Fig 1.
The timeline of the leptospirosis outbreak in Jakarta, with daily reported cases, precipitation data and the number of flood-affected subdistricts from December 2019 to February 2020.
Bars represent suspected (blue), probable (green), and confirmed (red) cases recorded by the surveillance. The left y-axis expresses the total daily cases of leptospirosis (coloured bars), and the right y-axis represents the number of flood-affected subdistricts (black dots). The horizontal colour gradient at the top indicates daily precipitation in millimetres per day (mm/day).
Fig 2.
Incidence rate of leptospirosis and spatial distribution of flood-affected subdistricts and districts from December 2019 through February 2020 in Jakarta.
The gradient from white to red represents the incidence rate, while not-flooded subdistricts are shaded. Maps were created in QGIS version 3.32 using basemaps from the Geospatial Information Agency of Indonesia (https://geoservices.big.go.id).
Table 1.
Patient characteristics and laboratory test results.
Fig 3.
*) Probable cases based on Leptospirosis IgM RDT positives = 91.5% (140/153) and based on clinical symptoms combined = 8.5% (13/153). Abbreviations: MLST, multi-locus sequence typing; PCR, polymerase chain reaction; RDT, rapid diagnostic test; RT-PCR, real-time polymerase chain reaction.
Fig 4.
Spider chart showing clinical characteristics of the 282 leptospirosis cases.
Table 2.
Case detection by use of RDT and TaqMan RT-PCR lipL32 for leptospirosis surveillance.
Table 3.
The result of MLST, allele assignation, presumptive STs and serovar of Leptospira in clinical samples.
Fig 5.
Maximum Likelihood tree of Leptospira using concatenated sequences from MLST scheme 3 loci gene sequences alignment, constructed under GTR + G + I substitution model.
Clinical samples (01, 04, 14, 55, and 71) are shown in relation to commonly reported reference pathogenic Leptospira sequence types (STs) from the PubMLST database. Bootstrap values (×1000) are displayed at the branch nodes to demonstrate the reliability of phylogenetic relationships. Corresponding sequence type isolate IDs and allele information from the PubMLST database are provided in S4 Table.