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Rapid diagnosis of intra-amniotic infection using nanopore-based sequencing

OBJECTIVES: Early diagnosis and treatment of intra-amniotic infection is crucial. Rapid pathogen identification allows for a definite diagnosis and enables proper management. We determined whether the 16S amplicon sequencing performed by a nanopore sequencing technique make possible rapid bacterial...

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Detalles Bibliográficos
Autores principales: Chaemsaithong, Piya, Romero, Roberto, Pongchaikul, Pisut, Vivithanaporn, Pornpun, Lertrut, Waranyu, Jaovisidha, Adithep, Mongkolsuk, Paninee, Nitayanon, Perapon, Pongsuktavorn, Khontawan, Kamlungkuea, Threebhorn, Jung, Eunjung, Suksai, Manaphat, Singhsnaeh, Arunee, Jenjaroenpun, Piroon, Thaipisuttikul, Iyarit, Wongsurawat, Thidathip
Formato: Online Artículo Texto
Lenguaje:English
Publicado: De Gruyter 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10261508/
https://www.ncbi.nlm.nih.gov/pubmed/36503654
http://dx.doi.org/10.1515/jpm-2022-0504
Descripción
Sumario:OBJECTIVES: Early diagnosis and treatment of intra-amniotic infection is crucial. Rapid pathogen identification allows for a definite diagnosis and enables proper management. We determined whether the 16S amplicon sequencing performed by a nanopore sequencing technique make possible rapid bacterial identification at the species level in intra-amniotic infection. METHODS: Five cases of confirmed intra-amniotic infection, determined by either cultivation or 16S rDNA polymerase chain reaction (PCR) Sanger sequencing, and 10 cases of women who underwent mid-trimester genetic amniocentesis were included. DNA was extracted from amniotic fluid and PCR was performed on the full-length 16S rDNA. Nanopore sequencing was performed. The results derived from nanopore sequencing were compared with those derived from cultivation and Sanger sequencing methods. RESULTS: Bacteria were successfully detected from amniotic fluid using nanopore sequencing in all cases of intra-amniotic infection. Nanopore sequencing identified additional bacterial species and polymicrobial infections. All patients who underwent a mid-trimester amniocentesis had negative cultures, negative 16S PCR Sanger sequencing and nanopore sequencing. Identification of the microorganisms using nanopore sequencing technique at the bacterial species level was achieved within 5–9 h from DNA extraction. CONCLUSIONS: This is the first study demonstrating that the nanopore sequencing technique is capable of rapid diagnosis of intra-amniotic infection using fresh amniotic fluid samples.