Biology subjects

Psaltis, A. J.

Publications and source records attributed to Psaltis, A. J..

9 recordsLinked to original sources

bioRxiv2026

Genus-wide re-speciation of Corynebacterium and genomic characterisation of 87 sinus isolates resolves taxonomic conflicts and identifies four candidate novel species

Corynebacterium species are common members of the sinonasal microbiome and have shown conflicting associations with sinus health and chronic rhinosinusitis (CRS) in genus-level surveys. To better resolve the taxonomy and species-level functions of sinus corynebacteria, we generated complete long-read genome assemblies for 87 isolates, sourced from the middle meatus of 71 patients (51 with CRS, 20 healthy controls). We re-derived species boundaries de novo across the whole genus by average nucleotide identity (ANI), clustering 4,661 quality-filtered genomes retrieved from public databases and delineating higher-order species complexes. Our re-speciation assigned a species to 282 unlabelled corynebacteria, and corrected taxonomy for 266 NCBI accessions. We identified four novel candidate species from our isolate collection, and 39 public genomes fell within these species' boundaries. Whole-genome assignment reclassified 41 of our 87 isolates relative to mass-spectrometry (MALDI-TOF MS) identification, which only resolved to the species-complex level. Comparison of genome annotation characterised accessory functions that partitioned along species-complex lines, including glycogen and glycan utilisation, fatty-acid biosynthesis, cofactor (biotin and thiamine) auxotrophy, and iron-acquisition systems. Virulence and antimicrobial-resistance determinants were sparse, and the diphtheria toxin gene was universally absent. Acquired antimicrobial resistance was enriched on plasmids, whilst virulence genes were depleted from horizontally transferred compartments. Contrary to its frequent report in sinus microbiome studies, no C. tuberculostearicum genome publicly accessible via NCBI was found to be isolated from the sinonasal tract. Continued genome-level interrogation of Corynebacterium and contribution of sinus-commensals to reference databases will improve species-level understanding of the role of corynebacteria in the sinonasal microbiome.

microbiology↗

bioRxiv2026

Mutations in mfd cause Staphylococcus aureus mucoid hyper-biofilm phenotype in chronic rhinosinusitis

Chronic Rhinosinusitis (CRS) is a common chronic inflammation of the paranasal sinus mucosa. Staphylococcus aureus contributes to its severity through biofilm formation. In this study, we isolated eight sequential methicillin-resistant S. aureus (MRSA) isolates from a patient with severe CRS over a period of 672 days (T1-T8). The isolates were phenotypically and genomically characterised, and the extracellular biofilm proteome analysed. We identified an accumulation of mutations that included the acquisition of an IS21 family insertion sequence inactivating the icaR gene and nucleotide variants in various genes including the transcription repair coupling factor (mfd). The genomic changes were associated with a switch to a mucoid phenotype from T3 onwards (Day 178), with a significant increase in biofilm-forming capacity and the secretion of multiple enterotoxins. Targeted mutagenesis confirmed mfd is a regulator of strain mucoidy with enhanced biofilm and enterotoxin production. These findings support mfd as a target for novel anti-virulence therapies.

microbiology↗

bioRxiv2025

Protein Structure Informed Bacteriophage Genome Annotation with Phold

Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilising protein structural information that combines the ProstT5 protein language model and structural alignment tool Foldseek. Phold assigns annotations using a database of over 1.36 million predicted phage protein structures with high quality functional labels. Benchmarking reveals that Phold outperforms existing sequence-based homology approaches in functional annotation sensitivity whilst maintaining speed, consistency and scalability. Applying Phold to diverse cultured and metagenomic phage genomes shows it consistently annotates over 50% of genes on an average phage and 40% on an average archaeal virus. Comparisons of phage protein structures to other protein structures across the tree of life reveals that phage proteins commonly have structural homology to proteins shared across the tree of life, particularly those that have nucleic acid metabolism and enzymatic functions. Phold is available as free and open-source software at https://github.com/gbouras13/phold.

bioinformatics↗

bioRxiv2025

LicD-Mediated Cell Wall Decoration Governs Phage Sensitivity in Enterococcus faecalis Clinical Isolates

Enterococcus faecalis has emerged as a prevalent antibiotic-resistant pathogen in clinical settings. Herein, we report the identification of three novel lytic phages targeting vancomycin-resistant E. faecalis. While the isolated phages all belonged to the Kochikohdavirus genus, there were distinctive differences in their tail fibre proteins, affecting their adsorption. The phages showed strong antibacterial activity with wide host range, infecting >90% of the tested E. faecalis clinical and hospital wastewater isolates (n=13) with variable efficiency. The variation in host range was genomically correlated to the presence of the LicD gene in phage sensitive bacteria, which is responsible for phosphorylcholine decoration of the bacterial cell wall. Furthermore, the isolated phages were predicted to harbour genes encoding for depolymerase enzymes, which was confirmed by in vitro testing showing a >80% reduction in biofilm biomass. Phages inhibited bacterial growth for [≥]12 hours, followed by the emergence of bacteriophage insensitive mutants (BIMs) that were 4-fold more sensitive to vancomycin compared to parent strains. In addition, the isolated BIMs showed less capability of evading THP-1 macrophage and produced weaker biofilms. These findings underpin the potential of the isolated phages in combating recalcitrant E. faecalis associated biofilm-mediated infections.

