Fig. 5

Identification of Balamuthia mandrillaris infection by metagenomic next-generation sequencing (NGS). a Coverage maps (blue gradient) and pairwise identity plots (magenta gradient) of two of the three available sequences from Balamuthia (16S/18S rRNA genes) in the NCBI nt reference database as of August 2015. Shown are coverage maps corresponding to day 6 DNA and RNA libraries from CSF and a day 6 mRNA library from brain biopsy. No hits to 16S and 18S Balamuthia sequences were seen from day 1 samples. The asterisk denotes an area with artificially low coverage after taxonomic classification of the NGS reads due to high conservation among eukaryotic sequences (for example, human, Balamuthia, and so on) within that region. b A bar graph of the number of species-specific NGS reads aligning to Balamuthia 16S/18S rRNA (blue) or the Balamuthia genome (orange) in day 1 or day 6 samples. Note that with the availability of the newly assembled 44 Mb Balamuthia genome, diagnosis of Balamuthia mandrillaris encephalitis at day 1 would have possible by detection of nine species-specific reads (red boldface). c Coverage maps of two large scaffolds, approximately 216 kB and 222 kB in size, from the Balamuthia draft genome, showing eight out of 926 hits to Balamuthia in the day 6 CSF DNA library that are identified by SURPI after the draft genome sequence is added to the reference database (versus only 13 hits previously)