Open AccessA Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing
Author(s) -
Stefan Neuenschwander,
Miguel Angel Terrazos Miani,
Heiko Amlang,
Carmen Perroulaz,
Pascal Bittel,
Carlo Casanova,
Sara Droz,
JeanPierre Flandrois,
Stephen L. Leib,
Franziska SuterRiniker,
Alban Ramette
Publication year - 2020
Publication title -
journal of clinical microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.349
H-Index - 255
eISSN - 1070-633X
pISSN - 0095-1137
DOI - 10.1128/jcm.00060-20
Subject(s) - amplicon , sanger sequencing , nanopore sequencing , computational biology , turnaround time , dna sequencing , massive parallel sequencing , biology , identification (biology) , ion semiconductor sequencing , amplicon sequencing , minion , sequence analysis , sample (material) , 16s ribosomal rna , polymerase chain reaction , genetics , computer science , gene , chromatography , chemistry , botany , operating system
Amplicon sequencing of the 16S rRNA gene is commonly used for the identification of bacterial isolates in diagnostic laboratories and mostly relies on the Sanger sequencing method. The latter, however, suffers from a number of limitations, with the most significant being the inability to resolve mixed amplicons when closely related species are coamplified from a mixed culture. This often leads to either increased turnaround time or absence of usable sequence data. Short-read next-generation sequencing (NGS) technologies could solve the mixed amplicon issue but would lack both cost efficiency at low throughput and fast turnaround times.