sodC-Based Real-Time PCR for Detection of Neisseria meningitidis
Publication Date
May 05, 2011
Journal
PLOS ONE
Authors
Jennifer Dolan Thomas, Cynthia P. Hatcher, Dara A. Satterfield, M. Jordan Theodore, et al
Volume
6
Issue
5
Pages
e19361
DOI
https://dx.plos.org/10.1371/journal.pone.0019361
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0019361
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/21573213
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3088665
Europe PMC
http://europepmc.org/abstract/MED/21573213
Web of Science
000290256400007
Scopus
79955874796
Mendeley
http://www.mendeley.com/research/sodcbased-realtime-pcr-detection-neisseria-meningitidis-2
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Mendeley | Further Information

{"title"=>"SodC-based real-time PCR for detection of neisseria meningitidis", "type"=>"journal", "authors"=>[{"first_name"=>"Jennifer", "last_name"=>"Dolan Thomas", "scopus_author_id"=>"37123815800"}, {"first_name"=>"Cynthia P.", "last_name"=>"Hatcher", "scopus_author_id"=>"23976299900"}, {"first_name"=>"Dara A.", "last_name"=>"Satterfield", "scopus_author_id"=>"52564262800"}, {"first_name"=>"M. Jordan", "last_name"=>"Theodore", "scopus_author_id"=>"26041136200"}, {"first_name"=>"Michelle C.", "last_name"=>"Bach", "scopus_author_id"=>"52563207000"}, {"first_name"=>"Kristin B.", "last_name"=>"Linscott", "scopus_author_id"=>"57189899697"}, {"first_name"=>"Xin", "last_name"=>"Zhao", "scopus_author_id"=>"52564855600"}, {"first_name"=>"Xin", "last_name"=>"Wang", "scopus_author_id"=>"56648218600"}, {"first_name"=>"Raydel", "last_name"=>"Mair", "scopus_author_id"=>"23976789700"}, {"first_name"=>"Susanna", "last_name"=>"Schmink", "scopus_author_id"=>"6603143738"}, {"first_name"=>"Kathryn E.", "last_name"=>"Arnold", "scopus_author_id"=>"35483029100"}, {"first_name"=>"David S.", "last_name"=>"Stephens", "scopus_author_id"=>"7402939607"}, {"first_name"=>"Lee H.", "last_name"=>"Harrison", "scopus_author_id"=>"7402529732"}, {"first_name"=>"Rosemary A.", "last_name"=>"Hollick", "scopus_author_id"=>"6503891701"}, {"first_name"=>"Ana Lucia", "last_name"=>"Andrade", "scopus_author_id"=>"23024318600"}, {"first_name"=>"Juliana", "last_name"=>"Lamaro-Cardoso", "scopus_author_id"=>"16068642800"}, {"first_name"=>"Ana Paula S.", "last_name"=>"de Lemos", "scopus_author_id"=>"6602923096"}, {"first_name"=>"Jenna", "last_name"=>"Gritzfeld", "scopus_author_id"=>"37115591600"}, {"first_name"=>"Stephen", "last_name"=>"Gordon", "scopus_author_id"=>"7401829209"}, {"first_name"=>"Ahmet", "last_name"=>"Soysal", "scopus_author_id"=>"23468003500"}, {"first_name"=>"Mustafa", "last_name"=>"Bakir", "scopus_author_id"=>"7004618935"}, {"first_name"=>"Dolly", "last_name"=>"Sharma", "scopus_author_id"=>"36872317400"}, {"first_name"=>"Shabnam", "last_name"=>"Jain", "scopus_author_id"=>"55366192300"}, {"first_name"=>"Sarah W.", "last_name"=>"Satola", "scopus_author_id"=>"6603089107"}, {"first_name"=>"Nancy E.", "last_name"=>"Messonnier", "scopus_author_id"=>"24344675200"}, {"first_name"=>"Leonard W.", "last_name"=>"Mayer", "scopus_author_id"=>"55414847600"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-79955874796", "pui"=>"361746711", "doi"=>"10.1371/journal.pone.0019361", "sgr"=>"79955874796", "pmid"=>"21573213"}, "id"=>"7728bb3e-b1db-3957-af5c-10186b5843d3", "abstract"=>"Real-time PCR (rt-PCR) is a widely used molecular method for detection of Neisseria meningitidis (Nm). Several rt-PCR assays for Nm target the capsule transport gene, ctrA. However, over 16% of meningococcal carriage isolates lack ctrA, rendering this target gene ineffective at identification of this sub-population of meningococcal isolates. The Cu-Zn superoxide dismutase gene, sodC, is found in Nm but not in other Neisseria species. To better identify Nm, regardless of capsule genotype or expression status, a sodC-based TaqMan rt-PCR assay was developed and validated. Standard curves revealed an average lower limit of detection of 73 genomes per reaction at cycle threshold (C(t)) value of 35, with 100% average reaction efficiency and an average R(2) of 0.9925. 