microbiology↗

bioRxiv2023

Prophage acquisition by Staphylococcus aureus contributes to the expansion of Staphylococcal immune evasion

Staphylococcus aureus colonizes 30% of the human population, but only a few clones cause severe infections. S. aureus virulence varies and partly depends on the presence of prophages, viral DNA embedded in the S. aureus core genome, such as hlb-converting prophage ({phi}Sa3int). Human-adapted S. aureus often harbours a {phi}Sa3int group of prophages preferentially integrated into their {beta}-hemolysin (hlb) gene that encodes human immune evasion cluster (IEC) genes. Exotoxins and immune modulatory molecules encoded by this prophage can inhibit human innate immunity increasing S. aureus pathogenicity. This study aims to investigate the genomic and phenotypic plasticity of S. aureus and changes in its extracellular proteome after the acquisition of {phi}Sa3int prophage. To achieve this, we used S. aureus strains isolated from the sinus cavities of a patient with severe chronic rhinosinusitis (CRS) at two different time points (S. aureus SA222 and S. aureus SA333) and hybrid sequenced the strains using short-read Illumina and long-read Oxford nanopore technology. In silico analysis showed the presence of a {phi}Sa3int prophage in the later isolate but not in the earlier isolate while most of the core genes remained identical. Using mitomycin C, we induced the {phi}Sa3int prophage, and transduced it into the Sa3int-prophage-free SA222 isolate to obtain a laboratory generated double lysogen. We confirmed the successful lysogenisation with culture methods (spot assay, blood agar) and also by sequencing. We compared growth kinetics, biofilm biomass and metabolic activity between parent and the lysogen by establishing growth curves, crystal violet and resazurin assays. Exoproteins were identified and quantified using mass spectrophotometry. Integration of {phi}Sa3int prophage in SA222 down-regulated the beta-hemolysin expression of the lysogen. In silico analysis of the S. aureus genome confirmed the insertion of a [~]43.8 kb {phi}Sa3int prophage into hlb gene. Insertion of prophage DNA did not alter the growth kinetics, biofilm formation, adhesion to primary human nasal epithelial cells and the metabolic activity in a biofilm. However, the acquisition of {phi}Sa3int prophage significantly changed the expression of various secreted proteins, both bacterial and prophage-encoded. Altogether, thirty-eight exoproteins were significantly differentially regulated in the laboratory created lysogen, compared to its recipient strain SA222. Among these proteins, there was significant upregulation of 21 exoproteins (55.3 %) including staphylokinase (sak), SCIN (scn), and intercellular adhesion protein B (icaB) and downregulation of 17 exoproteins (44.7 %), including {beta}-hemolysin (hlb/sph) and outer membrane porin (phoE). Most of the upregulated proteins were involved in immunomodulation that help S. aureus escape human innate immunity and help cause chronic infection. These findings may contribute to the development of novel approaches to render S. aureus susceptible to the immune response by blocking prophage-associated defence mechanisms. HighlightsO_LIA {phi}Sa3int prophage preferentially integrates into the {beta}-haemolysin gene (hlb) gene thereby disrupting the beta-hemolysin function. C_LIO_LIA [~]43.8 kb {phi}Sa3int prophage acquisition by S. aureus has no impact on its growth kinetics, biofilm formation and adhesion to primary human nasal epithelial cells (HNECs). C_LIO_LIThe presence of a {phi}Sa3int group prophage likely enhances Staphylococcus aureus human immune evasion capability as the prophage encodes a complete set of immune evasion cluster (IEC) genes. C_LIO_LITargeted identification of virulence factors in addition to species and strain identification may lead to better-personalized therapy as not all S. aureus carry the same virulence genes. C_LI

microbiology↗

bioRxiv2023

Staphylococcus aureus biofilm secreted factors cause mucosal damage, mast cell infiltration and goblet cell hyperplasia in a rat rhinosinusitis model

Chronic Rhinosinusitis (CRS) is an inflammatory condition of the paranasal sinus mucosa. Despite being a common health issue, the exact cause of CRS is yet to be understood. However, research suggests that Staphylococcus aureus, particularly in the biofilm form, drives the disease. This study aimed to investigate the impact of long-term exposure to secreted factors of Staphylococcus aureus biofilm (SABSF), harvested from clinical isolates of non-CRS carriers and CRS patients, on the nasal mucosa in a rat model. Wistar rats were randomised (n=5/group) to receive daily intranasal instillations of 40 L (200 g/L) SABSF for 28 days or vehicle control with S. aureus isolated from the sinuses of a non-CRS carrier, a type 2 endotype CRS with nasal polyps (CRSwNP) patient, and a non-type 2 endotype CRS without nasal polyps (CRSsNP) patient. The sinonasal samples of the rats were then analysed through histopathology and transcriptome profiling. The results showed that all three intervention groups displayed significant lymphocytic infiltration (p[≤]0.05). However, only the SABSF collected from the CRSwNP patient caused significant mucosal damage, mast cell infiltration, and goblet cell hyperplasia compared to the control. The transcriptomics results indicated that SABSF significantly enriched multiple inflammatory pathways and showed distinct transcriptional expression differences between the control group and the SABSF collected from CRS patients (p[≤]0.05). Additionally, the SABSF challenges induced the expression of IgA and IgG but not IgE. In conclusion, this in vivo study indicates that long-term exposure to SABSF leads to an inflammatory response in the nasal mucosa with increased severity for S. aureus isolated from a CRSwNP patient. The findings of this study shed light on the role of S. aureus in the development of CRS and could inform future research and treatment efforts.

