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Malaysia has committed to eliminate indigenous human malaria transmission by 2020. The objective of this descriptive study is to understand the epidemiology of malaria in Malaysia from 2000 through 2018 and to highlight the threat posed by zoonotic malaria to the National Malaria Elimination Strategic Plan.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Malaria is a notifiable infection in Malaysia. The data used in this study were extracted from the Disease Control Division, Ministry of Health Malaysia, contributed by the hospitals and health clinics throughout Malaysia. The population data used in this study was extracted from the Department of Statistics Malaysia. Data analyses were performed using Microsoft Excel. Data used for mapping are available at EPSG:4326 WGS84 CRS (Coordinate Reference System). Shapefile was obtained from igismap. Mapping and plotting of the map were performed using QGIS.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Between 2000 and 2007, human malaria contributed 100% of reported malaria and 18\u201346 deaths per year in Malaysia. Between 2008 and 2017, indigenous malaria cases decreased from 6071 to 85 (98.6% reduction), while during the same period, zoonotic<jats:italic>Plasmodium knowlesi<\/jats:italic>cases increased from 376 to 3614 cases (an 861% increase). The year 2018 marked the first year that Malaysia did not report any indigenous cases of malaria caused by human malaria parasites. However, there was an increasing trend of<jats:italic>P. knowlesi<\/jats:italic>cases, with a total of 4131 cases reported in that year. Although the increased incidence of<jats:italic>P. knowlesi<\/jats:italic>cases can be attributed to various factors including improved diagnostic capacity, reduction in human malaria cases, and increase in awareness of<jats:italic>P. knowlesi<\/jats:italic>, more than 50% of<jats:italic>P. knowlesi<\/jats:italic>cases were associated with agriculture and plantation activities, with a large remainder proportion linked to forest-related activities.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Malaysia has entered the elimination phase of malaria control. Zoonotic malaria, however, is increasing exponentially and becoming a significant public health problem. Improved inter-sectoral collaboration is required in order to develop a more integrated effort to control zoonotic malaria. Local political commitment and the provision of technical support from the World Health Organization will help to create focused and concerted efforts towards ensuring the success of the National Malaria Elimination Strategic Plan.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s40101-020-00247-5","type":"journal-article","created":{"date-parts":[[2020,11,23]],"date-time":"2020-11-23T15:10:21Z","timestamp":1606144221000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":87,"title":["Malaria elimination in Malaysia and the rising threat of Plasmodium knowlesi"],"prefix":"10.1186","volume":"39","author":[{"given":"Abraham Zefong","family":"Chin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marilyn Charlene Montini","family":"Maluda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jenarun","family":"Jelip","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad Saffree Bin","family":"Jeffree","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Culleton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1869-3701","authenticated-orcid":false,"given":"Kamruddin","family":"Ahmed","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,11,23]]},"reference":[{"key":"247_CR1","first-page":"63","volume-title":"Current status of malaria and anti-malaria programme in Malaysia. 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