{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T00:13:50Z","timestamp":1788308030551,"version":"build-2803163510"},"publisher-location":"New York, NY","reference-count":31,"publisher":"Springer US","isbn-type":[{"value":"9781071654996","type":"print"},{"value":"9781071655009","type":"electronic"}],"license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026]]},"DOI":"10.1007\/978-1-0716-5500-9_4","type":"book-chapter","created":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T23:26:16Z","timestamp":1788305176000},"page":"29-47","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["High Resolution Genotyping of Leptospira Direct from Clinical Samples Using Multiplexed Amplicon Sequencing"],"prefix":"10.1007","author":[{"given":"Nathan E.","family":"Stone","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason W.","family":"Sahl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,2]]},"reference":[{"issue":"9","key":"4_CR1","doi-asserted-by":"publisher","first-page":"e0004990","DOI":"10.1371\/journal.pntd.0004990","volume":"10","author":"V Barragan","year":"2016","unstructured":"Barragan V et al (2016) High Leptospira diversity in animals and humans complicates the search for common reservoirs of human disease in rural Ecuador. PLoS Negl Trop Dis 10(9):e0004990","journal-title":"PLoS Negl Trop Dis"},{"issue":"1","key":"4_CR2","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1016\/j.femsle.2005.06.011","volume":"249","author":"F Merien","year":"2005","unstructured":"Merien F et al (2005) A rapid and quantitative method for the detection of Leptospira species in human leptospirosis. FEMS Microbiol Lett 249(1):139\u2013147","journal-title":"FEMS Microbiol Lett"},{"issue":"3","key":"4_CR3","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1016\/j.diagmicrobio.2009.03.014","volume":"64","author":"RA Stoddard","year":"2009","unstructured":"Stoddard RA et al (2009) Detection of pathogenic Leptospira spp. through TaqMan polymerase chain reaction targeting the LipL32 gene. Diagn Microbiol Infect Dis 64(3):247\u2013255","journal-title":"Diagn Microbiol Infect Dis"},{"issue":"6","key":"4_CR4","doi-asserted-by":"publisher","first-page":"e0247522","DOI":"10.1128\/spectrum.02475-22","volume":"10","author":"MA Matthias","year":"2022","unstructured":"Matthias MA et al (2022) Culture-independent detection and identification of Leptospira serovars. Microbiol Spectr 10(6):e0247522","journal-title":"Microbiol Spectr"},{"issue":"6","key":"4_CR5","doi-asserted-by":"publisher","first-page":"e0128913","DOI":"10.1371\/journal.pone.0128913","volume":"10","author":"BT Backstedt","year":"2015","unstructured":"Backstedt BT et al (2015) Efficient detection of pathogenic leptospires using 16S ribosomal RNA. PLoS One 10(6):e0128913","journal-title":"PLoS One"},{"issue":"4","key":"4_CR6","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1016\/j.diagmicrobio.2016.01.001","volume":"84","author":"H Iwasaki","year":"2016","unstructured":"Iwasaki H et al (2016) Combined antibody and DNA detection for early diagnosis of leptospirosis after a disaster. Diagn Microbiol Infect Dis 84(4):287\u2013291","journal-title":"Diagn Microbiol Infect Dis"},{"issue":"2","key":"4_CR7","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1590\/0037-8682-0364-2016","volume":"50","author":"D Benacer","year":"2017","unstructured":"Benacer D et al (2017) A duplex endpoint PCR assay for rapid detection and differentiation of Leptospira strains. Rev Soc Bras Med Trop 50(2):239\u2013242","journal-title":"Rev Soc Bras Med Trop"},{"issue":"10","key":"4_CR8","doi-asserted-by":"publisher","first-page":"e15335","DOI":"10.1371\/journal.pone.0015335","volume":"5","author":"GM Cerqueira","year":"2010","unstructured":"Cerqueira GM et al (2010) Bioinformatics describes novel Loci for high resolution discrimination of Leptospira isolates. PLoS One 5(10):e15335","journal-title":"PLoS