immunology↗

bioRxiv2023

The Intra-Host Evolutionary Landscape And Pathoadaptation Of Persistent Staphylococcus aureus In Chronic Rhinosinusitis

Chronic rhinosinusitis (CRS) is a common chronic sinonasal mucosal inflammation associated with Staphylococcus aureus biofilm and relapsing infections. This study aimed to determine rates of S. aureus persistence and pathoadaptation in CRS patients by investigating the genomic relatedness and antibiotic resistance/tolerance in longitudinally collected S. aureus clinical isolates. A total of 68 S. aureus isolates were sourced from 34 CRS patients at least six months apart. Isolates were grown into 48-hour biofilms and tested for tolerance to antibiotics. A hybrid sequencing strategy was used to obtain high-quality reference-grade assemblies of all isolates. Single nucleotide variants (SNV) divergence in the core genome and sequence type clustering were used to analyse the relatedness of the isolate pairs. Single nucleotide and structural genome variations, plasmid similarity, and plasmid copy numbers between pairs were examined. Our analysis revealed that 41% (14/34 pairs) of S. aureus isolates were persisters, while 59% (20/34 pairs) were non-persisters. Persister isolates showed episode-specific mutational changes over time with a bias towards events in genes involved in adhesion to the host and mobile genetic elements such as plasmids, prophages, and insertion sequences. A significant increase in the copy number of conserved plasmids of persister strains (p<0.05) was seen, indicating a role of the "mobilome" in promoting persistence. This was accompanied by a significant increase in biofilm tolerance against all tested antibiotics (p<0.001), which was linked to a significant increase in biofilm biomass (p<0.05) over time, indicating a biofilm central pathoadaptive process in persisters. In conclusion, our study provides important insights into the mutational changes underlying S. aureus persistence in CRS patients highlighting pathoadaptive mechanisms in S. aureus persisters culminating in increased biofilm biomass linked to an increase in plasmid copy number over time.

microbiology↗

bioRxiv2019

Microbiotyping the sinonasal microbiome

This study offers a novel description of the sinonasal microbiome, through an unsupervised machine learning approach combining dimensionality reduction and clustering. We apply our method to the International Sinonasal Microbiome Study (ISMS) dataset of 410 sinus swab samples. We propose three main sinonasal microbiotypes or states: the first is Corynebacterium-dominated, the second is Staphylococcus-dominated, and the third dominated by the other core genera of the sinonasal microbiome (Streptococcus, Haemophilus, Moraxella, and Pseudomonas). The prevalence of the three microbiotypes studied did not differ between healthy and diseased sinuses, but differences in their distribution were evident based on geography. We also describe a potential reciprocal relationship between Corynebacterium species and Staphylococcus aureus, suggesting that a certain microbial equilibrium between various players is reached in the sinuses. We validate our approach by applying it to a separate 16S rRNA gene sequence dataset of 97 sinus swabs from a different patient cohort. Sinonasal microbiotyping may prove useful in reducing the complexity of describing sinonasal microbiota. It may drive future studies aimed at modeling microbial interactions in the sinuses and in doing so may facilitate the development of a tailored patient-specific approach to the treatment of sinus disease in the future.

microbiology↗

bioRxiv2019

The international sinonasal microbiome study (ISMS): a multi centre, international characterization of sinonasal bacterial ecology

The sinonasal microbiome remains poorly defined, with our current knowledge based on a few cohort studies whose findings are inconsistent. Furthermore, the variability of the sinus microbiome across geographical divides remains unexplored. We characterise the sinonasal microbiome and its geographical variations in both health and disease using 16S rRNA gene sequencing of 410 individuals from across the world. Although the sinus microbial ecology is highly variable between individuals, we identify a core microbiome comprised of Corynebacterium, Staphylococcus, Streptococcus, Haemophilus, and Moraxella species in both healthy and chronic rhinosinusitis (CRS) cohorts. Corynebacterium (mean relative abundance = 44.02%) and Staphylococcus (mean relative abundance = 27.34%) appear particularly dominant in the majority of patients sampled. There was a significant variation in microbial diversity between countries (p = 0.001). Amongst patients suffering from CRS with nasal polyps, a significant depletion of Corynebacterium (40.29% vs 50.43%; p = 0.02) and over-representation of Streptococcus (7.21% vs 2.73%; p = 0.032) was identified. The delineation of the sinonasal microbiome and standardised methodology described within our study will enable further characterisation and translational application of the sinus microbiota.

microbiology↗