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Data from an observational study conducted from 2013 to 2016 in seven cities across Indonesia was used to estimate the incidence of leptospirosis and document its clinical manifestations in patients requiring hospitalization.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Methods<\/jats:title>\n<jats:p>Specimens from patients hospitalized with acute fever were collected at enrollment, 14\u201328\u2009days, and 3 months. Demographic and clinical information were collected during study visits and\/or retrieved from medical records and double-entered into clinical report forms. After initially screening for dengue virus and other pathogens, specimens were tested at a central Reference Laboratory for anti-<jats:italic>Leptospira<\/jats:italic> IgM using commercial ELISA kits and for <jats:italic>Leptospira<\/jats:italic> DNA using an in-house quantitative real-time PCR assay.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Results<\/jats:title>\n<jats:p>Of 1464 patients enrolled, 45 (3.1%) confirmed cases (by PCR and\/or sero-coversion or four-fold increase of IgM) and 6 (0.4%) probable cases (by high titer IgM) of leptospirosis were identified by the Reference Laboratory. Disease incidence at sites ranged from 0 (0%) cases in Denpasar to 17 (8.9%) cases in Semarang. The median age of patients was 41.2\u2009years (range of 5.3 to 85.0\u2009years), and 67% of patients were male. Twenty-two patients (43.1%) were accurately diagnosed at sites, and 29 patients (56.9%) were clinically misdiagnosed as having another infection, most commonly dengue fever (11, 37.9%). Clinically, 20 patients (39.2%) did not present with hyperbilirubinemia or increased creatinine levels. Two patients (3.9%) died, both from respiratory failure. Fifteen patients (29.4%) clinically diagnosed with leptospirosis at sites were negative based on IgM ELISA and\/or PCR at the Reference Laboratory.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Conclusions<\/jats:title>\n<jats:p>Leptospirosis remains an important cause of hospitalization in Indonesia. It can have diverse clinical presentations, making it difficult to differentiate from other common tropical infections. PCR combined with ELISA is a powerful alternative to the cumbersome gold-standard microscopic agglutination test, particularly in resource-limited settings.<\/jats:p>\n<\/jats:sec>","DOI":"10.1186\/s12879-020-4903-5","type":"journal-article","created":{"date-parts":[[2020,2,27]],"date-time":"2020-02-27T10:02:32Z","timestamp":1582797752000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":36,"title":["Leptospirosis in Indonesia: diagnostic challenges associated with atypical clinical manifestations and limited laboratory capacity"],"prefix":"10.1186","volume":"20","author":[{"given":"Muhammad Hussein","family":"Gasem","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Usman","family":"Hadi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bachti","family":"Alisjahbana","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emiliana","family":"Tjitra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. 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The study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the IRBs of Faculty of Medicine, University of Indonesia\/ Dr. Cipto Mangunkusumo Hospital (451\/PT02.FK\/ETIK\/2012), Dr. Soetomo Hospital (192\/Panke.KKE\/VIII\/2012), and the National Institute of Health and Research and Development (NIHRD), Ministry of Health, Indonesia (KE.01.05\/EC\/407\/2012).","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"179"}}