99.7% (624/626) of Nm isolates tested were sodC-positive, with a range of average C(t) values from 13.0 to 29.5. The mean sodC C(t) value of these Nm isolates was 17.6±2.2 (±SD). Of the 626 Nm tested, 178 were nongroupable (NG) ctrA-negative Nm isolates, and 98.9% (176/178) of these were detected by sodC rt-PCR. The assay was 100% specific, with all 244 non-Nm isolates testing negative. Of 157 clinical specimens tested, sodC detected 25/157 Nm or 4 additional specimens compared to ctrA and 24 more than culture. Among 582 carriage specimens, sodC detected Nm in 1 more than ctrA and in 4 more than culture. This sodC rt-PCR assay is a highly sensitive and specific method for detection of Nm, especially in carriage studies where many meningococcal isolates lack capsule genes.", "link"=>"http://www.mendeley.com/research/sodcbased-realtime-pcr-detection-neisseria-meningitidis-2", "reader_count"=>18, "reader_count_by_academic_status"=>{"Researcher"=>7, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>2, "Student > Postgraduate"=>1, "Student > Master"=>2, "Other"=>1, "Student > Bachelor"=>3, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Researcher"=>7, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>2, "Student > Postgraduate"=>1, "Student > Master"=>2, "Other"=>1, "Student > Bachelor"=>3, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>2, "Medicine and Dentistry"=>2, "Agricultural and Biological Sciences"=>5, "Chemistry"=>1, "Psychology"=>1, "Social Sciences"=>1, "Immunology and Microbiology"=>3, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Psychology"=>{"Psychology"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>5}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"India"=>1}, "group_count"=>0}

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Scopus | Further Information

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  • {"files"=>["https://ndownloader.figshare.com/files/777500"], "description"=>"1<p>Serogroup-specific PCR testing was performed to detect serogroups A,\n B, C, W135, X, and Y; isolates not positive for one of these\n serogroups were termed NG by PCR. Serogroup-specific PCR was not\n performed on carriage study isolates that were\n <i>ctrA</i>-negative.</p>2<p>All <i>ctrA</i> C<sub>t</sub> values were generated at CDC\n except the MD carriage isolates, which were tested at the MD\n Department of Health and Mental Hygiene.</p>3<p>All <i>sodC</i> results were an average of 2 C<sub>t</sub>\n values except M17304, which is an average of 4 C<sub>t</sub>s.</p>4<p>24 <i>ctrA</i>-negative, <i>sodC</i>-positive NG\n Nm from this carriage study yielded No C<sub>t</sub> for\n <i>ctrA</i>. However, one such isolate, M05046, gave a\n negative <i>ctrA</i> C<sub>t</sub> value of 36.0.</p>5<p>MLEE results for the isolates collected in the Kellerman et al.\n carriage study were previously reported <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019361#pone.0019361-Kellerman1\" target=\"_blank\">[21]</a>.</p>6<p>Where ST is given, this isolate was previously characterized <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019361#pone.0019361-DolanLivengood1\" target=\"_blank\">[12]</a>. Where no ST is given, MLST data is to be\n published elsewhere.