Single-molecule long-read 16S sequencing to characterize the lung microbiome from mechanically ventilated patients with suspected pneumonia

Ian Toma, Marc O. Siegel, John Keiser, Anna Yakovleva, Alvin Kim, Lionel Davenport, Joseph Devaney, Eric P. Hoffman, Rami Alsubail, Keith A. Crandall, Eduardo Castro-Nallar, Marcos Pérez-Losada, Sarah K. Hilton, Lakhmir S. Chawla, Timothy A. McCaffrey, Gary L. Simon

Resultado de la investigación: Contribución a una revistaArtículorevisión exhaustiva

37 Citas (Scopus)

Resumen

In critically ill patients, the development of pneumonia results in significant morbidity and mortality and additional health care costs. The accurate and rapid identification of the microbial pathogens in patients with pulmonary infections might lead to targeted antimicrobial therapy with potentially fewer adverse effects and lower costs. Major advances in next-generation sequencing (NGS) allow culture-independent identification of pathogens. The present study used NGS of essentially full-length PCRamplified 16S ribosomal DNA from the bronchial aspirates of intubated patients with suspected pneumonia. The results from 61 patients demonstrated that sufficient DNA was obtained from 72% of samples, 44% of which (27 samples) yielded PCR amplimers suitable for NGS. Out of the 27 sequenced samples, only 20 had bacterial culture growth, while the microbiological and NGS identification of bacteria coincided in 17 (85%) of these samples. Despite the lack of bacterial growth in 7 samples that yielded amplimers and were sequenced, the NGS identified a number of bacterial species in these samples. Overall, a significant diversity of bacterial species was identified from the same genus as the predominant cultured pathogens. The numbers of NGS identifiable bacterial genera were consistently higher than identified by standard microbiological methods. As technical advances reduce the processing and sequencing times, NGS-based methods will ultimately be able to provide clinicians with rapid, precise, culture-independent identification of bacterial, fungal, and viral pathogens and their antimicrobial sensitivity profiles.

Idioma originalInglés
Páginas (desde-hasta)3913-3921
Número de páginas9
PublicaciónJournal of Clinical Microbiology
Volumen52
N.º11
DOI
EstadoPublicada - 1 nov 2014

Áreas temáticas de ASJC Scopus

  • Microbiología (médica)

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