs do not originate from the rectum.