Development of a SNP barcode to genotype Babesia microti infections
Babesia microti is tick-borne disease that is an emerging threat to public health due to increasing prevalence and expanding geographic range. Detection and constant surveillance of babesiosis is imperative for predicting pathogen expansion. Leveraging our whole genome sequence (WGS) analyses of B....
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| Veröffentlicht in: | PLoS neglected tropical diseases 2019-03, Vol.13 (3), p.e0007194-e0007194 |
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| creator | Baniecki, Mary Lynn Moon, Jade Sani, Kian Lemieux, Jacob E Schaffner, Stephen F Sabeti, Pardis C |
| description | Babesia microti is tick-borne disease that is an emerging threat to public health due to increasing prevalence and expanding geographic range. Detection and constant surveillance of babesiosis is imperative for predicting pathogen expansion. Leveraging our whole genome sequence (WGS) analyses of B. microti, we developed a single nucleotide polymorphism (SNP)-based high resolution melt (HRM) surveillance tool. We developed our HRM assay using available sequence data and identified 775 SNPs. From these candidate SNPs, we developed a 32-SNP barcode that is robust and differentiates geographically distinct populations; it contains SNPs that are putatively neutral, located in nuclear, mitochondrial, and apicoplastal regions. The assays are reproducible and robust, requiring a small quantity of DNA (limit of detection as low as 10 pg.). We analyzed the performance of our HRM assay using 26 B. microti clinical samples used in our WGS study from babesiosis endemic regions in the United States. We identified a minimal barcode consisting of 25 SNPs that differentiate geographically distinct populations across all clinical samples evaluated (average minor allele frequency > 0.22). Supporting our previous WGS findings, our 25-SNP barcode identified distinct barcode signatures that segregate B. microti into two lineages: Northeast and Midwest, with the Northeast having three subpopulations: Connecticut/Rhode Island, Nantucket, and the R1 reference group. Our 25-SNP HRM barcode provides a robust means genetic marker set that will aid in tracking the increasing incidence and expanding geographic range of B. microti infections. |
| doi_str_mv | 10.1371/journal.pntd.0007194 |
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Detection and constant surveillance of babesiosis is imperative for predicting pathogen expansion. Leveraging our whole genome sequence (WGS) analyses of B. microti, we developed a single nucleotide polymorphism (SNP)-based high resolution melt (HRM) surveillance tool. We developed our HRM assay using available sequence data and identified 775 SNPs. From these candidate SNPs, we developed a 32-SNP barcode that is robust and differentiates geographically distinct populations; it contains SNPs that are putatively neutral, located in nuclear, mitochondrial, and apicoplastal regions. The assays are reproducible and robust, requiring a small quantity of DNA (limit of detection as low as 10 pg.). We analyzed the performance of our HRM assay using 26 B. microti clinical samples used in our WGS study from babesiosis endemic regions in the United States. We identified a minimal barcode consisting of 25 SNPs that differentiate geographically distinct populations across all clinical samples evaluated (average minor allele frequency > 0.22). Supporting our previous WGS findings, our 25-SNP barcode identified distinct barcode signatures that segregate B. microti into two lineages: Northeast and Midwest, with the Northeast having three subpopulations: Connecticut/Rhode Island, Nantucket, and the R1 reference group. Our 25-SNP HRM barcode provides a robust means genetic marker set that will aid in tracking the increasing incidence and expanding geographic range of B. microti infections.</description><identifier>ISSN: 1935-2735</identifier><identifier>ISSN: 1935-2727</identifier><identifier>EISSN: 1935-2735</identifier><identifier>DOI: 10.1371/journal.pntd.0007194</identifier><identifier>PMID: 30908478</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Arachnids ; Assaying ; Babesia microti ; Babesiosis ; Bar codes ; Biology and Life Sciences ; Chromosomes ; Deoxyribonucleic acid ; Detection ; Diagnosis ; Disease ; DNA ; Evolutionary biology ; Gene frequency ; Gene polymorphism ; Genetic aspects ; Genetic markers ; Genetic polymorphisms ; Genetic testing ; Genomes ; Genomics ; Genotypes ; Health risks ; Hospitals ; Identification ; Identification and classification ; Infections ; Innovations ; Malaria ; Medical laboratories ; Medicine and Health Sciences ; Mitochondria ; Nucleotide sequence ; Nucleotides ; Parasitic diseases ; Pathogens ; People and places ; Polymorphism ; Population genetics ; Populations ; Public health ; Regions ; Research and Analysis Methods ; Robustness ; Samples ; Sentinel surveillance ; Sequencing ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism ; Subpopulations ; Surveillance ; Tick-borne diseases ; Tropical diseases ; Zoonoses</subject><ispartof>PLoS neglected tropical diseases, 2019-03, Vol.13 (3), p.e0007194-e0007194</ispartof><rights>COPYRIGHT 2019 Public Library of Science</rights><rights>2019 Baniecki et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2019 Baniecki et al 2019 Baniecki et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c624t-1146e115df2d24c6b0de2e77cc71c98f693df88a6355341b894157aad946cd953</citedby><cites>FETCH-LOGICAL-c624t-1146e115df2d24c6b0de2e77cc71c98f693df88a6355341b894157aad946cd953</cites><orcidid>0000-0003-3862-7231 ; 0000-0002-0907-8643</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6448979/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6448979/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30908478$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Baniecki, Mary Lynn</creatorcontrib><creatorcontrib>Moon, Jade</creatorcontrib><creatorcontrib>Sani, Kian</creatorcontrib><creatorcontrib>Lemieux, Jacob E</creatorcontrib><creatorcontrib>Schaffner, Stephen F</creatorcontrib><creatorcontrib>Sabeti, Pardis C</creatorcontrib><title>Development of a SNP barcode to genotype Babesia microti infections</title><title>PLoS neglected tropical diseases</title><addtitle>PLoS Negl Trop Dis</addtitle><description>Babesia microti is tick-borne disease that is an emerging threat to public health due to increasing prevalence and expanding geographic range. Detection and constant surveillance of babesiosis is imperative for predicting pathogen expansion. Leveraging our whole genome sequence (WGS) analyses of B. microti, we developed a single nucleotide polymorphism (SNP)-based high resolution melt (HRM) surveillance tool. We developed our HRM assay using available sequence data and identified 775 SNPs. From these candidate SNPs, we developed a 32-SNP barcode that is robust and differentiates geographically distinct populations; it contains SNPs that are putatively neutral, located in nuclear, mitochondrial, and apicoplastal regions. The assays are reproducible and robust, requiring a small quantity of DNA (limit of detection as low as 10 pg.). We analyzed the performance of our HRM assay using 26 B. microti clinical samples used in our WGS study from babesiosis endemic regions in the United States. We identified a minimal barcode consisting of 25 SNPs that differentiate geographically distinct populations across all clinical samples evaluated (average minor allele frequency > 0.22). Supporting our previous WGS findings, our 25-SNP barcode identified distinct barcode signatures that segregate B. microti into two lineages: Northeast and Midwest, with the Northeast having three subpopulations: Connecticut/Rhode Island, Nantucket, and the R1 reference group. Our 25-SNP HRM barcode provides a robust means genetic marker set that will aid in tracking the increasing incidence and expanding geographic range of B. microti infections.</description><subject>Arachnids</subject><subject>Assaying</subject><subject>Babesia microti</subject><subject>Babesiosis</subject><subject>Bar codes</subject><subject>Biology and Life Sciences</subject><subject>Chromosomes</subject><subject>Deoxyribonucleic acid</subject><subject>Detection</subject><subject>Diagnosis</subject><subject>Disease</subject><subject>DNA</subject><subject>Evolutionary biology</subject><subject>Gene frequency</subject><subject>Gene polymorphism</subject><subject>Genetic aspects</subject><subject>Genetic markers</subject><subject>Genetic polymorphisms</subject><subject>Genetic testing</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotypes</subject><subject>Health risks</subject><subject>Hospitals</subject><subject>Identification</subject><subject>Identification and classification</subject><subject>Infections</subject><subject>Innovations</subject><subject>Malaria</subject><subject>Medical laboratories</subject><subject>Medicine and Health Sciences</subject><subject>Mitochondria</subject><subject>Nucleotide sequence</subject><subject>Nucleotides</subject><subject>Parasitic diseases</subject><subject>Pathogens</subject><subject>People and places</subject><subject>Polymorphism</subject><subject>Population genetics</subject><subject>Populations</subject><subject>Public health</subject><subject>Regions</subject><subject>Research and Analysis Methods</subject><subject>Robustness</subject><subject>Samples</subject><subject>Sentinel surveillance</subject><subject>Sequencing</subject><subject>Single nucleotide