Detection of Vector-Borne Pathogens by Metagenomic Shotgun Sequencing

Vector-borne pathogens are associated with 17% of the global infections and considered a major contributor to emerging infections [1] whereby the infections might be under-recognized due to a lack of diagnostic tests. Metagenomic shotgun sequencing is a promising method with the potential of untargeted detection of bacteria, viruses, fungi, protozoa and helminths in one test.

Vijayvargiya and colleagues [1] developed a protocol considering the excess of host DNA, sufficient lysis of microbial cells and the limited presence of sequences in the databases. The workflow was established with blood samples containing the intracellular pathogens Babesia microti, Plasmodium falciparum, Ehrlichia chaffeensis and Anaplasma phagocytophilum and the extracellular pathogens Mansonella perstans and Borrelia hermsii. Host DNA was depleted and microbial DNA isolated with the MolYsis™ Complete5 kit (Molzym, Germany). After whole genome amplification with the REPLI-g Single Cell Kit (Qiagen, Germany) samples were sequenced on a HiSeq 2500 in rapid run mode (Illumina, USA).

Four analytical tools were applied and compared regarding the genus level identification [1]. Of the six pathogens, Babesia microti, Plasmodium falciparum, Anaplasma phagocytophilum and Borrelia hermsii were identified at the genus level by at least one analytical tool but with different sensitivities. Mansonella perstans was missed by all analytical tools but the presence of filarial DNA was indicated by reads assigned to other nematodes [1]. This might be associated with the quality and availability of sequences in the databases used for identifying the pathogens.

The authors concluded that metagenomic shotguns sequencing is a promising tool for vector-borne pathogens but sample preparation and sequence availability in databases need further improvement.