Biology subjects

Fritz, B. G.

Publications and source records attributed to Fritz, B. G..

5 recordsLinked to original sources

bioRxiv2023

What is Slough?A pilot study to define the proteomic and microbial composition of wound slough and its implications for wound healing.

Slough is a well-known feature of non-healing wounds. This study aims to determine the proteomic and microbiologic components of slough as well as interrogate the associations between wound slough components and wound healing. Twenty-three subjects with slow-to-heal wounds and visible slough were enrolled. Etiologies included venous stasis ulcers, post-surgical site infections, and pressure ulcers. Patient co-morbidities and wound healing outcome at 3-months post-sample collection was recorded. Debrided slough was analyzed microscopically, through untargeted proteomics, and high-throughput bacterial 16S-ribosomal gene sequencing. Microscopic imaging revealed wound slough to be amorphous in structure and highly variable. 16S-profiling found slough microbial communities to associate with wound etiology and location on the body. Across all subjects, slough largely consisted of proteins involved in skin structure and formation, blood-clot formation, and immune processes. To predict variables associated with wound healing, protein, microbial, and clinical datasets were integrated into a supervised discriminant analysis. This analysis revealed that healing wounds were enriched for proteins involved in skin barrier development and negative regulation of immune responses. While wounds that deteriorated over time started off with a higher baseline Bates-Jensen Wound Assessment Score and were enriched for anerobic bacterial taxa and chronic inflammatory proteins. To our knowledge, this is the first study to integrate clinical, microbiome, and proteomic data to systematically characterize wound slough and integrate it into a single assessment to predict wound healing outcome. Collectively, our findings underscore how slough components can help identify wounds at risk of continued impaired healing and serves as an underutilized biomarker.

microbiology↗

bioRxiv2023

Inhibition of Pseudomonas aeruginosa quorum sensing by chemical induction of the MexEF-oprN efflux pump

The cell-to-cell communication system quorum sensing (QS), used by various pathogenic bacteria to synchronize gene expression and increase host invasion potentials, is studied as a potential target for persistent infection control. To search for novel molecules targeting the QS system in the Gram-negative opportunistic pathogen Pseudomonas aeruginosa a chemical library consisting of 3280 small compounds from LifeArc was screened. A series of ten conjugated phenones that have not previously been reported to target bacteria were identified as inhibitors of QS in P. aeruginosa. Two lead compounds (ethylthio enynone and propylthio enynone) were resynthesized for verification of activity and further elucidation of the mode of action. The isomeric pure Z-ethylthio enynone was used for RNA sequencing revealing a strong inhibitor of QS-regulated genes and the QS-regulated virulence factors rhamnolipid and pyocyanin were significantly decreased by treatment with the compounds. A transposon mutagenesis screen performed in a newly constructed lasB-gfp monitor strain identified the target of Z-ethylthio enynone in P. aeruginosa to be the MexEF-OprN efflux pump, which was further established using defined mex knockout mutants. Our data indicate that the QS inhibitory capabilities of Z-ethylthio enynone were caused by the drainage of intracellular signal molecules as a response to chemical-induced stimulation of the MexEF-oprN efflux pump thereby inhibiting the auto-generated positive feedback and its enhanced signal-molecule synthesis.

microbiology↗

bioRxiv2023

Biofilms and core pathogens shape the tumour microenvironment and immune phenotype in colorectal cancer

ObjectiveGrowing evidence links bacterial dysbiosis with colorectal cancer (CRC) carcinogenesis, characterized by an increased presence of core pathogens such as Bacteroides fragilis and Fusobacterium nucleatum. Here, we characterized the in situ biogeography and transcriptional interactions between bacteria and the host in mucosal colon biopsies. DesignThe influence of CRC core pathogens and biofilms on the tumour microenvironment (TME) was investigated in biopsies from patients with and without CRC (paired normal tissue and healthy tissue biopsies) using fluorescence in situ hybridization and dual-RNA sequencing. ResultsTissue-invasive, mixed-species biofilms enriched for B. fragilis and F. nucleatum were observed in CRC tissue, especially in right-sided tumours. Fusobacterium spp. was associated with increased bacterial biomass and inflammatory response in CRC samples. CRC samples with high bacterial activity demonstrated increased expression of pro-inflammatory cytokines, defensins, matrix-metalloproteases, and immunomodulatory factors. In contrast, the gene expression profiles of CRC samples with low bacterial activity resembled healthy tissue samples. Moreover, immune cell profiling showed that B. fragilis and F. nucleatum modulated the TME and correlated with increased infiltration of neutrophils and CD4+ T-cells. Overall, bacterial activity was critical for the immune phenotype and correlated with the infiltration of several immune cell subtypes, including M2 macrophages and regulatory T-cells. ConclusionBiofilms and core pathogens shape the TME and immune phenotype in CRC. Our results support that Fusobacterium spp. may provide a future therapeutic target to reduce biofilms and the inflammatory response in the TME while highlighting the importance of widening the scope of bacterial pathogenesis in CRC beyond core pathogens.

