Biology subjects

Van den Bergh, B.

Publications and source records attributed to Van den Bergh, B..

4 recordsLinked to original sources

bioRxiv2025

Reprogramming the EnvZ-OmpR two-component system confers ethanol tolerance in Escherichia coli by stabilizing the outer membrane and altering iron homeostasis.

Ethanol is a fermentation product widely used as a fuel and chemical precursor in various applications. However, its accumulation imposes severe stress on the microbial producer, leading to significant production losses. To address this, improving a strains ethanol tolerance is considered an effective strategy to enhance production. In our previous research, we conducted an adaptive evolution experiment with Escherichia coli growing under gradually increasing concentrations of ethanol, which gave rise to multiple hypertolerant populations. Based on the genomic mutational data, we demonstrated in this work that adaptive alleles in the EnvZ-OmpR two-component system drive the development of ethanol tolerance in E. coli. Specifically, when a single leucine was substituted for a proline residue within the periplasmic domain using CRISPR, the mutated EnvZ osmosensor caused a significant increase in ethanol tolerance. Through promoter fusion assays, we showed that this particular mutation stabilizes EnvZ in a kinase-dominating state, which reprograms signal transduction involving its cognate OmpR response regulator. Whole-genome proteomics analysis revealed that this altered signaling pathway predominantly maintains outer membrane stability by upregulating global porin levels and attenuating iron metabolism in the tolerant envZ*L116P mutant. Moreover, we demonstrated that the hypertolerant envZ*L116P allele also promotes ethanol productivity in fermentation, providing valuable insights for enhancing industrial ethanol production. AUTHOR SUMMARYEthanol is a versatile chemical with many applications, but producing it in high quantities remains a challenge. This is because Escherichia coli, a candidate ethanol production strain, is naturally sensitive to this short-chain alcohol, especially when levels are gradually accumulating during fermentation. To resolve this bottleneck, we have investigated how E. coli can acquire tolerance to its own toxic fermentation product. Our research indicated that a single amino acid substitution in EnvZ-a key sensor protein that normally protects E. coli against extreme osmotic stress-is sufficient to confer ethanol tolerance. Further analysis revealed that the mutation perturbs the EnvZ-mediated signaling cascade, which, in turn, changes the transporter composition in the outer membrane and attenuates the cells iron metabolism. These adaptations enable E. coli to survive under high-ethanol conditions, thereby promoting its ethanol production efficiency. This discovery provides a suitable strategy to increase ethanol titers in industrial settings using fermentation.

microbiology↗

bioRxiv2022

In vitro persistence level reflects in vivo antibiotic survival of natural Pseudomonas aeruginosa isolates in a murine lung infection model

Nowadays, clinicians are more and more confronted with the limitations of antibiotics to completely cure bacterial infections in patients. It has long been assumed that only antibiotic resistance plays a pivotal role in this. Indeed, the worldwide emergence of antibiotic resistance is considered as one of the major health threats of the 21st century. However, the presence of persister cells also has a significant influence on treatment outcomes. These antibiotic-tolerant cells are present in every bacterial population and are the result of the phenotypic switching of normal, antibiotic-sensitive cells. Persister cells complicate current antibiotic therapies and contribute to the development of resistance. In the past, extensive research has been performed to investigate persistence in laboratory settings, however, antibiotic tolerance in conditions that mimic the clinical setting is still poorly understood. In this study, we have optimized a mouse model for lung infections of the opportunistic pathogen Pseudomonas aeruginosa. In this model, mice are intratracheally infected with P. aeruginosa embedded in seaweed alginate beads and subsequently treated with tobramycin via nasal droplets. A strain panel of 18 P. aeruginosa isolates originating from environmental, human and animal clinical sources was selected to assess survival in the animal model. These survival levels were positively correlated with the survival levels determined via time-kill assays which is a common method to study persistence in the laboratory. We showed that both survival levels are comparable and thus that the classical persister assays are indicative for antibiotic tolerance in a clinical setting. The optimized animal model also allows us to test potential antipersister molecules and study persistence. ImportanceThe importance of targeting persister cells in antibiotic therapies becomes more evident as these antibiotic-tolerant cells underlie relapsing infections and resistance development. Here, we studied persistence in a clinically relevant pathogen, Pseudomonas aeruginosa. It is one of the six ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, P. aeruginosa, Enterobacter spp.) that are considered as a major health threat. P. aeruginosa is mostly known for causing chronic lung infections in cystic fibrosis patients. We mimicked these lung infections in a mouse model to study persistence in more clinical conditions. We showed that the survival levels of natural P. aeruginosa isolates in this model are positively correlated with the survival levels measured in classical persistence assays. These results not only validate the use of our current techniques to study persistence, but also open opportunities to study new persistence mechanisms or evaluate new antipersister compounds in vivo.