One"},{"issue":"9","key":"4_CR9","doi-asserted-by":"publisher","first-page":"310","DOI":"10.1007\/s00284-023-03414-w","volume":"80","author":"MIN Di Azevedo","year":"2023","unstructured":"Di Azevedo MIN et al (2023) Genetic analysis of LigA, LipL32, Loa22, and OmpL1 antigens from Leptospira spp. Sejroe serogroup: how close we are to a vaccine against bovine leptospirosis?. Curr Microbiol 80(9):310","journal-title":"Curr Microbiol"},{"issue":"9","key":"4_CR10","doi-asserted-by":"publisher","first-page":"e7093","DOI":"10.1371\/journal.pone.0007093","volume":"4","author":"A Ahmed","year":"2009","unstructured":"Ahmed A et al (2009) Development and validation of a real-time PCR for detection of pathogenic Leptospira species in clinical materials. PLoS One 4(9):e7093","journal-title":"PLoS One"},{"issue":"14","key":"4_CR11","doi-asserted-by":"publisher","first-page":"1707","DOI":"10.1017\/S0031182019001252","volume":"146","author":"S Rahelinirina","year":"2019","unstructured":"Rahelinirina S et al (2019) Leptospira in livestock in Madagascar: uncultured strains, mixed infections and small mammal-livestock transmission highlight challenges in controlling and diagnosing leptospirosis in the developing world. Parasitology 146(14):1707\u20131713","journal-title":"Parasitology"},{"issue":"9","key":"4_CR12","doi-asserted-by":"publisher","first-page":"2818","DOI":"10.1128\/JB.186.9.2818-2828.2004","volume":"186","author":"DA Haake","year":"2004","unstructured":"Haake DA et al (2004) Molecular evolution and mosaicism of leptospiral outer membrane proteins involves horizontal DNA transfer. J Bacteriol 186(9):2818\u20132828","journal-title":"J Bacteriol"},{"key":"4_CR13","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1186\/1476-0711-5-28","volume":"5","author":"N Ahmed","year":"2006","unstructured":"Ahmed N et al (2006) Multilocus sequence typing method for identification and genotypic classification of pathogenic Leptospira species. Ann Clin Microbiol Antimicrob 5:28","journal-title":"Ann Clin Microbiol Antimicrob"},{"issue":"1","key":"4_CR14","doi-asserted-by":"publisher","first-page":"e1954","DOI":"10.1371\/journal.pntd.0001954","volume":"7","author":"S Boonsilp","year":"2013","unstructured":"Boonsilp S et al (2013) A single multilocus sequence typing (MLST) scheme for seven pathogenic Leptospira species. PLoS Negl Trop Dis 7(1):e1954","journal-title":"PLoS Negl Trop Dis"},{"key":"4_CR15","doi-asserted-by":"publisher","first-page":"216","DOI":"10.1016\/j.meegid.2013.08.002","volume":"22","author":"V Varni","year":"2014","unstructured":"Varni V et al (2014) Reassessment of MLST schemes for Leptospira spp. typing worldwide. Infect Genet Evol 22:216\u2013222","journal-title":"Infect Genet Evol"},{"issue":"4","key":"4_CR16","doi-asserted-by":"publisher","first-page":"e0012966","DOI":"10.1371\/journal.pntd.0012966","volume":"19","author":"NE Stone","year":"2025","unstructured":"Stone NE et al (2025) Host population dynamics influence Leptospira spp. transmission patterns among Rattus norvegicus in Boston, Massachusetts, US. PLoS Negl Trop Dis 19(4):e0012966","journal-title":"PLoS Negl Trop Dis"},{"key":"4_CR17","doi-asserted-by":"crossref","unstructured":"Colman RE, et al (2015) Detection of low-level mixed-population drug resistance in Mycobacterium tuberculosis using high fidelity amplicon sequencing. PLoS One 10(5):e0126626","DOI":"10.1371\/journal.pone.0126626"},{"issue":"10","key":"4_CR18","doi-asserted-by":"publisher","first-page":"2582","DOI":"10.1128\/JCM.00927-16","volume":"54","author":"JR Bowers","year":"2016","unstructured":"Bowers JR et al (2016) KlebSeq, a diagnostic tool for surveillance, detection, and monitoring of Klebsiella pneumoniae. J Clin Microbiol 54(10):2582\u20132596","journal-title":"J Clin Microbiol"},{"issue":"15","key":"4_CR19","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114\u20132120","journal-title":"Bioinformatics"},{"issue":"4","key":"4_CR20","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357\u2013359","journal-title":"Nat