Molecular detection and genetic characterisation of a large flood-borne outbreak of human leptospirosis in Jakarta, Indonesia: A retrospective analysis of surveillance data

Abstract Recurring outbreaks of leptospirosis in flood-prone areas caused by heavy rainfall pose a major public health concern, particularly in megacities such as Indonesia’s capital city, Jakarta. From December 2019 through February 2020, Jakarta experienced a large leptospirosis outbreak due to extensive flooding following extreme monsoonal rainfall. We conducted a comprehensive retrospective analysis of the outbreak based on complete surveillance data from all five districts and 42 of 44 subdistricts in Jakarta. A total of 282 cases (97 suspected, 153 probable, and 32 confirmed) were reported in West (n=162), South (n=64), East (n=30), North (n=14) and Central (n=12) Jakarta. Cases were predominantly adult males exposed to floodwaters. Of 241 cases tested, 164 (68.0%) had a positive IgM-based rapid diagnostic test (RDT). Of 118 cases tested with TaqMan RT-PCR lipL32 , 32 (27.1%) were positive; RT-PCR detected an additional 5 cases who were RDT-negative (case detection increased by 4.2% [5/118]), all of whom had fever