Biology subjects

Shea, A. E.

Publications and source records attributed to Shea, A. E..

5 recordsLinked to original sources

bioRxiv2026

Carbapenem-resistant Klebsiella pneumoniae lineage CG307 displays urinary tract tropism

Carbapenem-resistant (CR) Klebsiella pneumoniae (Kp) are designated by the WHO as a top-priority pathogen due to their antibiotic resistance profiles, capacity to disseminate resistance, and associated mortality. The prototypical CRKp clade, CG258, is associated with acute respiratory infections; however, urinary tract infections (UTIs) caused by CRKp are increasing, and frequently linked to the emergent clade CG307. Notably, CG307 isolates have extensive accessory genomes that may drive adaptation to the urinary tract, including a novel capsule gene cluster and high-affinity urea transporter. In this study, we show that UTIs caused by Kp are increasing across the Southern US and that in addition to CG307s circulating within Houston, TX hospital systems, the lineage was also detected in healthcare systems in the broader Gulf Coast region. Characterization of CG307 isolates demonstrate that while these strains exhibit similar mucoviscosity compared to the reference UTI strain TOP52, the lineage displays significantly higher i) growth in artificial urine, ii) urease activity, and iii) UTI in a mouse model. These results suggest that CG307 is spreading across the Southern US and encodes distinct pathogenic features that promote urinary tract tropism, underscoring a need for targeted surveillance and future studies that mechanistically examine the factors that promote UTI.

microbiology↗

bioRxiv2026

Selective Sugar Transport Supports Proteus mirabilis Fitness in the Urinary Tract

Proteus mirabilis is a leading cause of complicated urinary tract infections (UTIs). Prior work showed P. mirabilis metabolizes sugars during experimental UTI, yet the role of sugar import systems in pathogenesis remains poorly defined. To investigate this, we generated a panel of 47 targeted mutants in predicted sugar transporter genes and assessed their growth in vitro and fitness in vivo. Growth screening in nutrient-rich and minimal media revealed carbon source-dependent defects in several phosphotransferase system (PTS) mutants, including ptsH and ptsI. Pooled insertion sequencing (In-seq) identified xapB, ptsH, and ptsI as in vivo fitness factors, with validation in a traditional murine co-challenge model. Functional studies showed that xapB, annotated as a xanthosine permease, did not support xanthosine or guanosine uptake in P. mirabilis, suggesting misannotation. Dissection of the PTS network revealed that a triple mutant lacking scrA, ulaC, and ptsG recapitulated the ptsH phenotype in vivo. To evaluate whether increased sugar availability exacerbates these defects, we modeled glucosuria using the SGLT2 inhibitor dapagliflozin in CBA/J mice. Dapagliflozin treatment significantly increased urinary glucose and enhanced P. mirabilis colonization. There was an inverse correlation between colonization and urinary glucose, but only in untreated mice. These findings reveal limitations in genome-based transporter annotation, establish a functional link between sugar import and P. mirabilis fitness during UTI, and demonstrate that host metabolic conditions such as glucosuria can influence the severity of infection. AUTHOR SUMMARYAll living organisms require nutrients to grow, survive, and cause disease. Bacteria like Proteus mirabilis, which causes urinary tract infections, rely on specialized systems to import and metabolize sugars available in the host environment. In this study, we systematically disrupted 47 genes predicted to encode sugar transporters in P. mirabilis and tested their contribution to infection in a mouse model. We identified three key genes (xapB, ptsH, and ptsI) that were critical for colonization. Further analysis showed that many sugar transporters in P. mirabilis were misannotated, and predicted substrates like sucrose and cellobiose were not utilized by the bacterium. We also demonstrated that high sugar conditions, mimicking diabetic urine using the drug dapagliflozin, worsened infection and increased disease severity. These results highlight the importance of carbohydrate acquisition for P. mirabilis during infection and emphasize the need to experimentally validate gene function rather than rely on predictions based on other bacteria like E. coli.

microbiology↗

bioRxiv2026

Emerging Pathogens in Urinary Tract Infections: Virulence and Phenotypic Characterization of Pseudomonas aeruginosa strains

