Potential utility of targeted Nanopore sequencing for improving etiologic diagnosis of bacterial and fungal respiratory infection.
Diagn Pathol
; 15(1): 41, 2020 Apr 27.
Article
em En
| MEDLINE
| ID: mdl-32340617
ABSTRACT
BACKGROUND:
Diversified etiology of lower respiratory tract infection renders diagnosis challenging. The mainstay microbial culture is time-consuming and constrained by variable growth requirements. In this study, we explored the use of Nanopore sequencing as a supplementary tool to alleviate this diagnostic bottleneck.METHODS:
We developed a targeted Nanopore method based on amplification of bacterial 16S rRNA gene and fungal internal transcribed spacer region. The performance was compared with routine infectious disease workups on 43 respiratory specimens.RESULTS:
Nanopore successfully identified majority of microbes (47/54, 87.04%) and 7 possible pathogens not detected by routine workups, which were attributable to the content of microbiological investigations (n = 5) and negative culture (n = 2). The average sequencing time for first target reads was 7 min (1-43 min) plus 5 h of pre-sequencing preparation.CONCLUSIONS:
The Nanopore method described here was rapid, economical and hypothesis-free, which might provide valuable hints to further microbiological follow-up for opportunistic pathogens missed or not detectable by conventional tests.Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Infecções Respiratórias
/
Infecções Bacterianas
/
Técnicas Bacteriológicas
/
Sequenciamento por Nanoporos
/
Pneumopatias Fúngicas
/
Micologia
Tipo de estudo:
Diagnostic_studies
/
Etiology_studies
/
Prognostic_studies
Limite:
Humans
Idioma:
En
Revista:
Diagn Pathol
Assunto da revista:
PATOLOGIA
Ano de publicação:
2020
Tipo de documento:
Article
País de afiliação:
China