Biology subjects

Tschudin-Sutter, S.

Publications and source records attributed to Tschudin-Sutter, S..

6 recordsLinked to original sources

bioRxiv2026

Monitoring intracellular antibiotic concentrations in real-time using allosteric biosensors

Antibiotic treatment can fail due to insufficient drug availability at the site of infection or limited accumulation within bacterial pathogens. However, it is poorly understood how antibiotics penetrate infected tissues and complex bacterial aggregates, limiting insights into the mechanisms of treatment failure. Here, we present genetically-encoded allosteric biosensors for two antibiotic classes, trimethoprim and tetracycline, which enable real-time monitoring of antibiotic concentrations inside bacterial cells. The biosensors consist of circularly permuted EGFP linked to the sensory domains DHFR or TetR. To extend this approach to low oxygen environments, we engineered an oxygen-independent trimethoprim biosensor by fusing DHFR to a circularly permuted version of the fluorogenic protein FAST. Using these biosensors, we monitored the antibiotic exposure dynamics of intracellular Salmonella enterica during macrophage infection at the single-cell level, and antibiotic penetration into anaerobic regions of Vibrio cholerae biofilms, as well as antibiotic availability in microoxic conditions in a human bladder tissue model infected with uropathogenic Escherichia coli. These fluorescent biosensors have the potential to be broadly applied for determining antibiotic distributions at infection sites with high spatial and temporal resolution.

microbiology↗

bioRxiv2025

Perfusable 3D human urothelial model for real-time analysis of bacterial infection dynamics and therapeutic interventions

Urinary tract infections (UTIs) remain a major health burden, yet mechanistic studies are limited by the lack of experimental models that enable high spatiotemporal resolution tracking of infection dynamics, while recapitulating the stratified architecture of the bladder epithelium, urine tolerance and fluid dynamics. Here, we present a modular microphysiological platform integrating a fully stratified, urine-tolerant human urothelium cultured on standard transwell inserts within a custom-designed perfusion device compatible with live imaging. Urine flow enables real-time, high-resolution imaging of uropathogenic Escherichia coli (UPEC) infections under physiologically relevant conditions, including clearance of planktonic bacteria and nutrients replenishment, while retaining tissue-associated populations. This system revealed UPEC attachment via the type 1 fimbrial adhesin FimH and its inhibition by D-mannose treatment. Moreover, the platform captured L-form formation upon treatment with the frontline antibiotic fosfomycin and regrowth of walled bacteria following drug withdrawal. The platform further uncovered strain-specific lysis through bacteriophages in contrast to the activity of broad-spectrum antibiotics. In summary, this system constitutes a scalable platform with high predictive power for studying UTI pathogenesis and preclinical therapeutic testing.

bioengineering↗

bioRxiv2025

Genome-scale CRISPRi profiling reveals metabolic vulnerabilities of uropathogenic Escherichia coli in human urine

Urinary tract infections (UTIs) are among the most common infectious diseases, causing over 400 million cases and 260,000 deaths annually. Women are disproportionately affected, with [~]50% experiencing at least one UTI during their lifetime and 20-30% suffering from recurrent infections. Uropathogenic Escherichia coli (UPEC), which accounts for [~]75% of cases, employs diverse virulence factors to persist and evade host immunity. Rising antibiotic resistance, driven by widespread antimicrobial misuse, is eroding treatment efficacy and highlights the urgent need for alternative therapeutic strategies. To uncover novel vulnerabilities under physiologically relevant conditions, we constructed a genome-wide CRISPR interference (CRISPRi) library in the UPEC reference strain E. coli CFT073 and systematically profiled gene fitness in rich media versus human urine. The screen revealed multiple pathways that are conditionally essential for UPEC growth in urine, including iron uptake, envelope maintenance, and the biosynthesis of arginine, methionine, and branched-chain amino acids. Notably, we identified acetolactate synthase (ALS) II as the sole active isoform supporting branched-chain amino acid synthesis in urine. Functional validation further demonstrated its druggability: introducing a re-sensitizing mutation overcame the proteins intrinsic resistance to the ALS-targeting herbicide sulfometuron methyl, restoring sensitivity. These findings establish ALS II as a promising therapeutic target against UPEC.

