Understanding leptospirosis ecoepidemiology by environmental dna metabarcoding of irrigation water from two agro-ecological regions of Sri Lanka

Abstract

Background Leptospirosis is one of the most significant zoonoses across the world not only because of its impact on human and animal health but also because of the economic and social impact on agrarian communities. Leptospirosis is endemic in Sri Lanka where paddy farming activities, the use of draught animals in agriculture, and peridomestic animals in urban and rural areas play important roles in maintaining the infection cycle of pathogenic Leptospira, especially concerning animals as a potential reservoir. In this study, an environmental DNA (eDNA) metabarcoding methodology was applied in two different agro-ecological regions of Sri Lanka to understand the eco-epidemiology of leptospirosis. Methodology/Principal findings Irrigation water samples were collected in Kandy District (wet zone mid-country region 2) and Girandurukotte, Badulla District (intermediate zone low-country region 2); and analysed for the presence of pathogenic Leptospira, associated microbiome and the potential reservoir animals. Briefly, we generated PCR products for high-throughput sequencing of multiple amplicons through next-generation sequencing. The analysis of eDNA showed different environmental microbiomes in both regions and a higher diversity of Leptospira species circulating in Kandy than in Girandurukotte. Moreover, the number of sequence reads of pathogenic Leptospira species associated with clinical cases such as L. interrogans was higher in Kandy than in Girandurukotte. Kandy also showed more animal species associated with pathogenic bacterial species than Girandurukotte. Finally, several pathogenic bacterial species including Arcobacter cryaerophilus, responsible for abortion in animals, was shown to be associated with pathogenic Leptospira. influences the formation of biofilms, and thus, the persistence of infectiousLeptospira in the environment. The etiological agents of leptospirosis in Sri Lanka belong to species of the P1 subclade/virulent group (L.interrogans,L.kirschneri,L.borgpetersenii,L.santorasaiandL. weilii) [22, 28]. Little to no information is available regarding the environmentalLeptospira species of Sri Lanka. The identification of the pathogenicLeptospira reservoir animals in the different agro-ecological regions of Sri Lanka will be useful to understand the eco-epidemiology of leptospirosis and establish proper prevention and intervention strategies. In this study, we applied an eDNA metabarcoding approach to compare the microbiome and species diversity of environmental leptospires in two different agro-ecological regions of Sri Lanka to understand how the different climate, soil and terrains conditions influence the environmental transmission of pathogenicLeptospira.