</p>7<p>There is no Z PCR serogrouping assay currently in use in the CDC\n Meningitis Laboratory. However, this isolate tested negative by\n rt-PCR for serogroup A, B, C, W135, X, and Y genes.</p>8<p>There is no 29E PCR serogrouping assay currently in use in the CDC\n Meningitis Laboratory. However, this isolate tested negative by\n rt-PCR for serogroup A, B, C, W135, X, and Y genes.</p>", "links"=>[], "tags"=>["626", "nm", "isolates", "the"], "article_id"=>447835, "categories"=>["Biotechnology", "Microbiology", "Biochemistry", "Genetics", "Infectious Diseases"], "users"=>["Jennifer Dolan Thomas", "Cynthia P. Hatcher", "Dara A. Satterfield", "M. Jordan Theodore", "Michelle C. Bach", "Kristin B. Linscott", "Xin Zhao", "Xin Wang", "Raydel Mair", "Susanna Schmink", "Kathryn E. Arnold", "David S. Stephens", "Lee H. Harrison", "Rosemary A. Hollick", "Ana Lucia Andrade", "Juliana Lamaro-Cardoso", "Ana Paula S. de Lemos", "Jenna Gritzfeld", "Stephen Gordon", "Ahmet Soysal", "Mustafa Bakir", "Dolly Sharma", "Shabnam Jain", "Sarah W. Satola", "Nancy E. Messonnier", "Leonard W. Mayer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0019361.t001", "stats"=>{"downloads"=>12, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_626_Nm_isolates_used_to_test_the_sensitivity_of_the_____sodC_assay_/447835", "title"=>"Summary of 626 Nm isolates used to test the sensitivity of the\n <i>sodC</i> assay.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-05 02:10:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/389850", "https://ndownloader.figshare.com/files/389904", "https://ndownloader.figshare.com/files/389939", "https://ndownloader.figshare.com/files/390072", "https://ndownloader.figshare.com/files/390110"], "description"=>"<div><p>Real-time PCR (rt-PCR) is a widely used molecular method for detection of <em>Neisseria meningitidis</em> (Nm). Several rt-PCR assays for Nm target the capsule transport gene, <em>ctrA</em>. However, over 16% of meningococcal carriage isolates lack <em>ctrA</em>, rendering this target gene ineffective at identification of this sub-population of meningococcal isolates. The Cu-Zn superoxide dismutase gene, <em>sodC</em>, is found in Nm but not in other <em>Neisseria</em> species. To better identify Nm, regardless of capsule genotype or expression status, a <em>sodC</em>-based TaqMan rt-PCR assay was developed and validated. Standard curves revealed an average lower limit of detection of 73 genomes per reaction at cycle threshold (C<sub>t</sub>) value of 35, with 100% average reaction efficiency and an average R<sup>2</sup> of 0.9925. 99.7% (624/626) of Nm isolates tested were <em>sodC</em>-positive, with a range of average C<sub>t</sub> values from 13.0 to 29.5. The mean <em>sodC</em> C<sub>t</sub> value of these Nm isolates was 17.6±2.2 (±SD). Of the 626 Nm tested, 178 were nongroupable (NG) <em>ctrA</em>-negative Nm isolates, and 98.9% (176/178) of these were detected by <em>sodC</em> rt-PCR. The assay was 100% specific, with all 244 non-Nm isolates testing negative. Of 157 clinical specimens tested, <em>sodC</em> detected 25/157 Nm or 4 additional specimens compared to <em>ctrA</em> and 24 more than culture. Among 582 carriage specimens, <em>sodC</em> detected Nm in 1 more than <em>ctrA</em> and in 4 more than culture. This <em>sodC</em> rt-PCR assay is a highly sensitive and specific method for detection of Nm, especially in carriage studies where many meningococcal isolates lack capsule genes.