Biology subjects

Maffei, E.

Publications and source records attributed to Maffei, E..

5 recordsLinked to original sources

bioRxiv2025

Coenzyme A depletion causes antibiotic tolerance in Pseudomonas aeruginosa

The widespread use of antibiotics promotes both resistance and tolerance. While resistance enables bacterial growth in the presence of drugs, tolerance allows survival during treatment, generating persisters that seed relapse and promote resistance. Despite its clinical relevance, the molecular basis of tolerance remains poorly understood. Using proteomic and metabolomic profiling combined with machine learning, we identified thiol oxidation as a robust predictor of tolerance in the human pathogen Pseudomonas aeruginosa. Single-cell analyses established a direct link between thiol oxidation and drug survival, indicating that redox imbalance drives persistence. Whereas depletion of coenzyme A (CoA), a central thiol-containing metabolite, scaled with tolerance, restoring CoA using engineered catalysts from Staphylococcus aureus abolished tolerance, establishing a causal relation between CoA availability and drug susceptibility. Thiol-based predictors also accurately capture tolerance of clinical P. aeruginosa isolates. These findings establish CoA-centered redox control as a key determinant of tolerance, opening opportunities for diagnostics and therapeutic interventions to prevent infection relapses.

microbiology↗

bioRxiv2024

Unlocking hidden phage diversity to complete the BASEL collection for systematic exploration of phage-host interactions

Research on bacteriophages, the viruses infecting bacteria, has fueled the development of modern molecular biology and inspired their therapeutic application to combat bacterial multidrug resistance. However, most work has so far focused on a few model phages which impedes direct applications of these findings in clinics and suggests that a vast potential of powerful molecular biology has remained untapped. We have therefore recently composed the BASEL collection of Escherichia coli phages (BActeriophage SElection for your Laboratory) which made a relevant diversity of phages infecting the E. coli K-12 laboratory strain accessible to the community. These phages are widely used, but their assorted diversity had remained limited by the E. coli K-12 host. We have therefore now genetically overcome the two major limitations of E. coli K-12, its lack of O-antigen glycans and the presence of resident bacterial immunity. Restoring O-antigen expression resulted in the isolation of diverse additional viral groups like Kagunavirus, Nonanavirus, Gordonclarkvirinae, and Gamaleyavirus, while eliminating all known antiviral defenses of E. coli K-12 additionally enabled us to isolate phages of Wifcevirus genus. Even though some of these viral groups appear to be common in nature, no phages from any of them had previously been isolated using E. coli laboratory strains and they had thus remained largely understudied. Overall, 37 new phage isolates have been added to complete the BASEL collection. These phages were deeply characterized genomically and phenotypically with regard to host receptors, sensitivity to antiviral defense systems, and host range. These results highlighted dominant roles of the O-antigen barrier for viral host recognition and of restriction-modification systems in bacterial immunity. We anticipate that the completed BASEL collection will propel research on phage-host interactions and their molecular mechanisms, deepening our understanding of viral ecology and fostering innovations in biotechnology and antimicrobial therapy.

microbiology↗

bioRxiv2022

Phage Paride hijacks bacterial stress responses to kill dormant, antibiotic-tolerant cells

Bacteriophages are fierce viral predators with no regard for pathogenicity or antibiotic resistance of their bacterial hosts1,2. Despite early recognition of their therapeutic potential and the current escalation of bacterial multidrug resistance, phages have so far failed to become a regular treatment option in clinical practice3-5. One reason is the occasional discrepancy between poor performance of selected phages in vivo despite high potency in vitro3,4,6,7. Similar resilience of supposedly drug-sensitive bacterial infections to antibiotic treatment has been linked to persistence of dormant cells inside patients8,9. Given the abundance of non-growing bacteria also in the environment10,11, we wondered whether some phages can infect and kill these antibiotic-tolerant cells. As shown previously12-16, most phages failed to replicate on dormant hosts and instead entered a state of hibernation or pseudolysogeny. However, we isolated a new Pseudomonas aeruginosa phage named Paride with the exciting ability to directly kill dormant, antibiotic-tolerant hosts by lytic replication, causing sterilization of deep-dormant cultures in synergy with the {beta}-lactam meropenem. Intriguingly, efficient replication of Paride on dormant hosts depends on the same bacterial stress responses that also drive antibiotic tolerance. We therefore suggest that Paride hijacks weak spots in the dormant physiology of antibiotic-tolerant bacteria that could be exploited as Achilles heels for the development of new treatments targeting resilient bacterial infections.

microbiology↗

bioRxiv2021

Systematic exploration of Escherichia coli phage-host interactions with the BASEL phage collection

Bacteriophages, the viruses infecting bacteria, hold great potential for the treatment of multidrug-resistant bacterial infections and other applications due to their unparalleled diversity and recent breakthroughs in their genetic engineering. However, fundamental knowledge of molecular mechanisms underlying phage-host interactions is mostly confined to a few traditional model systems and did not keep pace with the recent massive expansion of the field. The true potential of molecular biology encoded by these viruses has therefore remained largely untapped, and phages for therapy or other applications are often still selected empirically. We therefore sought to promote a systematic exploration of phage-host interactions by composing a well-assorted library of 66 newly isolated phages infecting the model organism Escherichia coli that we share with the community as the BASEL collection (BActeriophage SElection for your Laboratory). This collection is largely representative of natural E. coli phage diversity and was intensively characterized phenotypically and genomically alongside ten well-studied traditional model phages. We experimentally determined essential host receptors of all phages, quantified their sensitivity to eleven defense systems across different layers of bacterial immunity, and matched these results to the phages host range across a panel of pathogenic enterobacterial strains. Our results reveal clear patterns in the distribution of phage phenotypes and genomic features that highlight systematic differences in the potency of different immunity systems and point towards the molecular basis of receptor specificity in several phage groups. Strong trade-offs were detected between fitness traits like broad host recognition and resistance to bacterial immunity that might drive the divergent adaptation of different phage groups to specific niches. We envision that the BASEL collection will inspire future work exploring the biology of bacteriophages and their hosts by facilitating the discovery of underlying molecular mechanisms as the basis for an effective translation into biotechnology or therapeutic applications.

microbiology↗

bioRxiv2020

Evolution of Antibiotic Tolerance Shapes Resistance Development in Chronic Pseudomonas aeruginosa Infections

The widespread use of antibiotics promotes the evolution and dissemination of resistance and tolerance mechanisms. To assess the relevance of tolerance and its implications for resistance development, we used in vitro evolution and analyzed inpatient microevolution of Pseudomonas aeruginosa, an important human pathogen causing acute and chronic infections. We show that the development of tolerance precedes and promotes the acquisition of resistance in vitro and we present evidence that similar processes shape antibiotic exposure in human patients. Our data suggest that during chronic infections, P. aeruginosa first acquires moderate drug tolerance before following distinct evolutionary trajectories that lead to high-level multi-drug tolerance or to antibiotic resistance. Our studies propose that the development of antibiotic tolerance predisposes bacteria for the acquisition of resistance at early stages of infection and that both mechanisms independently promote bacterial survival during antibiotic treatment at later stages of chronic infections.

microbiology↗