Biology subjects

Psaltis, A.

Publications and source records attributed to Psaltis, A..

2 recordsLinked to original sources

bioRxiv2024

A comparison between full-length 16S rRNA Oxford Nanopore sequencing and Illumina V3-V4 16S rRNA sequencing in head and neck cancer tissues

IntroductionDescribing the microbial community within the tumour has been a key aspect in understanding the pathophysiology of the tumour microenvironment. In head and neck cancer (HNC), most studies on tissue samples have only performed 16S ribosomal RNA (rRNA) short-read sequencing (SRS) on V3-V5 region. SRS is mostly limited to genus level identification. In this study, we compared full-length 16S rRNA long-read sequencing (FL-ONT) from Oxford Nanopore Technology (ONT) to V3-V4 Illumina SRS (V3V4-Illumina). To date, this is the largest study using HNC tissues samples to perform FL-ONT of the 16S rRNA using ONT. MethodsSequencing of the full-length and the V3-V4 16S rRNA region was conducted on tumour samples from 26 HNC patients, using ONT and Illumina technologies respectively. Paired sample analysis was applied to compare differences in diversities and abundance of microbial communities. Further validation was also performed using culture-based methods in 16 bacterial isolates obtained from 4 patients using MALDI-TOF MS. ResultsWe observed similar alpha diversity indexes between FL-ONT and V3V4-Illumina technologies. However, beta-diversity was significantly different between techniques (PERMANOVA - R2 = 0.083, p < 0.0001). At higher taxonomic levels (Phylum to Family), all metrics were more similar among sequencing techniques, while lower taxonomy displayed more discrepancies. At higher taxonomic levels, correlation in microbial abundance from FL-ONT and V3V4-Illumina were higher, while this correlation decreased at lower levels. Finally, FL-ONT was able to identify more isolates at the species level that were identified using MALDI-TOF MS (81.3% v.s. 62.5%). ConclusionsFL-ONT was able to identify lower taxonomic levels at a better resolution as compared to V3V4-Illumina 16S rRNA sequencing. Depending on application purposes, both methods are suitable for identification of microbial communities, with FL-ONT being more superior at species level.

microbiology↗

bioRxiv2023

Bacteriophage in combination with ciprofloxacin against Pseudomonas aeruginosa infections in diabetic foot ulcer patients

BackgroundIn diabetic foot ulcer (DFU) patients, Pseudomonas aeruginosa (P. aeruginosa) infections are linked to poor wound healing. The ineffectiveness of antibiotics against these infections promotes the emergence of multidrug-resistant (MDR) strains. Bacteriophage (phage) therapy has recently gained popularity as an alternative to antibiotics. MethodologyBacterial and viral swabs and tissue were obtained from DFU infections (DFI). Bacteria were cultured followed by MALDI-TOF MS for identification. 16S rRNA long-read sequencing was used to identify the microbiota. Bacteriophages were isolated and underwent transmission electron microscopy, genomic sequencing, and stability testing. The antimicrobial activity of phages alone and in combination with ciprofloxacin against P. aeruginosa planktonic cells and biofilm grown in vitro and in ex vivo tissue was tested by measuring the optical density (OD), crystal violet assays and live/dead staining with visualisation using confocal scanning laser microscopy respectively. ResultsA total of 34 DFI patients were recruited from which microbiota were analysed for 25 patients. P. aeruginosa was the most prevalent pathogen cultured and was one of the top 6 most prevalent and abundant species in the microbiota analysis. Phage APTC-PA18 was isolated from DFIs, belonged to the myoviridae family and was strictly lytic. PA18 was stable between 4 and 70 degrees Celsius and between pH 3 and 11. Seven of eight P. aeruginosa clinical isolates were sensitive to APTC-PA18, and when APTC-PA18 was combined with ciprofloxacin against planktonic and biofilm of P. aeruginosa, synergistic effects were observed in vitro and in DFI tissue samples. ConclusionPhage APTC-PA18, when combined with ciprofloxacin, has the ability to kill P. aeruginosa clinical isolates both in vitro and ex vivo and is a promising treatment option for P. aeruginosa infections in DFUs.

microbiology↗