microbiology↗

bioRxiv2023

Ancient methicillin-resistant Staphylococcus aureus: expanding current knowledge using molecular epidemiological characterization of a Swiss legacy collection

Few methicillin-resistant Staphylococcus aureus (MRSA) from the early years of its global emergence have been sequenced. Knowledge about evolutionary factors promoting the success of specific MRSA multi-locus sequence types (MLSTs) remains scarce. We aimed to characterize a legacy MRSA collection isolated from 1965 to 1987 and compare it against publicly available international and local genomes. We accessed 451 ancient (1965-1987) Swiss MRSA isolates, stored in the Culture Collection of Switzerland. We determined phenotypic antimicrobial resistance (AMR) and performed Illumina short-read sequencing on all isolates and long-read sequencing on a selection with Oxford Nanopore Technology. For context, we included 103 publicly available international genomes from 1960 to 1992 and sequenced 1207 modern Swiss MRSA isolates from 2007 to 2022. We analyzed the core genome (cg)MLST and predicted SCCmec cassette types, AMR, and virulence genes. Among the 451 ancient Swiss MRSA isolates, we found 17 sequence types (STs) of which 11 have been previously described. Two STs were novel combinations of known loci and six isolates carried previously unsubmitted MLST alleles, representing five new STs (ST7843, ST7844, ST7837, ST7839, and ST7842). Most isolates (83% 376/451) represented ST247-MRSA-I isolated in the 1960s, followed by ST7844 (6% 25/451), a novel single locus variant (SLV) of ST239. Analysis by cgMLST indicated that isolates belonging to ST7844-MRSA-III cluster within the diversity of ST239-MRSA-IIII. Early MRSA were predominantly from clonal complex (CC) 8. From 1980 to the end of the 20th century we observed that CC22 and CC5 as well as CC8 were present, both locally and internationally. The combined analysis of 1761 ancient and contemporary MRSA isolates across more than 50 years uncovered novel STs and allowed us a glimpse into the lineage flux between Swiss and international MRSA across time.

microbiology↗

bioRxiv2021

The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies

The spread of antibiotic resistance genes on plasmids is a threat to human and animal health. Phylogenies of bacteria and their plasmids contain clues regarding the frequency of plasmid transfer events, as well as the co-evolution of plasmids and their hosts. However, whole genome sequencing data from diverse ecological or clinical bacterial samples is rarely used to study plasmid phylogenies and resistance gene transfer. This is partially due to the difficulty to extract plasmids from short-read sequencing data. Here, we use both short- and long-read sequencing data of 24 clinical extended-spectrum {beta}-lactamase producing Escherichia coli to estimate chromosomal and plasmid phylogenies. We compare the impact of different sequencing and assembly methodologies on these phylogenies and on the inference of horizontal gene transfer. We find chromosomal phylogenies can be estimated robustly with all methods, whereas plasmid phylogenies have more variable topology and branch lengths across the methods used. Specifically, hybrid methods that use long reads to resolve short-read assemblies (HybridSPAdes and Unicycler) perform better than those that started from long-reads during assembly graph generation (Canu). In contrast, the inference of plasmid and antibiotic resistance gene transfer using a parsimony-based criterion is mostly robust to the choice of sequencing and assembly method.

bioinformatics↗

bioRxiv2020

High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters

With two-thirds of the global population projected to be living in urban areas by 2050, understanding the transmission patterns of viral pathogens within cities is crucial for effective prevention strategies. Here, in unprecedented spatial resolution, we analysed the socioeconomic determinants of influenza transmission in a European city. We combined geographical and epidemiological data with whole genome sequencing of influenza viruses at the scale of urban quarters and statistical blocks, the smallest geographic subdivisions within a city. We observed annually re-occurring geographic clusters of influenza incidences, mainly associated with net income, and independent of population density and living space. Vaccination against influenza was also mainly associated with household income and was linked to the likelihood of influenza-like illness within an urban quarter. Transmissions patterns within and between quarters were complex. High-resolution city-level epidemiological studies combined with social science surveys such as this will be essential for understanding seasonal and pandemic transmission chains and delivering tailored public health information and vaccination programs at the municipal level.

microbiology↗