Single gene targeted nanopore sequencing enables simultaneous identification and antimicrobial resistance detection of sexually transmitted infections
| Autor: | Natalia Romero Sandoval, Andrea A. Lopez Rodas, Luz Marina Llangarí, Sadiq Tariq Sadiq, Liqing Zhou, Philip J. Cooper |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2022 |
| Předmět: |
Gene Sequencing
Mycoplasma genitalium Artificial Gene Amplification and Extension medicine.disease_cause Polymerase Chain Reaction Biochemistry Medical Conditions Medicine and Health Sciences DNA sequencing Pathogen Trichomonas Vaginalis Multidisciplinary biology Database and informatics methods Sequence analysis Eukaryota Protists Anti-Bacterial Agents Nucleic acids RNA Ribosomal 23S Infectious Diseases Ribosomal RNA DNA Gyrase Vagina Trichomonas Medicine Female Ecuador Macrolides Fluoroquinolones Research Article Cell biology Cellular structures and organelles Bioinformatics Science Sexually Transmitted Diseases Real-Time Polymerase Chain Reaction Research and Analysis Methods Microbiology Antibiotic resistance Microbial Control Drug Resistance Bacterial medicine Humans Molecular Biology Techniques Sequencing Techniques Non-coding RNA Molecular Biology BLAST algorithm Pharmacology Sex Workers Organisms Biology and Life Sciences biology.organism_classification Virology Neisseria gonorrhoeae Nanopore Sequencing RNA Trichomonas vaginalis Nanopore sequencing Antimicrobial Resistance Chlamydia trachomatis Ribosomes |
| Zdroj: | PLoS ONE, Vol 17, Iss 1, p e0262242 (2022) PLoS ONE PLoS ONE, Vol 17, Iss 1 (2022) |
| ISSN: | 1932-6203 |
| Popis: | Objectives To develop a simple DNA sequencing test for simultaneous identification and antimicrobial resistance (AMR) detection of multiple sexually transmitted infections (STIs). Methods Real-time PCR (qPCR) was initially performed to identify Neisseria gonorrhoeae (NG), Chlamydia trachomatis (CT), Mycoplasma genitalium (MG) and Trichomonas vaginalis (TV) infections among a total of 200 vulvo-vaginal swab samples from female sex workers in Ecuador. qPCR positive samples plus qPCR negative controls for these STIs were subjected to single gene targeted PCR MinION-nanopore sequencing using the smartphone operated MinIT. Results Among 200 vulvo-vaginal swab samples 43 were qPCR positive for at least one of the STIs. Single gene targeted nanopore sequencing generally yielded higher pathogen specific read counts in qPCR positive samples than qPCR negative controls. Of the 26 CT, NG or MG infections identified by qPCR, 25 were clearly distinguishable from qPCR negative controls by read count. Discrimination of TV qPCR positives from qPCR negative controls was poorer as many had low pathogen loads (qPCR cycle threshold >35) which produced few specific reads. Real-time AMR profiling revealed that 3/3 NG samples identified had gyrA mutations associated with fluoroquinolone resistance, 2/10 of TV had mutations related to metronidazole resistance, while none of the MG samples possessed 23S rRNA gene mutations contributing to macrolide resistance. Conclusions Single gene targeted nanopore sequencing for diagnosing and simultaneously identifying key antimicrobial resistance markers for four common genital STIs shows promise. Further work to optimise accuracy, reduce costs and improve speed may allow sustainable approaches for managing STIs and emerging AMR in resource poor and laboratory limited settings. |
| Databáze: | OpenAIRE |
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