Urinary tract infections (UTIs) affect a broad patient population and inflict a substantial financial burden on the U.S. healthcare system. While uropathogenic Escherichia coli (UPEC) causes the majority of cases, other pathogens are emerging. Analysis of patient data from our healthcare system in the Gulf Coast region of Alabama revealed that Pseudomonas aeruginosa accounted for 4.0% of UTI cases, roughly double the national average, prompting further investigation into this historically understudied uropathogen. Here, we performed whole-genome sequencing and phenotypic assays on 55 urinary P. aeruginosa isolates to identify key drivers of pathogenicity in the context of UTI. Multilocus sequence typing identified 19 novel sequence types, underscoring the uncharacterized diversity of urinary P. aeruginosa isolates. Serotype O6 was most common and enriched in patients with indwelling catheters, whereas O4 was linked to diabetes mellitus. Antibiotic susceptibility testing (AST) revealed high levofloxacin resistance (30.9%), with 23.6% multidrug-resistant (MDR) and 9.1% extensively drug-resistant (XDR) isolates. Resistance patterns correlated with demographics, including significantly higher meropenem and aztreonam resistance in isolates from African American patients. Phenotypic assays of growth, motility, and biofilm formation revealed negative correlations between antibiotic resistance and virulence. Specific virulence genes predicted enhanced iron acquisition, hemolysis, and colonization potential. Notably, motility and exotoxin profiles emerged as strong predictors of P. aeruginosa ascension in a murine UTI model. Together, these findings provide new biological and clinical insight into P. aeruginosa as a uropathogen and emphasize the need for continued research. IMPORTANCEPseudomonas aeruginosa is an emerging but understudied pathogen in urinary tract infections (UTIs). Given its resilience, adaptability, and the growing threat of multidrug resistance, P. aeruginosa remains a significant challenge in clinical microbiology and infection control. Our data reveal an increased prevalence of P. aeruginosa in our local patient population. In this study, we examined both genotypic and phenotypic traits of clinical isolates and correlated them with colonization in murine models and extensive patient metadata. We identified strong associations between antibiotic resistance patterns and patient demographics. Novel sequence type strains were linked to motility phenotypes in vitro. Additionally, specific flagellar alleles were associated with enhanced murine kidney colonization and recurrent UTIs in patients. These findings provide new insight into the evolutionary adaptations that contribute to P. aeruginosa uropathogenicity and support a more nuanced understanding of its clinical significance.

microbiology↗

bioRxiv2025

Human bladder organoids model urinary tract infection and bacteriophage therapy

Urinary tract infections (UTIs), primarily caused by uropathogenic Escherichia coli (UPEC), are among the most common antibiotic-resistant infections. Despite this, currently available preclinical UTI models lack the breadth of morphotypic and heterogenous cell populations of the human bladder, impairing the development of novel therapies. To address these limitations, we developed human bladder organoids derived from the bladder stem cells of multiple healthy donors which recapitulate cellular diversity of the urothelium. Using bulk and single cell RNA-sequencing, we characterized organoid responses to UPEC and phage exposure individually and in combination to model phage therapy. Although phage minimally affected the uroepithelium in the absence of infection, during UTI, phage treatment reduced bacterial burdens and dampened inflammatory responses and barrier disruption. Collectively, our findings highlight human bladder organoids as a tool for capturing conserved and individual-specific uroepithelial responses to infection while also providing preclinical efficacy and safety testing for therapeutic development.

microbiology↗

bioRxiv2024

Distinct maternofetal immune signatures delineate preterm birth onset following urinary tract infection

Preterm birth is the leading cause of infant mortality resulting in over one million neonatal deaths annually. Maternal urinary tract infection (UTI) during pregnancy increases risk for preterm birth; however, biological processes mediating UTI-associated preterm birth are not well-described. We established a murine maternal UTI model in which challenge with uropathogenic E. coli resulted in preterm birth in about half of dams. Dams experiencing preterm birth displayed excessive bladder inflammation and altered uteroplacental T cell polarization compared to non-laboring infected dams, with no differences in bacterial burdens. Additional factors associated with preterm birth included higher proportions of male fetuses and lower maternal serum IL-10. Furthermore, exogenous maternal IL-10 treatment absolved UTI-associated preterm birth but contributed to fetal growth restriction in this model. Using urine samples from a cohort of human pregnancies with or without UTI, we correlated urinary cytokines with birth outcomes and urine culture status. These analyses yielded a non-invasive, highly predictive three-model system for evaluating preterm birth risk implicating cytokines IL-10, IL-15, IL-1{beta}, and IL-1RA. Our unique bimodal murine model coupled with patient samples provides a platform to investigate immunological and microbial factors governing UTI-associated preterm birth, revealing novel therapeutic opportunities to predict or prevent preterm birth.

immunology↗