</p> </div>", "links"=>[], "tags"=>["Real-time", "pcr", "detection", "of"], "article_id"=>136969, "categories"=>["Biotechnology", "Cancer", "Biochemistry", "Genetics", "Microbiology"], "users"=>["Jennifer Dolan Thomas", "Cynthia P. Hatcher", "Dara A. Satterfield", "M. Jordan Theodore", "Michelle C. Bach", "Kristin B. Linscott", "Xin Zhao", "Xin Wang", "Raydel Mair", "Susanna Schmink", "Kathryn E. Arnold", "David S. Stephens", "Lee H. Harrison", "Rosemary A. Hollick", "Ana Lucia Andrade", "Juliana Lamaro-Cardoso", "Ana Paula S. de Lemos", "Jenna Gritzfeld", "Stephen Gordon", "Ahmet Soysal", "Mustafa Bakir", "Dolly Sharma", "Shabnam Jain", "Sarah W. Satola", "Nancy E. Messonnier", "Leonard W. Mayer"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0019361.s001", "https://dx.doi.org/10.1371/journal.pone.0019361.s002", "https://dx.doi.org/10.1371/journal.pone.0019361.s003", "https://dx.doi.org/10.1371/journal.pone.0019361.s004", "https://dx.doi.org/10.1371/journal.pone.0019361.s005"], "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_sodC_Based_Real_Time_PCR_for_Detection_of____Neisseria_meningitidis_/136969", "title"=>"<em>sodC</em>-Based Real-Time PCR for Detection of\n <em>Neisseria meningitidis</em>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-05-05 01:56:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/777568"], "description"=>"<p>Primers and probe used in this study.</p>", "links"=>[], "tags"=>["probe"], "article_id"=>447911, "categories"=>["Biotechnology", "Microbiology", "Biochemistry", "Genetics", "Infectious Diseases"], "users"=>["Jennifer Dolan Thomas", "Cynthia P. Hatcher", "Dara A. Satterfield", "M. Jordan Theodore", "Michelle C. Bach", "Kristin B. Linscott", "Xin Zhao", "Xin Wang", "Raydel Mair", "Susanna Schmink", "Kathryn E. Arnold", "David S. Stephens", "Lee H. Harrison", "Rosemary A. Hollick", "Ana Lucia Andrade", "Juliana Lamaro-Cardoso", "Ana Paula S. de Lemos", "Jenna Gritzfeld", "Stephen Gordon", "Ahmet Soysal", "Mustafa Bakir", "Dolly Sharma", "Shabnam Jain", "Sarah W. Satola", "Nancy E. Messonnier", "Leonard W. Mayer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0019361.t004", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Primers_and_probe_used_in_this_study_/447911", "title"=>"Primers and probe used in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-05 02:11:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/777360"], "description"=>"1<p>92 <i>N. lactamica</i>, 4 <i>N. gonorrhoeae</i>,\n 19 <i>M. catarrhalis</i>, and 2 <i>H</i>. spp.\n from this panel were collected in a Georgia Nm carriage study <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019361#pone.0019361-Clark1\" target=\"_blank\">[20]</a>.\n 3 <i>N</i>. spp., 1 <i>N. polysaccharea</i>, 2\n <i>M. catarrhalis</i>, 9 <i>H.\n parainfluenzae</i>, 1 <i>H. haemolyticus</i>, 75\n NTHi, and 1 Hie were collected in a Georgia Hib carriage study <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019361#pone.0019361-Sharma1\" target=\"_blank\">[24]</a>.</p>", "links"=>[], "tags"=>["non-nm", "isolates", "specificity", "the"], "article_id"=>447694, "categories"=>["Biotechnology", "Microbiology", "Biochemistry", "Genetics", "Infectious Diseases"], "users"=>["Jennifer Dolan Thomas", "Cynthia P. Hatcher", "Dara A. Satterfield", "M. Jordan Theodore", "Michelle C. Bach", "Kristin B. Linscott", "Xin Zhao", "Xin Wang", "Raydel Mair", "Susanna Schmink", "Kathryn E. Arnold", "David S. Stephens", "Lee H. Harrison", "Rosemary A. Hollick", "Ana Lucia Andrade", "Juliana Lamaro-Cardoso", "Ana Paula S. de Lemos", "Jenna Gritzfeld", "Stephen Gordon", "Ahmet Soysal", "Mustafa Bakir", "Dolly Sharma", "Shabnam Jain", "Sarah W. Satola", "Nancy E. Messonnier", "Leonard W. Mayer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0019361.t002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_244_non_Nm_isolates_were_used_to_test_the_specificity_of_the_____sodC_assay_/447694", "title"=>"244 non-Nm isolates were used to test the specificity of the\n <i>sodC</i> assay.