Single nucleotide polymorphism (SNP)-based differentiation of Shigella isolates by pyrosequencing
► We applied single nucleotide polymorphism (SNP) discovery and analysis for distinguishing Shigella serogroups. ► Twenty four informative SNPs were located in nine genes by in silico analysis of eight Shigella whole genome sequences. ► SNPs were verified by pyrosequencing. ► The combination of the...
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| creator | Hayford, Alice E. Mammel, Mark K. Lacher, David W. Brown, Eric W. |
| description | ► We applied single nucleotide polymorphism (SNP) discovery and analysis for distinguishing Shigella serogroups. ► Twenty four informative SNPs were located in nine genes by in silico analysis of eight Shigella whole genome sequences. ► SNPs were verified by pyrosequencing. ► The combination of the 24 SNPs resulted in the identification of 26 SNP genotypes among the four Shigella serogroups. ► Phylogenetic tree based on data from the 24 SNPs constructed identified six lineages among the 26 SNP profiles.
Analysis of single nucleotide polymorphisms (SNPs) is an important genetic tool that provides molecular markers for rapid differentiation of closely related strains. We have applied SNP discovery and analysis for distinguishing each of the four Shigella serogroups (Boydii, Dysenteriae, Flexneri, and Sonnei) and for discriminating individual strains within the same serogroup by using 24 SNPs selected from nine genes. Five SNPs were identified from sequence analysis of two housekeeping genes (gapA and thrB) used previously in our lab to differentiate Shigella isolates into distinct lineages. The remaining 19 SNPs were identified by in silico analyses of eight Shigella genomes and are within the genes lpxC, sanA, yaaH, ybaP, ygaZ, yhbO, and ynhA. A total of 118 Shigella strains comprising 20 Boydii, 29 Dysenteriae, 42 Flexneri, and 27 Sonnei isolates were analyzed using the SNP typing scheme reported here. The combination of the 24 SNPs resulted in the identification of 26 SNP genotypes among the four Shigella serogroups and also provided some discriminatory resolution among individual strains within the same serogroup. The SNPs presented here should prove useful in identifying Shigella using PCR amplification and rapid sequence typing strategies. |
| doi_str_mv | 10.1016/j.meegid.2011.07.015 |
| format | Article |
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Analysis of single nucleotide polymorphisms (SNPs) is an important genetic tool that provides molecular markers for rapid differentiation of closely related strains. We have applied SNP discovery and analysis for distinguishing each of the four Shigella serogroups (Boydii, Dysenteriae, Flexneri, and Sonnei) and for discriminating individual strains within the same serogroup by using 24 SNPs selected from nine genes. Five SNPs were identified from sequence analysis of two housekeeping genes (gapA and thrB) used previously in our lab to differentiate Shigella isolates into distinct lineages. The remaining 19 SNPs were identified by in silico analyses of eight Shigella genomes and are within the genes lpxC, sanA, yaaH, ybaP, ygaZ, yhbO, and ynhA. A total of 118 Shigella strains comprising 20 Boydii, 29 Dysenteriae, 42 Flexneri, and 27 Sonnei isolates were analyzed using the SNP typing scheme reported here. The combination of the 24 SNPs resulted in the identification of 26 SNP genotypes among the four Shigella serogroups and also provided some discriminatory resolution among individual strains within the same serogroup. The SNPs presented here should prove useful in identifying Shigella using PCR amplification and rapid sequence typing strategies.</description><identifier>ISSN: 1567-1348</identifier><identifier>EISSN: 1567-7257</identifier><identifier>DOI: 10.1016/j.meegid.2011.07.015</identifier><identifier>PMID: 21839856</identifier><language>eng</language><publisher>Kidlington: Elsevier B.V</publisher><subject>Bacterial Typing Techniques ; Base Sequence ; Biological and medical sciences ; DNA, Bacterial - genetics ; Dysentery, Bacillary - microbiology ; Epidemiology. Vaccinations ; Food Microbiology ; General aspects ; Genome, Bacterial ; Humans ; Infectious diseases ; Medical sciences ; Phylogenetics ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Pyrosequencing ; Sequence Analysis, DNA ; Serotyping ; Shigella ; Shigella - classification ; Shigella - genetics ; Shigella - isolation & purification ; Shigella - pathogenicity ; Single nucleotide polymorphisms</subject><ispartof>Infection, genetics and evolution, 2011-10, Vol.11 (7), p.1761-1768</ispartof><rights>2011</rights><rights>2015 INIST-CNRS</rights><rights>Published by Elsevier B.V.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c391t-e1a8003d2cc3a4236faabb96b51f46fa5d9fa3507c01262621a6bc1aa17a72f23</citedby><cites>FETCH-LOGICAL-c391t-e1a8003d2cc3a4236faabb96b51f46fa5d9fa3507c01262621a6bc1aa17a72f23</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.meegid.2011.07.015$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=24628534$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21839856$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Hayford, Alice E.</creatorcontrib><creatorcontrib>Mammel, Mark K.</creatorcontrib><creatorcontrib>Lacher, David W.</creatorcontrib><creatorcontrib>Brown, Eric W.</creatorcontrib><title>Single nucleotide polymorphism (SNP)-based differentiation of Shigella isolates by pyrosequencing</title><title>Infection, genetics and evolution</title><addtitle>Infect Genet Evol</addtitle><description>► We applied single nucleotide polymorphism (SNP) discovery and analysis for distinguishing Shigella serogroups. ► Twenty four informative SNPs were located in nine genes by in silico analysis of eight Shigella whole genome sequences. ► SNPs were verified by pyrosequencing. ► The combination of the 24 SNPs resulted in the identification of 26 SNP genotypes among the four Shigella serogroups. ► Phylogenetic tree based on data from the 24 SNPs constructed identified six lineages among the 26 SNP profiles.