microbiology↗

bioRxiv2022

Antibiotic-tolerant persisters are pervasive among clinical Streptococcus pneumoniae isolates and show strong condition-dependence

Streptococcus pneumoniae is an important human pathogen, being one of the most common causes of community-acquired pneumonia and otitis media. Antibiotic resistance in S. pneumoniae is an emerging problem as it depletes our arsenal of effective drugs. In addition, persistence also contributes to the antibiotic crisis in many other pathogens, yet, in S. pneumoniae nothing is known about antibiotic-tolerant persisters. Persister cells are phenotypic variants that exist as a subpopulation within a clonal culture. Being tolerant to lethal antibiotics, they underly the chronic nature of a variety of infections and even help in acquiring genetic resistance. Here, we set out to identify and characterize persistence in S. pneumoniae. Specifically, we followed different strategies to overcome the self-limiting nature of S. pneumoniae as confounding factor in the prolonged monitoring of antibiotic survival needed to study persistence. In optimized conditions, we identified genuine persisters in various growth phases and for four relevant antibiotics through biphasic survival dynamics and heritability assays. Finally, we detected a high variety in antibiotic survival levels across a diverse collection of S. pneumoniae clinical isolates, which shows that a high natural diversity in persistence is widely present in S. pneumoniae. Collectively, this proof-of-concept significantly progresses the understanding of the importance of antibiotic persistence in S. pneumoniae infections which will set stage for characterizing its relevance to clinical outcomes and advocates for increased attention to the phenotype in both fundamental and clinical research. IMPORTANCES. pneumoniae is considered a serious threat by the Centers of Disease Control and Prevention through arising antibiotic resistance. In addition to resistance, bacteria can also survive lethal antibiotic treatment by developing antibiotic tolerance and more specifically by antibiotic tolerance through persistence. This phenotypic variation seems omnipresent among bacterial life, is linked to therapy failure and acts as a catalyst for resistance development. This study gives the first proof of the presence of persister cells in S. pneumoniae and shows a high variety in persistence levels among diverse strains, suggesting persistence is a general trait in S. pneumoniae cultures and that a broad range of genetic elements are controlling the phenotype. Together, our work advocates for higher interest for persistence in S. pneumoniae as a contributing factor for therapy failure and resistance development.

microbiology↗

bioRxiv2019

Isolation of persisters enabled by ss-lactam-induced filamentation reveals their single-cell awakening characteristics

When exposed to lethal doses of antibiotics, bacterial populations are most often not completely eradicated. A small number of phenotypic variants, defined as persisters, are refractory to antibiotics and survive treatment. Despite their involvement in relapsing infections caused by major pathogens, processes determining phenotypic switches from and to the persister state largely remain elusive. This is mainly due to the low frequency of persisters in a population and the lack of reliable persistence markers, both hampering studies of persistence at the single-cell level. Problematically, existing methods to enrich for persisters result in samples with very low persister densities and/or a too high abundance of other cell types. Here we present a novel and highly effective persister isolation method involving cephalexin, an antibiotic that induces extensive filamentation of susceptible cells. We show that antibiotic-tolerant cells can easily be separated by size after a short cephalexin treatment, and that the isolated cells are genuine persisters. We used our isolation method to monitor persister outgrowth at the single-cell level in a microfluidic device, thereby conclusively demonstrating that awakening is a stochastic phenomenon. We anticipate that our novel approach can have far-reaching consequences in the persistence field, by allowing single-cell studies at a much higher throughput than previously reported.

microbiology↗