RT Journal
A1 McLean, Jeffrey S.
A1 Lombardo, Mary-Jane
A1 Ziegler, Michael G.
A1 Novotny, Mark
A1 Yee-Greenbaum, Joyclyn
A1 Badger, Jonathan H.
A1 Tesler, Glenn
A1 Nurk, Sergey
A1 Lesin, Valery
A1 Brami, Daniel
A1 Hall, Adam P.
A1 Edlund, Anna
A1 Allen, Lisa Z.
A1 Durkin, Scott
A1 Reed, Sharon
A1 Torriani, Francesca
A1 Nealson, Kenneth H.
A1 Pevzner, Pavel A.
A1 Friedman, Robert
A1 Venter, J. Craig
A1 Lasken, Roger S.
T1 Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform
JF Genome Research 
JO Genome Research 
YR 2013 
FD May 01 
VO 23 
IS 5 
SP 867 
OP 877 
DO 10.1101/gr.150433.112 
UL http://genome.cshlp.org/content/23/5/867.abstract 
AB Although biofilms have been shown to be reservoirs of pathogens, our knowledge of the microbial diversity in biofilms within critical areas, such as health care facilities, is limited. Available methods for pathogen identification and strain typing have some inherent restrictions. In particular, culturing will yield only a fraction of the species present, PCR of virulence or marker genes is mainly focused on a handful of known species, and shotgun metagenomics is limited in the ability to detect strain variations. In this study, we present a single-cell genome sequencing approach to address these limitations and demonstrate it by specifically targeting bacterial cells within a complex biofilm from a hospital bathroom sink drain. A newly developed, automated platform was used to generate genomic DNA by the multiple displacement amplification (MDA) technique from hundreds of single cells in parallel. MDA reactions were screened and classified by 16S rRNA gene PCR sequence, which revealed a broad range of bacteria covering 25 different genera representing environmental species, human commensals, and opportunistic human pathogens. Here we focus on the recovery of a nearly complete genome representing a novel strain of the periodontal pathogen Porphyromonas gingivalis (P. gingivalis JCVI SC001) using the single-cell assembly tool SPAdes. Single-cell genomics is becoming an accepted method to capture novel genomes, primarily in the marine and soil environments. Here we show for the first time that it also enables comparative genomic analysis of strain variation in a pathogen captured from complex biofilm samples in a healthcare facility.