cancer biology↗

bioRxiv2020

Metabolic flux fingerprinting differentiates planktonic and biofilm states of Pseudomonas aeruginosa and Staphylococcus aureus

The challenges of defining the biofilm phenotype has been clear for decades. Many biomarkers for biofilm are known, but methods for identifying these are often invasive and/or complicated. These methods often rely on disrupting the biofilm matrix or examining virulence factors and compounds, which may only be expressed under certain conditions. We used microcalorimetric measurements of metabolic energy release to investigate whether unchallenged, planktonic Pseudomonas aeruginosa displayed differences in metabolism compared to surface-bound and non-attached biofilms. The pattern of energy release observed in the recorded microcalorimetric thermograms clearly depended on growth state, though the total energy expenditure was not different between growth states. To characterize these differences, we developed a classification pipeline utilizing machine learning algorithms to classify growth state, based on the observed patterns of energy release. With this approach, we could with high accuracy detect the growth form of blinded samples. To challenge the algorithm, we attempted to limit the amount of training data. By training the algorithm with only a single data point from each growth form, we obtained a mean accuracy of 90.5% using two principal components. Further validation of the classification pipeline showed that the approach was not limited to P. aeruginosa but could also be used for detection of gram-positive Staphylococcus aureus biofilm. We propose that microcalorimetric measurements, in combination with this new quantitative framework, can be used as a non-invasive biomarker to detect the presence of biofilm. These results could have a significant potential in clinical settings where the detection of biofilms in infections often means a different outcome and treatment regime for the patient.

microbiology↗

bioRxiv2018

Oxygen restriction induces a viable but non-culturable population in bacteria

Induction of a non-culturable state has been demonstrated for many bacteria. In a clinical perspective, the lack of growth due to these non-culturable bacteria can have major consequences for the diagnosis and treatment of patients. Here we show how anoxic conditioning (restriction of molecular oxygen, O2) generates difficult-to-culture (DTC) bacteria during biofilm growth. A significant subpopulation of Pseudomonas aeruginosa entered a DTC state after anoxic conditioning, ranging from five to 90 % of the total culturable population, in both planktonic and biofilm models. Anoxic conditioning also generated DTC subpopulations of Staphylococcus aureus and Staphylococcus epidermidis. Growth of the DTC populations were achieved by substituting O2 with 10 mM NO3- as an alternative electron acceptor for anaerobic respiration or, in the case of P. aeruginosa, by adding sodium pyruvate or catalase as scavengers against reactive oxygen species (ROS) during aerobic respiration. An increase in normoxic plating due to addition of catalase suggests the molecule hydrogen peroxide as a possible mechanism for induction of DTC P. aeruginosa. Anoxic conditioning also generated a true viable but non-culturable (VBNC) population of P. aeruginosa that was not resurrected by substituting O2 with NO3- during anaerobic respiration. Moreover, bacterial detection in clinical samples was improved significantly by supplementing 10 mM NO3- to LB plates and incubating under anoxic conditions. These results demonstrate that habituation to an infectious anoxic micro-environment complicates diagnostic culturing of bacteria, especially in the case of chronic infections where oxygen is restricted due to the host immune response. ImportanceDiagnostics of bacteria from chronic infections by standard culture-based methods is challenging. Bacteria in a non-culturable state may contribute to the lack of culturing from these infections. Many stressors are known to induce a non-culturable state, among others the absence of molecular oxygen, which is evident in chronic infections due to high rates of oxygen consumption by the host response. In this study, we have shown that Pseudomonas aeruginosa, Staphylococcus aureus and Staphylococcus epidermidis can enter a difficult-to-culture state after oxygen restriction. Regrowth was not possible using conventional normoxic plating where oxygen served as electron acceptor. Instead, regrowth was enabled during anoxic conditions with added nitrate as alternative electron acceptor. Our findings show that bacteria can habituate to their environment and that it has to be taken into consideration especially when culturing clinical samples e.g. from chronic infections.

microbiology↗