PRJNA555084
Augmentation of Standard Clinical Microbiological Culture with Next Generation Sequencing Improves Diagnosis in Bronchoalveolar Lavage Specimens
Immunocompromised patients are at increased risk for pneumonia. Standard microbiological culture may fail to identify unusual or unexpected organisms; culture-independent methods have improved our ability to deconvolute polymicrobial patient samples. We hypothesized that a more complete assessment of the microbial composition of bronchoalveolar lavage (BAL) samples would identify changes to routine clinical laboratory procedures that improve pathogen recovery. 20 consecutive BAL samples from oncology or transplant patients were plated to three standard and four additional media, and cultivable bacteria present were identified by next-generation 16S rRNA gene sequencing (NGS16S) analysis of DNA extracted from washed culture plates. NGS16S analysis was also performed on DNA extracted directly from patient samples. 96% of all organisms identified were cultivable, but only 21% were reported by standard culture, indicating that standard work-up can be further optimized. Direct NGS16S correlated well with standard culture results, identifying the same predominant organism in 50% of samples. When different predominant organisms were identified, NGS16S most often detected anaerobes, whose growth is unsupported by standard culture conditions. Brucella agar was the best single value-added media, supporting the growth of the largest number of organisms for the most specimens. Anaerobes are underappreciated BAL constituents. NGS16S identifies more organisms per sample and allows identification of fastidious organisms, while culture is better at capturing organisms when bacterial load is low, and allows incidental recovery of non-bacterial pathogens such as yeast or molds. Molecular and culture-based methods together detect more relevant organisms in clinical samples than either method alone.