A metagenomics survey of microbes in febrile illness patients in Kenya
The commonly used diagnostic platforms such as cell culture serology and PCR have a limitation of requiring a priori knowledge of the identity of the target pathogen. Unfortunately febrile illnesses have similar presentations. Therefore conventional approaches to laboratory diagnosis limit our ability to detect causes of infectious diseases.
We used RNA shotgun sequencing on the Illumina Miseq platform to profile the transcriptomes of 1000 blood samples in pools of 10 collected from patients with febrile illnesses. Sequence data was quality filtered mapped to the human genome to remove host contaminating reads and the unmapped reads used for de novo assemblies. Resulting contigs were then taxonomically classified by querying the contigs against a reference database using BLAST. Seven eukaryotic genera that are human pathogens were detected.
Of these Plasmodium was detected in all sites in all pools tested and reads were highest in the lake region of Kenya. Twenty six pathogenic bacteria genera were detected of which Shigella infections were the most abundant across the sites. Nine viral families were detected three of these were human pathogens with Hepatitis A virus being the most abundant.
These findings provide a better profile of human disease pathogens in patients with acute febrile patients in Kenya and demonstrate the utility of high-throughput shotgun sequencing in disease surveillance.
Publication Information
Focus County(s):
Programme Area(s):
Natural Products Research & Drug Development (NAPREDA)
Research Priority Area(s):
Disease Domain(s):
Acute febrile illness
Document History:
Publication Date: 01.Jan.1970
Conference Title:
KASH 2018 Conference Proceedings