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9 results on '"Sadiq, Syed T."'

3. P459: Anorectal and vulvovaginal microbiota in Ecuadorian female sex workers with anorectal and urogenital STIs: evidence for crossanatomical impact.

Author

Sadiq, Syed T., Broad, Claire, Cooper, Philip, Llangari Arizo, Luz Marina, and Romero, Natalia

Abstract

Background: Vaginal microbiota changes associated with Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Mycoplasma genitalium (MG) and Trichomonas vaginalis (TV), can be linked to adverse reproductive health outcomes. Evidence suggests gastrointestinal tract (GIT) infections may affect extra-GIT microbiota. Full-length 16S rRNA gene sequencing may better identify microbiota to species level. We used long-read, full-length 16S rRNA gene sequencing to characterise vulvovaginal (VVS) and anorectal microbiota and their associations with urogenital and anorectal STIs in Ecuadorian female sex workers (FSWs). Methods: VVS and anorectal DNA extracts were subselected from a wider study of FSWs from north-west Ecuador, previously tested for urogenital and anorectal CT, NG, MG and urogenital TV. Full-length 16S rRNA amplicon sequencing was performed using PacBio Hi-Fidelity (HiFi) circular consensus sequencing, reads mapped to a 16S rRNA NCBI database and analyses performed using R-based packages including phyloseq. Significance values were corrected for multiple testing. Results: A total of 124 samples were sequenced, of which 83 were VVS and 43 anorectal, including 36 VVS-anorectal pairs from the same FSWs. Following normalisation, distinct species numbers were lower in VVS compared with anorectal samples (p β = -42, p = 0.018) with no impact on anorectal Shannon and Simpson diversity. In contrast, anorectal CT or NG infection was associated with greater VVS microbiota evenness (Simpson β = 0.31, p = 0.003; Shannon β = 0.67, p = 0.01) independent of urogenital STI status, with 5-fold increased Actinobacteria abundance (p = 0.02), dominated by G. vaginalis and F. vaginae, and 43% decreased Firmicutes abundance (p = 0.05), predominantly decreased L. iners. Conclusions: Amongst vulnerable, highly sexually active Ecuadorian FSWs with high usage of vaginal products, anorectal STIs were independently associated with increased vulvovaginal microbial diversity with changes in vulvovaginal microbiota traditionally associated with poor reproductive health outcomes. [ABSTRACT FROM AUTHOR]

Published
2024

7. P1.32 Hand-held rapid whole genome nanopore sequencing to predictneisseria gonorrhoeaeantibiotic susceptibility: steps towards clinic based tailored antimicrobial therapy

Author

Phillips, Laura T, primary, Witney, Adam, additional, Izquierdo-Carrasco, Fernando, additional, Mayes, Simon, additional, Wright, Amber, additional, Laing, Ken, additional, Gould, Kate, additional, Pond, Marcus, additional, Hall, Catherine L, additional, Harding-Esch, Emma M, additional, Butcher, Phillip, additional, Zhou, Liqing, additional, and Sadiq, Syed T, additional

Published
2017
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8. Modular development of a prototype point of care molecular diagnostic platform for sexually transmitted infections

Author

Branavan, Manoharanehru, Mackay, Ruth E., Craw, Pascal, Naveenathayalan, Angel, Ahern, Jeremy C., Sivanesan, Tulasi, Hudson, Chris, Stead, Thomas, Kremer, Jessica, Garg, Neha, Baker, Mark, Sadiq, Syed T., and Balachandran, Wamadeva

Subjects
Point-of-care, Microfluidics, Biophysics, Biomedical Engineering, Molecular diagnostics, Microengineering
Abstract