Analysis of single nucleotide polymorphisms (SNPs) is an important genetic tool that provides molecular markers for rapid differentiation of closely related strains. We have applied SNP discovery and analysis for distinguishing each of the four Shigella serogroups (Boydii, Dysenteriae, Flexneri, and Sonnei) and for discriminating individual strains within the same serogroup by using 24 SNPs selected from nine genes. Five SNPs were identified from sequence analysis of two housekeeping genes (gapA and thrB) used previously in our lab to differentiate Shigella isolates into distinct lineages. The remaining 19 SNPs were identified by in silico analyses of eight Shigella genomes and are within the genes lpxC, sanA, yaaH, ybaP, ygaZ, yhbO, and ynhA. A total of 118 Shigella strains comprising 20 Boydii, 29 Dysenteriae, 42 Flexneri, and 27 Sonnei isolates were analyzed using the SNP typing scheme reported here. The combination of the 24 SNPs resulted in the identification of 26 SNP genotypes among the four Shigella serogroups and also provided some discriminatory resolution among individual strains within the same serogroup. The SNPs presented here should prove useful in identifying Shigella using PCR amplification and rapid sequence typing strategies.</description><subject>Bacterial Typing Techniques</subject><subject>Base Sequence</subject><subject>Biological and medical sciences</subject><subject>DNA, Bacterial - genetics</subject><subject>Dysentery, Bacillary - microbiology</subject><subject>Epidemiology. Vaccinations</subject><subject>Food Microbiology</subject><subject>General aspects</subject><subject>Genome, Bacterial</subject><subject>Humans</subject><subject>Infectious diseases</subject><subject>Medical sciences</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Polymerase Chain Reaction</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Pyrosequencing</subject><subject>Sequence Analysis, DNA</subject><subject>Serotyping</subject><subject>Shigella</subject><subject>Shigella - classification</subject><subject>Shigella - genetics</subject><subject>Shigella - isolation & purification</subject><subject>Shigella - pathogenicity</subject><subject>Single nucleotide polymorphisms</subject><issn>1567-1348</issn><issn>1567-7257</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kF2L1DAUhoso7of-A5HciOtFaz6apL1ZkMUvWFQYvQ6nyclshrapSUeYf2-GGfVOcpEEnnPel6eqXjDaMMrU210zIW6DazhlrKG6oUw-qi6ZVLrWXOrH5zcTbXdRXeW8o5Rpyrun1QVnneg7qS4r2IR5OyKZ93bEuAaHZInjYYppeQh5IjebL9_e1ANkdMQF7zHhvAZYQ5xJ9GTzELY4jkBCjiOsmMlwIMshxYw_9zjbsvxZ9cTDmPH5-b6ufnx4__3uU33_9ePnu3f3tRU9W2tk0FEqHLdWQMuF8gDD0KtBMt-Wj3S9ByGptpRxVQ4DNVgGwDRo7rm4rl6f9i4pluy8milkeyw3Y9xn01OhFJddW8j2RNrSMyf0ZklhgnQwjJqjW7MzJ7fm6NZQbYrbMvbyHLAfJnR_h_7ILMCrMwDZwugTFAH5H9cq3klxzL89cVh0_AqYTLahyEIXEtrVuBj-3-Q3TVaamw</recordid><startdate>20111001</startdate><enddate>20111001</enddate><creator>Hayford, Alice E.</creator><creator>Mammel, Mark K.</creator><creator>Lacher, David W.</creator><creator>Brown, Eric W.</creator><general>Elsevier B.V</general><general>Elsevier</general><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>20111001</creationdate><title>Single nucleotide polymorphism (SNP)-based differentiation of Shigella isolates by pyrosequencing</title><author>Hayford, Alice E. ; Mammel, Mark K. ; Lacher, David W. ; Brown, Eric W.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c391t-e1a8003d2cc3a4236faabb96b51f46fa5d9fa3507c01262621a6bc1aa17a72f23</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Bacterial Typing Techniques</topic><topic>Base Sequence</topic><topic>Biological and medical sciences</topic><topic>DNA, Bacterial - genetics</topic><topic>Dysentery, Bacillary - microbiology</topic><topic>Epidemiology. Vaccinations</topic><topic>Food Microbiology</topic><topic>General aspects</topic><topic>Genome, Bacterial</topic><topic>Humans</topic><topic>Infectious diseases</topic><topic>Medical sciences</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Polymerase Chain Reaction</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Pyrosequencing</topic><topic>Sequence Analysis, DNA</topic><topic>Serotyping</topic><topic>Shigella</topic><topic>Shigella - classification</topic><topic>Shigella - genetics</topic><topic>Shigella - isolation & purification</topic><topic>Shigella - pathogenicity</topic><topic>Single nucleotide polymorphisms</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hayford, Alice E.