Rapid diagnosis of intra-amniotic infection using nanopore-based sequencing
1
Issued Date
2022-01-01
Resource Type
ISSN
03005577
eISSN
16193997
Scopus ID
2-s2.0-85144338383
Pubmed ID
36503654
Journal Title
Journal of Perinatal Medicine
Rights Holder(s)
SCOPUS
Bibliographic Citation
Journal of Perinatal Medicine (2022)
Suggested Citation
Chaemsaithong P., Romero R., Pongchaikul P., Vivithanaporn P., Lertrut W., Jaovisidha A., Mongkolsuk P., Nitayanon P., Pongsuktavorn K., Kamlungkuea T., Jung E., Suksai M., Singhsnaeh A., Jenjaroenpun P., Thaipisuttikul I., Wongsurawat T. Rapid diagnosis of intra-amniotic infection using nanopore-based sequencing. Journal of Perinatal Medicine (2022). doi:10.1515/jpm-2022-0504 Retrieved from: https://repository.li.mahidol.ac.th/handle/123456789/87396
Title
Rapid diagnosis of intra-amniotic infection using nanopore-based sequencing
Author's Affiliation
Ramathibodi Hospital
Siriraj Hospital
University of Michigan Medical School
Detroit Medical Center
Michigan State University
University of Liverpool
Wayne State University School of Medicine
National Institute of Child Health and Human Development (NICHD)
Faculty of Medicine Ramathibodi Hospital, Mahidol University
Mahidol University
National Institutes of Health (NIH)
Siriraj Hospital
University of Michigan Medical School
Detroit Medical Center
Michigan State University
University of Liverpool
Wayne State University School of Medicine
National Institute of Child Health and Human Development (NICHD)
Faculty of Medicine Ramathibodi Hospital, Mahidol University
Mahidol University
National Institutes of Health (NIH)
Other Contributor(s)
Abstract
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. 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. 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. 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.