• 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, and Gary L Simon.
• Department of Medicine, Division of Genomic Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA Department of Physical Therapy and Health Care Sciences, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA itoma@gwu.edu msiegel@mfa.gwu.edu.
• J. Clin. Microbiol. 2014 Nov 1; 52 (11): 3913-21.

AbstractIn 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 PCR-amplified 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. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

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