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-05 02:08:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/777432"], "description"=>"1<p>Exact binomial 95% confidence interval.</p>2<p>Culture was attempted for all 120 Turkey CSF specimens. With the\n exception of the one <i>ctrA</i>-negative,\n <i>sodC</i>-positive U.S. CSF specimen that was\n culture-positive, culture was either not attempted, not reported or,\n in one case, the isolate was nonviable two times for the other 36\n U.S. clinical specimens.</p>3<p>n/a, not applicable.</p>", "links"=>[], "tags"=>["specimens", "tested", "compared"], "article_id"=>447766, "categories"=>["Biotechnology", "Microbiology", "Biochemistry", "Genetics", "Infectious Diseases"], "users"=>["Jennifer Dolan Thomas", "Cynthia P. Hatcher", "Dara A. Satterfield", "M. Jordan Theodore", "Michelle C. Bach", "Kristin B. Linscott", "Xin Zhao", "Xin Wang", "Raydel Mair", "Susanna Schmink", "Kathryn E. Arnold", "David S. Stephens", "Lee H. Harrison", "Rosemary A. Hollick", "Ana Lucia Andrade", "Juliana Lamaro-Cardoso", "Ana Paula S. de Lemos", "Jenna Gritzfeld", "Stephen Gordon", "Ahmet Soysal", "Mustafa Bakir", "Dolly Sharma", "Shabnam Jain", "Sarah W. Satola", "Nancy E. Messonnier", "Leonard W. Mayer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0019361.t003", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_U_S_and_Turkey_clinical_specimens_tested_for_sod_C____and_ctrA_and_compared_to_culture_/447766", "title"=>"U.S. and Turkey clinical specimens tested for <i>sod C</i>\n and <i>ctrA</i> and compared to culture.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-05 02:09:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/777640"], "description"=>"1<p>Exact binomial 95% confidence interval.</p>2<p>This <i>ctrA</i>-positive NP swab eluate was\n <i>sodC</i>-negative.</p>3<p>Both of these <i>sodC</i>-positive NP swab eluates were\n <i>ctrA</i>-positive.</p>4<p>This Nm culture-positive NW was <i>ctrA</i>-positive,\n <i>sodC</i>-positive.</p>5<p>n/a, not applicable.</p>", "links"=>[], "tags"=>["specimens", "tested", "and", "compared"], "article_id"=>447977, "categories"=>["Biotechnology", "Microbiology", "Biochemistry", "Genetics", "Infectious Diseases"], "users"=>["Jennifer Dolan Thomas", "Cynthia P. Hatcher", "Dara A. Satterfield", "M. Jordan Theodore", "Michelle C. Bach", "Kristin B. Linscott", "Xin Zhao", "Xin Wang", "Raydel Mair", "Susanna Schmink", "Kathryn E. Arnold", "David S. Stephens", "Lee H. Harrison", "Rosemary A. Hollick", "Ana Lucia Andrade", "Juliana Lamaro-Cardoso", "Ana Paula S. de Lemos", "Jenna Gritzfeld", "Stephen Gordon", "Ahmet Soysal", "Mustafa Bakir", "Dolly Sharma", "Shabnam Jain", "Sarah W. Satola", "Nancy E. Messonnier", "Leonard W. Mayer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0019361.t005", "stats"=>{"downloads"=>2, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Carriage_specimens_tested_for_sodC_and_____ctrA_and_compared_to_culture_/447977", "title"=>"Carriage specimens tested for <i>sodC</i> and\n <i>ctrA</i> and compared to culture.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-05 02:12:57"}

PMC Usage Stats | Further Information

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  • {"scanned-page-browse"=>"0", "month"=>"9", "cited-by"=>"0", "abstract"=>"0", "full-text"=>"22", "unique-ip"=>"21", "pdf"=>"10", "year"=>"2011", "figure"=>"0", "scanned-summary"=>"0", "supp-data"=>"0"}
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