Diversidade microbiana no líquido cefalorraquidiano de pacientes com neuroinfecção

Abstract

Background: Nervous system infections are a challenge for clinical neurology, as late diagnosis can contribute to disability and, sometimes, death. Considering that much of the diagnosis remains without identification of the infectious agent, new technologies have been developed to contribute to the diagnosis. Objective: This study's main objective is to identify microbial diversity using metagenomics in cerebrospinal fluid (CSF) samples from patients with suspected neuroinfection. Methods: This is an observational, descriptive and retrospective study, which analyzed CSF samples from confirmed and suspected cases of viral and bacterial infections. Sequencing was performed on the Illumina MiSeq System platform based on the ligation of DNA fragments onto magnetic beads, and returned a total of 15,696,300 reads with information from five CSF samples. All data generated was downloaded, validated and analyzed for quality to check loss on each read. Furthermore, to improve the quality of the reads, adapters, low-quality sequences and about 10 nucleotides at the ends of the DNA strand were cut. The DRAGEN metagenomics and KRAKEN2 pipelines were used for the taxonomic classification of the reads. Results: The quality analysis of reads with q score ≥ 30 was 86.10%, of which in 15.3% it was possible to classify 167 species of microorganisms in the selected samples. About 1,399,082 reads were aligned to the host genome. However, the analysis showed a predominance of the phylum Proteobacteria (9.9%), Firmicutes (2.59%) and Actinobacteria (0.29%). Among the 17 samples selected, only 5 (29.4%) were able to perform metagenomic analysis. In 3/4 (75%) of the samples with etiological identification, the NGS result corroborated the findings using conventional methods. In the sample without etiological identification, species of the genera Staphylococcus, Streptococcus and Burkholderia were identified, where the B. cepacia complex was considered the possible pathogen causing the mastoiditis and meningitis. Conclusion: The use of mNGS associated with other tests to detect microorganisms in CSF is important for identifying these pathogens in CSF. In this way, this study can generate future research that allows the exploration of the reads obtained for each sample, especially those that did not have hits with any taxonomic group, in order to further increase the sensitivity of the test.