Fig 1.
Climate zones according to rainfall, districts and location of sampling sites (Polonnaruwa, Kurunegala and Gampaha) in Sri Lanka where field work was conducted in smallholder food storage facilities.
Source base layer & credit base layer: https://data.humdata.org/ published under creative commons attribution for intergovernmental organisations: https://data.humdata.org/m/dataset/cod-ab-lka.
Fig 2.
Typical smallholder rice growing environment in Sri Lanka.
A. Smallholder rice field embedded in a matrix of surrounding tropical forest. B. Storage facility structure with harvested rice in white storage bags. C. Farmers house and surrounding paddy fields.
Table 1.
Individuals per species per climate zone.
In the dry zone, trapping effort was only half that of the trapping effort in the intermediate and wet zone.
Table 2.
Observed prevalence of pathogenic Leptospira spp. in each climate zone with number of infected individuals indicated in brackets.
Fig 3.
Occurrence of pathogenic Leptospira spp. infection in small mammal species at the three climate zones in Sri Lanka.
Blue triangles indicate occurrence of L. borgpetersenii, yellow squares occurrence of L. interrogans and the red star the occurrence of L. kirschneri. The size of triangles and squares is proportional to the number of infected animals within storage facility. The large red circle indicates a cluster of increased risk of L. borgpetersenii infection. Land use and land cover base layer obtained from https://land.copernicus.eu/global/products/lc.
Table 3.
Leptospira prevalence in rodent species and shrews present in smallholder food storage facilities in Sri Lanka including pest and conservation status.
L. borg is L. borgpetersenii, L. inter is L. Interrogans, L. kirsch is L. kirschneri and L. sp is total Leptospira spp. N is sample size, LC—least concern, VU—vulnerable.
Fig 4.
A. Variance partitioning. Variation in Leptospira spp. occurrence partitioned into responses to grouped fixed effect for host (species), ecological (climate zone and Shannon diversity), temporal (season) and spatial random effect. B. Parameter estimates and posterior Bayesian support (cutoff probability = 0.9) for either a negative (blue) or positive (red) response.
Fig 5.
Evolutionary analysis of concatenated MLST allele sequences The tree was inferred in MEGA X using the Maximum Likelihood method and Tamura 3-parameter model.
Bootstrap values above 70% are shown next to the branches. MLST sequences from Leptospira interrogans (L.i.), Leptospira borgpetersenii (L.b.) and Leptospira kirschneri (L.k.) obtained from specimen collected in this study are shown (○). For comparison, MLST sequences from human clinical isolates originating from Sri Lanka were included in the analysis (●). The tree was rooted using concatenated MLST sequences of Leptospira santarosai (L.s.) strain Alice.
Table 4.
Occurrence of Leptospira MLST sequence types in each small mammal species and climate zone.
n is the number of samples with specific ST in the respective category, N is the total number of samples with specific ST.