This paper presents the design of a modular point of care test platform that integrates a proprietary sample collection device directly with a microfluidic cartridge. Cell lysis, within the cartridge, is conducted using a chemical method and nucleic acid purification is done on an activated cellulose membrane. The microfluidic device incorporates passive mixing of the lysis-binding buffers and sample using a serpentine channel. Results have shown extraction efficiencies for this new membrane of 69% and 57% compared to the commercial Qiagen extraction method of 85% and 59.4% for 0.1ng/μL and 100ng/μL salmon sperm DNA respectively spiked in phosphate buffered solution. Extraction experiments using the serpentine passive mixer cartridges incorporating lysis and nucleic acid purification showed extraction efficiency around 80% of the commercial Qiagen kit. Isothermal amplification was conducted using thermophillic helicase dependant amplification and recombinase polymerase amplification. A low cost benchtop real-time isothermal amplification platform has been developed capable of running six amplifications simultaneously. Results show that the platform is capable of detecting 1.32×106 of sample DNA through thermophillic helicase dependant amplification and 1×105 copy numbers Chlamydia trachomatis genomic DNA within 10min through recombinase polymerase nucleic acid amplification tests. This work is funded under the UKCRC Translational Infection Research (TIR) Initiative supported by the Medical Research Council (Grant number G0901608) with contributions to the grant from the Biotechnology and Biological Sciences Research Council, the National Institute for Health Research on behalf of the Department of Health, the Chief Scientist Office of the Scottish Government Health Directorates and the Wellcome Trust. Axxin are thanked for sup- plying the T16-ISO platform.

Published
2015

9. P1.32 Hand-held rapid whole genome nanopore sequencing to predict neisseria gonorrhoeaeantibiotic susceptibility: steps towards clinic based tailored antimicrobial therapy

Author

Phillips, Laura T, Witney, Adam, Izquierdo-Carrasco, Fernando, Mayes, Simon, Wright, Amber, Laing, Ken, Gould, Kate, Pond, Marcus, Hall, Catherine L, Harding-Esch, Emma M, Butcher, Phillip, Zhou, Liqing, and Sadiq, Syed T

Abstract

IntroductionNext generation sequencing can accurately predict antibiotic susceptibility in Neisseria gonorrhoeae(NG) allowing preservation of first-line treatments in the face of widespread antimicrobial resistance (AMR). The rapid nature of novel hand-held nanopore sequencing (NPS) gives promise for utility at the point of care. We evaluated time to result post DNA extraction, and accuracy of MinION (Oxford Nanopore Technologies) NPS to predict phenotypic antimicrobial susceptibility (PAMS) of NG to ciprofloxacin and azithromycin.MethodsOne-directional (1-D) NPS using bar-coded DNA library preparations from 48 NG isolates, prospectively collected from a London clinic, were run on NPS flow cells (3 per R9.0 flow cell) and illumina MiSeq as a comparator. NPS raw sequences were transferred to the cloud for base-calling, alignment, and variant calling using standard tools.ResultsMean time for 1-D library preparation was roughly 1 hour; NPS and alignment took <40 min per sample with single nucleotide polymorphism (SNP) calling adding little extra time. NPS genome coverage was >30X per isolate. Of 48 samples, PAMS to ciprofloxacin, and azithromycin was 74% and 87% respectively. Accuracy of NPS-based genotypic susceptibility, defined as absence of any known AMR-associated SNP’s, to predict PAMS for ciprofloxacin and azithromycin, was 34/34 (100%; 95% CI 89.8%–100%) and 35/40 (87.5%; 95% CI 73.9%–94.5%) respectively. Accuracies improved significantly for azithromycin when only high quality reads were included, and with Illumina sequencing. 30 of the 34 isolates susceptible to azithromycin were also susceptible to ciprofloxacin, and 3 of 6 isolates resistant to azithromycin were also resistant to Ciprofloxacin.ConclusionNPS accurately predicted ciprofloxacin PAMS but was less accurate for azithromycin. With new iterations of the technology, imminent rapid barcoded library preparation (10 min) and rapid DNA extraction from clinical samples, NPS may allow accurate ceftriaxone-adjunctive treatment combinations, for a substantial proportion of patients.

Published
2017
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