Genome-wide Analysis for Variants in Philippine Trypanosoma evansi Isolates with Varying Drug Resistance Profiles

Jose Enrico H. Lazaro^1§, Neil Andrew D. Bascos^1,3§, Francis A. Tablizo^3§,
Nancy S. Abes², Renlyn Ivy DG. Paynaganan¹, Michelle A. Miguel²,
Hector M. Espiritu2, Mary Rose D. Uy2, Claro N. Mingala², and Cynthia P. Saloma^1,3*

¹National Institute of Molecular Biology and Biotechnology, College of Science,
University of the Philippines Diliman, Quezon City 1101 Philippines
²Philippine Carabao Center, Department of Agriculture,
Science City of Munoz, Nueva Ecija 3120 Philippines
³Philippine Genome Center, University of the Philippines, Diliman,
Quezon City 1101 Philippines
^§These authors contributed equally to this work

*Corresponding Author: cpsaloma@up.edu.ph; cpsaloma@mbb.up.edu.ph

 

ABSTRACT

Surra, a parasitic disease transmitted by hematophagous flies and caused by Trypanosoma evansi, affects many domesticated animals – including water buffaloes, camels, horses, pigs, dogs, and other carnivores – throughout the world. When left untreated, this disease can cause anemia, significant loss of weight, abortion, and death in affected animals. Among Philippine isolates of T. evansi, variability has been reported in terms of virulence as well as response to drug treatment. In this study, trypanosoma-positive blood was obtained from 15 Philippine water buffalo samples from different sites in the country. The collected T. evansi strains were propagated in mice then subjected to in vivo virulence, in vitro drug sensitivity testing, and whole genome sequencing. One strain (O14) was found to be highly virulent in vivo, and was found to be resistant to three commonly used drugs [i.e., isometamidium chloride (IC), diminazene diaceturate (DD), and melarsamine hydrochloride (CY for Cymelarsan®)] in vitro. This highly resistant sample was compared with two less-virulent strains using genome-wide analysis of single nucleotide polymorphisms (SNPs) and short insertions and deletions (indels) relative to the reference strain STIB 805. Variant analysis between O14 and the less virulent strains (M4 and C117) identified a number of distinctive SNPs, many of which corroborate previous data. Genes with relatively high copy numbers were observed in mutation hotspots. These included genes that code for variant surface glycoproteins (VSGs), expression site-associated genes (ESAGs), retrotransposon hot spot (RHS) proteins, and leucine rich repeat proteins. Notable mutations were also predicted from genes coding for membrane transporters and cysteine peptidases, as well as those involved in RNA degradation. The whole genome sequences acquired from the Philippine isolates (O14, M4, and C117) vary greatly from the reference strain (STIB 805). These WGS data serve as a good resource for the discovery of genetic and phenotypic features that may be translated to effective treatment strategies, relevant to the Philippine setting. . . . . read more