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Current screening technologies are limited by the number of samples and genes that can easily be screened. We demonstrate here digital multiplex ligation assay (dMLA) as a low-cost targeted genomic detection workflow capable of highly-parallel screening of bacterial isolates for multiple target gene regions simultaneously. Here, dMLA is used for simultaneous detection of 1187 \u03b2-lactamase-encoding genes, including extended spectrum \u03b2-lactamase (ESBL) genes, in 74 bacterial isolates. We demonstrate dMLA as a light-weight and cost-efficient workflow which provides a highly scalable tool for antimicrobial resistance surveillance and is also adaptable to genetic screening applications beyond antibiotic resistance.<\/jats:p>","DOI":"10.1038\/s42003-020-0980-7","type":"journal-article","created":{"date-parts":[[2020,5,25]],"date-time":"2020-05-25T10:02:44Z","timestamp":1590400964000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Digital multiplex ligation assay for highly multiplexed screening of \u03b2-lactamase-encoding genes in bacterial isolates"],"prefix":"10.1038","volume":"3","author":[{"given":"Manu","family":"Tamminen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jenny","family":"Spaak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lea","family":"Caduff","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanna","family":"Schiff","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ramon","family":"Lang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven","family":"Schmid","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Camila","family":"Montealegre","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1000-0306","authenticated-orcid":false,"given":"Timothy R.","family":"Julian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,5,25]]},"reference":[{"key":"980_CR1","doi-asserted-by":"publisher","first-page":"1432","DOI":"10.1038\/s41564-019-0503-9","volume":"4","author":"S Hernando-Amado","year":"2019","unstructured":"Hernando-Amado, S., Coque, T. 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High genomic diversity and heterogenous origins of pathogenic and antibiotic-resistant escherichia coli in household settings represent a challenge to reducing transmission in low-income settings. mSphere. 5, 1\u201317 (2020).","journal-title":"mSphere"}],"container-title":["Communications Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s42003-020-0980-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-020-0980-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-020-0980-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,7]],"date-time":"2022-12-07T02:12:51Z","timestamp":1670379171000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s42003-020-0980-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,5,25]]},"references-count":28,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2020,12]]}},"alternative-id":["980"],"URL":"https:\/\/doi.org\/10.1038\/s42003-020-0980-7","relation":{},"ISSN":["2399-3642"],"issn-type":[{"value":"2399-3642","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,5,25]]},"assertion":[{"value":"24 October 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 April 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 May 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Authors M.T., T.R.J., J.S., L.C. and H.S. hold a patent (Patent # CA3072650A1) on a similar method for detection and quantification of genetic targets in human, animal, and environmental samples. The workflow presented in this study is distinct from that covered by the patent, though it is conceptually related. R.L., S.S. and M.C.M. declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"264"}}