Metagenomic study of blood samples from bats, Uganda

Abstract

Background: The unique ecosystem of Uganda enables close interaction between humans and wildlife. This milieu creates a hot spot for emergence of infectious diseases. In the last decade bats were found to be a major reservoir of zoonotic pathogens and their proximity to humans provides direct or indirect conditions for spillover events. Methods & Materials: Whole blood samples were collected from 4 different districts of Uganda (Bundibugyo, Buikwe, Kaabong, Lamwo). RNA from six pools of blood, consisting of 9-26 individual bats, each representing specific location, was extracted by Purelink RNA kit (Invitrogen, Thermo Fischer Scientific) and were subjected to NGS of the transcriptome. Sequencing of RNA samples was performed by Illumina Hiseq 2500 with single 60 bp reads. The results were analyzed using de novo assembly with Velvet, followed by BLAST analysis. Based on these analyses, reads were re-aligned to known virus and Plasmodium genomes using Bowtie and normalized per library by correcting for sequencing depth. Results: Plasmodium spp. represents between 0.56%-0.74% of total reads. The top 10 normalized read counts obtained, were from Plasmodium berghei, P.falciparum, P. yoeli. and P. chabaudi, at this order. The highest number of reads were related to P. berghei gene and was found in a pool consisting of mixed frugivorous and insectivorous bats at Buikwe district. The highest number of reads related to P. falciparum was obtained from the northern part of Uganda. Noteworthy, the reads of all 4 Plasmodium serotypes were abundantly found in all sampling sites. Conclusion: Three species of Plasmodium primarily maintained in rodents and one species found in humans were found in four different ecosystems in Uganda. Two main points to be stressed include the ability to switch Plasmodium spp. between rodents and bats and the well tolerated and adapted immune responses of bats to newly introduced spp. No viruses have been found.