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Int. J. Mol. Sci. 2017, 18(9), 2011; doi:10.3390/ijms18092011

Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing

1
Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals (HUG), 1205 Geneva, Switzerland
2
Service of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, 1205 Geneva, Switzerland
3
Bacteriology Laboratory, Geneva University Hospitals and Faculty of Medicine, 1205 Geneva, Switzerland
*
Author to whom correspondence should be addressed.
Received: 15 August 2017 / Revised: 10 September 2017 / Accepted: 13 September 2017 / Published: 20 September 2017
(This article belongs to the Special Issue Deciphering the Human Microbiota: Methods and Impact on Human Health)
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Abstract

The applications of whole-metagenome shotgun sequencing (WMGS) in routine clinical analysis are still limited. A combination of a DNA extraction procedure, sequencing, and bioinformatics tools is essential for the removal of human DNA and for improving bacterial species identification in a timely manner. We tackled these issues with a broncho-alveolar lavage (BAL) sample from an immunocompromised patient who had developed severe chronic pneumonia. We extracted DNA from the BAL sample with protocols based either on sequential lysis of human and bacterial cells or on the mechanical disruption of all cells. Metagenomic libraries were sequenced on Illumina HiSeq platforms. Microbial community composition was determined by k-mer analysis or by mapping to taxonomic markers. Results were compared to those obtained by conventional clinical culture and molecular methods. Compared to mechanical cell disruption, a sequential lysis protocol resulted in a significantly increased proportion of bacterial DNA over human DNA and higher sequence coverage of Mycobacterium abscessus, Corynebacterium jeikeium and Rothia dentocariosa, the bacteria reported by clinical microbiology tests. In addition, we identified anaerobic bacteria not searched for by the clinical laboratory. Our results further support the implementation of WMGS in clinical routine diagnosis for bacterial identification. View Full-Text
Keywords: whole-metagenome shotgun; clinical metagenomics; broncho-alveolar lavage whole-metagenome shotgun; clinical metagenomics; broncho-alveolar lavage
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Leo, S.; Gaïa, N.; Ruppé, E.; Emonet, S.; Girard, M.; Lazarevic, V.; Schrenzel, J. Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing. Int. J. Mol. Sci. 2017, 18, 2011.

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