Biology subjects

Dodson, K. W.

Publications and source records attributed to Dodson, K. W..

5 recordsLinked to original sources

bioRxiv2025

The lac operon in uropathogenic Escherichia coli enhances intracellular growth by enabling host glycan utilization

The lac operon in Escherichia coli has been used as a model of gene regulation throughout biology since its characterization in the early 1960s. Despite the myriad of biotechnology applications that arose from characterization of the lac system, the explanation for the importance of a functional lac operon in normal bladder colonization by uropathogenic E. coli remains unknown given that the prototypical substrate, lactose, is not normally known to be readily available within the urinary tract. Here, we identified a unique uropathogenic clinical isolate (5.3r) that has a two codon deletion in the LacY permease, leading to impaired {beta}-galactoside metabolism and attenuation of development of critical intracellular bacterial communities (IBCs) in which UPEC replicates to high numbers, and then disseminates during urinary tract infection. Further, we show that expression of a functional lacY permease gene is sufficient to rescue defects in IBC size and number in 5.3r. In addition, we demonstrate that UPEC are able to utilize the disaccharide galactose {beta}-1,4 N-acetylglucosamine (LacNAc) - which appears as the terminal glycan in a subset of the glycoproteins that decorate the apical surface of bladder epithelial cells - as a sole carbon source in a lac system dependent manner. These data suggest that the lac operon is important to the growth and development of intracellular E. coli through metabolism of host bladder cell glycans.

microbiology↗

bioRxiv2025

Metabolic cross-talk promotes persistence of Enterococcus in a model of polymicrobial catheter-associated urinary tract infection

Catheter-associated urinary tract infections (CAUTI) account for 70%[~]80% of urinary tract infections (UTI) and can lead to adverse outcomes. Most CAUTIs are polymicrobial with resilient communities maintaining a consistent composition of species over time, despite antibiotic treatment and catheter replacement. However, the mechanisms promoting persistence are poorly understood. Here we examine how a chemical interaction between Gram-positive Enterococcus faecalis and Gram-negative Klebsiella pneumoniae can explain their high rate of co-occurrence on long-term indwelling urinary catheters. Sequence analyses of longitudinal isolates from several human patients co-infected with E. faecalis and K. pneumoniae revealed that despite frequent replacement, catheters became re-colonized with the same or a nearly identical consortium of strains throughout the study collection period. Using artificial urine medium (AUM), monoculture revealed that the K. pneumoniae isolates grew robustly and formed biofilm, while the E. faecalis isolates grew poorly and did not form biofilm. However, co-culture of paired isolates resulted in enhanced E. faecalis growth and biofilm, which could be reproduced by supplementing E. faecalis with cell-free K. pneumoniae conditioned AUM supernatant (KpAUMSup). Analyses using comparative transcriptomics, mutant strains and chemical inhibitors with cell culture and murine CAUTI models revealed that: i) KpAUMSup, but not AUM, stimulated expression of the E. faecalis Fsr quorum-sensing system; ii) Fsr was required for E. faecalis to respond to KpAUMSup; iii) E. faecalis cultured in KpAUMSup was more efficient in initiating CAUTI; and iv) Disruption of Fsr inhibited initiation of CAUTI. This interspecies signaling may help explain the high rate of co-colonization of these CAUTI pathogens and highlights new therapeutic strategies to treat polymicrobial CAUTI.

microbiology↗

bioRxiv2025

De Novo Design of Miniprotein Inhibitors of Bacterial Adhesins

The rise of multidrug-resistant bacterial infections necessitates the discovery of novel antimicrobial strategies. Here, we show that protein design provides a generalizable means of generating new antimicrobials by neutralizing the function of bacterial adhesins, which are virulence factors critical in host-pathogen interactions. We de novo designed high-affinity miniprotein binders to FimH and Abp chaperone usher pili adhesins from uropathogenic Escherichia coli and Acinetobacter baumannii, respectively, which are implicated in mediating both uncomplicated and catheter-associated urinary tract infections (UTI) responsible for significant morbidity worldwide. The designed antagonists have high specificity and stability, disrupt bacterial recognition of host receptors, block biofilm formation, and are effective in treating and preventing murine models of uncomplicated and catheter- associated UTIs in vivo.

microbiology↗

bioRxiv2024

Monoclonal antibodies targeting the FimH adhesin protect against uropathogenic E. coli UTI

As antimicrobial resistance increases, urinary tract infections (UTIs) are expected to pose an increased burden in morbidity and expense on the healthcare system, increasing the need for alternative antibiotic-sparing treatments. Most UTIs are caused by uropathogenic Escherichia coli (UPEC), while Klebsiella pneumoniae causes a significant portion of non-UPEC UTIs. Both bacteria express type 1 pili tipped with the mannose-binding FimH adhesin critical for UTI pathogenesis. We generated and biochemically characterized 33 murine monoclonal antibodies (mAbs) to FimH. Two mAbs protected mice from E. coli UTI. Mechanistically, we show that this protection is Fc-independent and mediated by the ability of these mAbs to sterically block FimH function. Our data reveals that FimH mAbs hold promise as an antibiotic-sparing treatment strategy.

microbiology↗

bioRxiv2023

Strain Tracking with Uncertainty Quantification

The ability to detect and quantify microbiota over time has a plethora of clinical, basic science, and public health applications. One of the primary means of tracking microbiota is through sequencing technologies. When the microorganism of interest is well characterized or known a priori, targeted sequencing is often used. In many applications, however, untargeted bulk (shotgun) sequencing is more appropriate; for instance, the tracking of infection transmission events and nucleotide variants across multiple genomic loci, or studying the role of multiple genes in a particular phenotype. Given these applications, and the observation that pathogens (e.g. Clostridioides difficile, Escherichia coli, Salmonella enterica) and other taxa of interest can reside at low relative abundance in the gastrointestinal tract, there is a critical need for algorithms that accurately track low-abundance taxa with strain level resolution. Here we present a sequence quality- and time-aware model, ChronoStrain, that introduces uncertainty quantification to gauge low-abundance species and significantly outperforms the current state-of-the-art on both real and synthetic data. ChronoStrain leverages sequences quality scores and the samples temporal information to produce a probability distribution over abundance trajectories for each strain tracked in the model. We demonstrate Chronostrains improved performance in capturing post-antibiotic Escherichia coli strain blooms among women with recurrent urinary tract infections (UTIs) from the UTI Microbiome (UMB) Project. Other strain tracking models on the same data either show inconsistent temporal colonization or can only track consistently using very coarse groupings. In contrast, our probabilistic outputs can reveal the relationship between low-confidence strains present in the sample that cannot be reliably assigned a single reference label (either due to poor coverage or novelty) while simultaneously calling high-confidence strains that can be unambiguously assigned a label. We also analyze samples from the Early Life Microbiota Colonisation (ELMC) Study demonstrating the algorithms ability to correctly identify Enterococcus faecalis strains using paired sample isolates as validation.

bioinformatics↗