Biology subjects

Wilks, S.

Publications and source records attributed to Wilks, S..

4 recordsLinked to original sources

bioRxiv2026

NGS-RFA/FRA: A High Throughput Experimental and Computational Pipeline for Selective Mutational Scanning in Parallel

Influenza viruses evade vaccine and infection mediated immunity by accumulating mutations in their hemagglutinin (HA) protein. Predicting this evolution might be possible via selective mutational scanning (SMS) - the generation of many specific mutants of interest from currently circulating viruses and characterizing their escape potential and fitness with high accuracy (Mogling 2016). However, this task is challenging, even when focusing on a reduced set of key HA positions (Koel et al. 2013). Here we describe a high-throughput SMS method to address this challenge. Our approach consists of a three-stage pipeline: (1) a parallel optimized virus rescue process that generates balanced target mutant virus libraries (2) an assay to assess replicative fitness and neutralisation of these variants as a mixture, and (3) a bespoke statistical model to quantify statistically significant differences between these observables. We tested the pipeline on libraries of up to 134 variants finding excellent correlation to classical hemagglutination inhibition (HI) and plaque growth assays used to assess antigenic phenotype and replicative fitness respectively, as well as remarkable repeatability overall. Notably, the method reduces the timeline required to carry out such assessments with classical methods from about a year to several weeks. By enabling rapid and efficient characterization of influenza virus variants, this approach has the potential to greatly enhance surveillance efforts, transforming reactive monitoring into proactive forecasting.

evolutionary biology↗

bioRxiv2025

LubriShieldTM - a unique permanent coating for indwelling urinary catheters that impedes surface-associated uropathogens from forming biofilm

Catheter-associated urinary tract infection (CAUTI) is one of the most common healthcare-associated infections and biofilm formation plays a key role in its pathogenesis. Indwelling medical devices introduce ideal pathways inside the body for invading pathogens and feature surfaces conducive to biofilm development. These devices are the root cause of severe clinical infections often recalcitrant to antimicrobials. When bacteria and fungi switch to biofilm mode of growth, they produce a matrix in the form of extracellular polymeric substances (EPS). This creates a unique environment for growing virulent colonizers and persisting cells while also forming a shielding barrier against immune system attacks, antimicrobial agents and mechanical removal by fluid shear forces. To address this challenge, LubriShield TM - a novel permanent coating was invented, and evenly applied to both the internal and external surfaces of indwelling urinary Foley catheters. Without releasing active substances, it effectively prevented pathogens from producing biofilm. The coating was superhydrophilic and incorporated a proprietary anti-fouling ligand, which created a surface that significantly inhibited up to 99% of colonizing uropathogens from forming biofilm for the duration of use without any microbial killing (p< 0.001). The predominant uropathogens, including Gram-positive and Gram-negative as well as Candida albicans, were inhibited from forming biofilm on the LubriShieldTM coated surfaces for up to 14 days in artificial urine medium. After challenging the adhering bacteria in a glass bladder flow model, the coating still significantly reduced biofilm formation by 83% (p<0.001). The growth mode and emergent properties of adhering bacteria on uncoated silicone catheter surfaces were compared with those on LubriShieldTM coated surfaces. RNA-seq analysis revealed that gene expression associated with microbial EPS formation was significantly downregulated on the coated surfaces. Additionally, microorganisms adhering to LubriShieldTM coated catheters were 46% more susceptible to antibiotics compared to those on uncoated silicone catheters (p<0.01).

microbiology↗

bioRxiv2021

Modelling of filamentous phage-induced antibiotic tolerance of P.aeruginosa

Filamentous molecules tend to spontaneously assemble into liquid crystalline droplets with a tactoid morphology in the environments with the high concentration on non-adsorbing molecules. Tactoids of filamentous Pf bacteriophage, such as those produced by Pseudomonas aeruginosa, have been linked with increased antibiotic tolerance. We modelled this system and show that tactoids, composed of filamentous Pf virions, can lead to antibiotic tolerance by acting as an adsorptive diffusion barrier. The continuum model, reminiscent of descriptions of reactive diffusion in porous media, has been solved numerically and good agreement was found with the analytical results, obtained using a homogenisation approach. We find that the formation of tactoids significantly increases antibiotic diffusion times leading to stronger antibiotic resistance.

microbiology↗

bioRxiv2020

Uncovering microbial populations in the lumen of neonatal enteral feeding tubes utilising 16s rRNA sequencing.

Gastrointestinal microbiome is increasingly implicated in the morbidity associated with being born preterm. Enteral tubes (ET) are essential for the nutritional care of preterm infants. Limited culture-based studies have suggested they are colonised by high densities of microorganisms. Microbial DNA was extracted from 60 ETs retrieved from infants in a tertiary neonatal unit and analysed by16s rRNA sequencing of the V4 variable region. Relative abundance analysis on dominant microorganisms demonstrated that compared to breast milk, formula significantly increased abundance of Streptococcus spp and significantly decreased Enterococcus spp and Enterobacteriaceae Vaginal birth was also associated with significantly increased relative abundance of Streptococcus. This study more accurately demonstrates the extent of microbial diversity in neonatal ETs, with feeding regime significantly influencing colonisation patterns. Colonisation with unwanted organisms, as a result of specific care regimes, could result in disruption of the fragile infant gut microbiome, with implications for long-term morbidity.

microbiology↗