polymorphisms</subject><subject>Single-nucleotide polymorphism</subject><subject>Subpopulations</subject><subject>Surveillance</subject><subject>Tick-borne diseases</subject><subject>Tropical 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of a SNP barcode to genotype Babesia microti infections</title><author>Baniecki, Mary Lynn ; Moon, Jade ; Sani, Kian ; Lemieux, Jacob E ; Schaffner, Stephen F ; Sabeti, Pardis C</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c624t-1146e115df2d24c6b0de2e77cc71c98f693df88a6355341b894157aad946cd953</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Arachnids</topic><topic>Assaying</topic><topic>Babesia microti</topic><topic>Babesiosis</topic><topic>Bar codes</topic><topic>Biology and Life Sciences</topic><topic>Chromosomes</topic><topic>Deoxyribonucleic acid</topic><topic>Detection</topic><topic>Diagnosis</topic><topic>Disease</topic><topic>DNA</topic><topic>Evolutionary biology</topic><topic>Gene frequency</topic><topic>Gene polymorphism</topic><topic>Genetic aspects</topic><topic>Genetic markers</topic><topic>Genetic polymorphisms</topic><topic>Genetic 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diseases</topic><topic>Tropical diseases</topic><topic>Zoonoses</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Baniecki, Mary Lynn</creatorcontrib><creatorcontrib>Moon, Jade</creatorcontrib><creatorcontrib>Sani, Kian</creatorcontrib><creatorcontrib>Lemieux, Jacob E</creatorcontrib><creatorcontrib>Schaffner, Stephen F</creatorcontrib><creatorcontrib>Sabeti, Pardis C</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Health and Safety Science Abstracts (Full archive)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 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microti is tick-borne disease that is an emerging threat to public health due to increasing prevalence and expanding geographic range. Detection and constant surveillance of babesiosis is imperative for predicting pathogen expansion. Leveraging our whole genome sequence (WGS) analyses of B. microti, we developed a single nucleotide polymorphism (SNP)-based high resolution melt (HRM) surveillance tool. We developed our HRM assay using available sequence data and identified 775 SNPs. From these candidate SNPs, we developed a 32-SNP barcode that is robust and differentiates geographically distinct populations; it contains SNPs that are putatively neutral, located in nuclear, mitochondrial, and apicoplastal regions. The assays are reproducible and robust, requiring a small quantity of DNA (limit of detection as low as 10 pg.). We analyzed the performance of our HRM assay using 26 B. microti clinical samples used in our WGS study from babesiosis endemic regions in the United States. We identified a minimal barcode consisting of 25 SNPs that differentiate geographically distinct populations across all clinical samples evaluated (average minor allele frequency > 0.22). Supporting our previous WGS findings, our 25-SNP barcode identified distinct barcode signatures that segregate B. microti into two lineages: Northeast and Midwest, with the Northeast having three subpopulations: Connecticut/Rhode Island, Nantucket, and the R1 reference group. Our 25-SNP HRM barcode provides a robust means genetic marker set that will aid in tracking the increasing incidence and expanding geographic range of B. microti infections.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>30908478</pmid><doi>10.1371/journal.pntd.0007194</doi><orcidid>https://orcid.org/0000-0003-3862-7231</orcidid><orcidid>https://orcid.org/0000-0002-0907-8643</orcidid><oa>free_for_read</oa></addata></record> |
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| source | DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; PubMed Central Open Access; Public Library of Science (PLoS) |
| subjects | Arachnids Assaying Babesia microti Babesiosis Bar codes Biology and Life Sciences Chromosomes Deoxyribonucleic acid Detection Diagnosis Disease DNA Evolutionary biology Gene frequency Gene polymorphism Genetic aspects Genetic markers Genetic polymorphisms Genetic testing Genomes Genomics Genotypes Health risks Hospitals Identification Identification and classification Infections Innovations Malaria Medical laboratories Medicine and Health Sciences Mitochondria Nucleotide sequence Nucleotides Parasitic diseases Pathogens People and places Polymorphism Population genetics Populations Public health Regions Research and Analysis Methods Robustness Samples Sentinel surveillance Sequencing Single nucleotide polymorphisms Single-nucleotide polymorphism Subpopulations Surveillance Tick-borne diseases Tropical diseases Zoonoses |
| title | Development of a SNP barcode to genotype Babesia microti infections |
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