</creatorcontrib><creatorcontrib>Mammel, Mark K.</creatorcontrib><creatorcontrib>Lacher, David W.</creatorcontrib><creatorcontrib>Brown, Eric W.</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Infection, genetics and evolution</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hayford, Alice E.</au><au>Mammel, Mark K.</au><au>Lacher, David W.</au><au>Brown, Eric W.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Single nucleotide polymorphism (SNP)-based differentiation of Shigella isolates by pyrosequencing</atitle><jtitle>Infection, genetics and evolution</jtitle><addtitle>Infect Genet Evol</addtitle><date>2011-10-01</date><risdate>2011</risdate><volume>11</volume><issue>7</issue><spage>1761</spage><epage>1768</epage><pages>1761-1768</pages><issn>1567-1348</issn><eissn>1567-7257</eissn><abstract>► We applied single nucleotide polymorphism (SNP) discovery and analysis for distinguishing Shigella serogroups. ► Twenty four informative SNPs were located in nine genes by in silico analysis of eight Shigella whole genome sequences. ► SNPs were verified by pyrosequencing. ► The combination of the 24 SNPs resulted in the identification of 26 SNP genotypes among the four Shigella serogroups. ► Phylogenetic tree based on data from the 24 SNPs constructed identified six lineages among the 26 SNP profiles.
Analysis of single nucleotide polymorphisms (SNPs) is an important genetic tool that provides molecular markers for rapid differentiation of closely related strains. We have applied SNP discovery and analysis for distinguishing each of the four Shigella serogroups (Boydii, Dysenteriae, Flexneri, and Sonnei) and for discriminating individual strains within the same serogroup by using 24 SNPs selected from nine genes. Five SNPs were identified from sequence analysis of two housekeeping genes (gapA and thrB) used previously in our lab to differentiate Shigella isolates into distinct lineages. The remaining 19 SNPs were identified by in silico analyses of eight Shigella genomes and are within the genes lpxC, sanA, yaaH, ybaP, ygaZ, yhbO, and ynhA. A total of 118 Shigella strains comprising 20 Boydii, 29 Dysenteriae, 42 Flexneri, and 27 Sonnei isolates were analyzed using the SNP typing scheme reported here. The combination of the 24 SNPs resulted in the identification of 26 SNP genotypes among the four Shigella serogroups and also provided some discriminatory resolution among individual strains within the same serogroup. The SNPs presented here should prove useful in identifying Shigella using PCR amplification and rapid sequence typing strategies.</abstract><cop>Kidlington</cop><pub>Elsevier B.V</pub><pmid>21839856</pmid><doi>10.1016/j.meegid.2011.07.015</doi><tpages>8</tpages></addata></record> |
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| subjects | Bacterial Typing Techniques Base Sequence Biological and medical sciences DNA, Bacterial - genetics Dysentery, Bacillary - microbiology Epidemiology. Vaccinations Food Microbiology General aspects Genome, Bacterial Humans Infectious diseases Medical sciences Phylogenetics Phylogeny Polymerase Chain Reaction Polymorphism, Single Nucleotide Pyrosequencing Sequence Analysis, DNA Serotyping Shigella Shigella - classification Shigella - genetics Shigella - isolation & purification Shigella - pathogenicity Single nucleotide polymorphisms |
| title | Single nucleotide polymorphism (SNP)-based differentiation of Shigella isolates by pyrosequencing |
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