Respiratory Treatment and Prevention (Advances in Experimental Medicine and Biology)

4 Discussion

Detection of individual pathogens in infections
of the central nervous system is often impractical
due to the sheer number of potential infectious
agents. NGS represents a novel and promising
tool in microbial diagnostics, as it can detect
multiple pathogens concurrently. NGS

techniques, combined with a metagenomics

approach, have enabled the identification of

new arenavirus (Palacios et al. 2008 ) and previ-

ously unknown species of Bundibugyo

ebolavirus(Towner et al. 2008 ). Other examples

of a successful use of NGS were the identifica-

tion ofLeptospirain CSF of a 14-year-old patient

with encephalitis of unknown etiology (Wilson

Fig. 1 Metagenomic analysis of next-generation
sequencing (NGS) of samples containing different
human immunodeficiency virus (HIV) and herpes sim-
plex virus (HSV-1) loads (10^1 ,10^2 ,10^3 , and 10^4 viral

copies per reaction). Percentages reflect the proportion of

HIV and HSV-1 reads in regard to all reads after trimming

Table 2 Next-generation sequencing (NGS) of negative controls: water (W1 and W2) and cerebrospinal fluid (CSF)
samples from a patient with motor neuron disease (MND)

Sample W1 W2 MND
Reads after trimming (n) 1,521,154 7,192,898 40,340,940
Human 168,102 967,092 36,634,692
(11.051 %) (13.445 %) (90.813 %)
Viral 711 36,231 6878
(0.047 %) (0.500 %) (0.017 %)
Bacterial 819,135 1,540,184 922,862
(5.850 %) (21.410 %) (2.288 %)
Fungal 8366 165,873 258,635
(0.550 %) (2.306 %) (0.641 %)
Archeal 0 0 500
(0.001 %)
Protozoan 69 28,830 106,155
(0.005 %) (0.401 %) (0.263 %)
Othera 477,933 4,339,215 1,256,859
(31.419 %) (60.326 %) (3.116 %)
No match 46,838 115,473 1,154,359
(3.079 %) (1.605 %) (2.862 %)
Sequences were compared to the NCBI-nt database
aSequences related to plants, plant viruses, and synthetic constructs

58 I. Bukowska-Os ́ko et al.