Methods"},{"issue":"16","key":"4_CR21","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li H et al (2009) The sequence alignment\/map format and SAMtools. Bioinformatics 25(16):2078\u20132079","journal-title":"Bioinformatics"},{"issue":"18","key":"4_CR22","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","volume":"34","author":"H Li","year":"2018","unstructured":"Li H (2018) Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34(18):3094\u20133100","journal-title":"Bioinformatics"},{"issue":"5","key":"4_CR23","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1038\/ng.806","volume":"43","author":"MA DePristo","year":"2011","unstructured":"DePristo MA et al (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43(5):491\u2013498","journal-title":"Nat Genet"},{"issue":"9","key":"4_CR24","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","volume":"20","author":"A McKenna","year":"2010","unstructured":"McKenna A et al (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20(9):1297\u20131303","journal-title":"Genome Res"},{"issue":"11","key":"4_CR25","doi-asserted-by":"publisher","first-page":"2478","DOI":"10.1093\/nar\/30.11.2478","volume":"30","author":"AL Delcher","year":"2002","unstructured":"Delcher AL et al (2002) Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res 30(11):2478\u20132483","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"4_CR26","first-page":"e000074","volume":"2","author":"JW Sahl","year":"2016","unstructured":"Sahl JW et al (2016) NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats. Microb Genom 2(8):e000074","journal-title":"Microb Genom"},{"issue":"2","key":"4_CR27","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1093\/bib\/bbs012","volume":"14","author":"I Milne","year":"2013","unstructured":"Milne I et al (2013) Using tablet for visual exploration of second-generation sequencing data. Brief Bioinform 14(2):193\u2013202","journal-title":"Brief Bioinform"},{"issue":"11","key":"4_CR28","doi-asserted-by":"publisher","first-page":"1138","DOI":"10.1089\/cmb.2017.0096","volume":"24","author":"A Kechin","year":"2017","unstructured":"Kechin A et al (2017) cutPrimers: a new tool for accurate cutting of primers from reads of targeted next generation sequencing. J Comput Biol 24(11):1138\u20131143","journal-title":"J Comput Biol"},{"issue":"1","key":"4_CR29","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-015-0176-9","volume":"7","author":"JW Sahl","year":"2015","unstructured":"Sahl JW et al (2015) Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic data. Genome Med 7(1):52","journal-title":"Genome Med"},{"issue":"3","key":"4_CR30","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1093\/sysbio\/syr010","volume":"60","author":"SA Berger","year":"2011","unstructured":"Berger SA, Krompass D, Stamatakis A (2011) Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood. Syst Biol 60(3):291\u2013302","journal-title":"Syst Biol"},{"issue":"9","key":"4_CR31","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","volume":"30","author":"A Stamatakis","year":"2014","unstructured":"Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9):1312\u20131313","journal-title":"Bioinformatics"}],"container-title":["Methods in Molecular Biology","Leptospira spp."],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-1-0716-5500-9_4","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T23:26:18Z","timestamp":1788305178000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-1-0716-5500-9_4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"ISBN":["9781071654996","9781071655009"],"references-count":31,"URL":"https:\/\/doi.org\/10.1007\/978-1-0716-5500-9_4","relation":{},"ISSN":["1064-3745","1940-6029"],"issn-type":[{"value":"1064-3745","type":"print"},{"value":"1940-6029","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026]]},"assertion":[{"value":"2 September 2026","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}}]}}