Multiplex Identification of Gram-Positive Bacteria and Resistance Determinants Directly from Positive Blood Culture Broths: Evaluation of an Automated Microarray-Based Nucleic Acid Test
Publication Date
July 02, 2013
Journal
PLoS Medicine
Authors
Blake W. Buchan, Christine C. Ginocchio, Ryhana Manii, Robert Cavagnolo, et al
Volume
10
Issue
7
Pages
e1001478
DOI
https://dx.plos.org/10.1371/journal.pmed.1001478
Publisher URL
http://journals.plos.org/plosmedicine/article?id=10.1371%2Fjournal.pmed.1001478
Web of Science
000322590800004
Scopus
84881261591
Mendeley
http://www.mendeley.com/research/multiplex-identification-grampositive-bacteria-resistance-determinants-directly-positive-blood-cultu
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Mendeley | Further Information

{"title"=>"Multiplex Identification of Gram-Positive Bacteria and Resistance Determinants Directly from Positive Blood Culture Broths: Evaluation of an Automated Microarray-Based Nucleic Acid Test", "type"=>"journal", "authors"=>[{"first_name"=>"Blake W.", "last_name"=>"Buchan", "scopus_author_id"=>"8632032400"}, {"first_name"=>"Christine C.", "last_name"=>"Ginocchio", "scopus_author_id"=>"7004518429"}, {"first_name"=>"Ryhana", "last_name"=>"Manii", "scopus_author_id"=>"55815675200"}, {"first_name"=>"Robert", "last_name"=>"Cavagnolo", "scopus_author_id"=>"36924025900"}, {"first_name"=>"Preeti", "last_name"=>"Pancholi", "scopus_author_id"=>"6701869604"}, {"first_name"=>"Lettie", "last_name"=>"Swyers", "scopus_author_id"=>"36165013900"}, {"first_name"=>"Richard B.", "last_name"=>"Thomson", "scopus_author_id"=>"7201360087"}, {"first_name"=>"Christopher", "last_name"=>"Anderson", "scopus_author_id"=>"56390879800"}, {"first_name"=>"Karen", "last_name"=>"Kaul", "scopus_author_id"=>"7007034089"}, {"first_name"=>"Nathan A.", "last_name"=>"Ledeboer", "scopus_author_id"=>"8404600600"}], "year"=>2013, "source"=>"PLoS Medicine", "identifiers"=>{"scopus"=>"2-s2.0-84881261591", "doi"=>"10.1371/journal.pmed.1001478", "sgr"=>"84881261591", "isbn"=>"1549-1676", "pmid"=>"23843749", "issn"=>"15491277", "pui"=>"369514189"}, "id"=>"f8258f8f-c166-3715-87f6-56096d69ea74", "abstract"=>"BACKGROUND A multicenter study was conducted to evaluate the diagnostic accuracy (sensitivity and specificity) of the Verigene Gram-Positive Blood Culture Test (BC-GP) test to identify 12 Gram-positive bacterial gene targets and three genetic resistance determinants directly from positive blood culture broths containing Gram-positive bacteria. METHODS AND FINDINGS 1,252 blood cultures containing Gram-positive bacteria were prospectively collected and tested at five clinical centers between April, 2011 and January, 2012. An additional 387 contrived blood cultures containing uncommon targets (e.g., Listeria spp., S. lugdunensis, vanB-positive Enterococci) were included to fully evaluate the performance of the BC-GP test. Sensitivity and specificity for the 12 specific genus or species targets identified by the BC-GP test ranged from 92.6%-100% and 95.4%-100%, respectively. Identification of the mecA gene in 599 cultures containing S. aureus or S. epidermidis was 98.6% sensitive and 94.3% specific compared to cefoxitin disk method. Identification of the vanA gene in 81 cultures containing Enterococcus faecium or E. faecalis was 100% sensitive and specific. Approximately 7.5% (87/1,157) of single-organism cultures contained Gram-positive bacteria not present on the BC-GP test panel. In 95 cultures containing multiple organisms the BC-GP test was in 71.6% (68/95) agreement with culture results. Retrospective analysis of 107 separate blood cultures demonstrated that identification of methicillin resistant S. aureus and vancomycin resistant Enterococcus spp. was completed an average of 41.8 to 42.4 h earlier using the BC-GP test compared to routine culture methods. The BC-GP test was unable to assign mecA to a specific organism in cultures containing more than one Staphylococcus isolate and does not identify common blood culture contaminants such as Micrococcus, Corynebacterium, and Bacillus. CONCLUSIONS The BC-GP test is a multiplex test capable of detecting most leading causes of Gram-positive bacterial blood stream infections as well as genetic markers of methicillin and vancomycin resistance directly from positive blood cultures.", "link"=>"http://www.mendeley.com/research/multiplex-identification-grampositive-bacteria-resistance-determinants-directly-positive-blood-cultu", "reader_count"=>50, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>2, "Librarian"=>1, "Researcher"=>10, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>3, "Student > Master"=>8, "Other"=>5, "Student > Bachelor"=>7, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>2, "Librarian"=>1, "Researcher"=>10, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>3, "Student > Master"=>8, "Other"=>5, "Student > Bachelor"=>7, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Engineering"=>2, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Medicine and Dentistry"=>16, "Agricultural and Biological Sciences"=>19, "Business, Management and Accounting"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>3}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>16}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>19}, "Computer Science"=>{"Computer Science"=>1}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>5}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Canada"=>2, "Kenya"=>1, "Portugal"=>1}, "group_count"=>7}

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1108868", "https://ndownloader.figshare.com/files/1108869", "https://ndownloader.figshare.com/files/1108870", "https://ndownloader.figshare.com/files/1108871"], "description"=>"<div><p>Background</p><p>A multicenter study was conducted to evaluate the diagnostic accuracy (sensitivity and specificity) of the Verigene Gram-Positive Blood Culture Test (BC-GP) test to identify 12 Gram-positive bacterial gene targets and three genetic resistance determinants directly from positive blood culture broths containing Gram-positive bacteria.</p><p>Methods and Findings</p><p>1,252 blood cultures containing Gram-positive bacteria were prospectively collected and tested at five clinical centers between April, 2011 and January, 2012. An additional 387 contrived blood cultures containing uncommon targets (e.g., <i>Listeria</i> spp., <i>S. lugdunensis</i>, <i>vanB</i>-positive Enterococci) were included to fully evaluate the performance of the BC-GP test. Sensitivity and specificity for the 12 specific genus or species targets identified by the BC-GP test ranged from 92.6%–100% and 95.4%–100%, respectively. Identification of the <i>mecA</i> gene in 599 cultures containing <i>S. aureus</i> or <i>S. epidermidis</i> was 98.6% sensitive and 94.3% specific compared to cefoxitin disk method. Identification of the <i>vanA</i> gene in 81 cultures containing <i>Enterococcus faecium</i> or <i>E. faecalis</i> was 100% sensitive and specific. Approximately 7.5% (87/1,157) of single-organism cultures contained Gram-positive bacteria not present on the BC-GP test panel. In 95 cultures containing multiple organisms the BC-GP test was in 71.6% (68/95) agreement with culture results. Retrospective analysis of 107 separate blood cultures demonstrated that identification of methicillin resistant <i>S. aureus</i> and vancomycin resistant <i>Enterococcus</i> spp. was completed an average of 41.8 to 42.4 h earlier using the BC-GP test compared to routine culture methods. The BC-GP test was unable to assign <i>mecA</i> to a specific organism in cultures containing more than one <i>Staphylococcus</i> isolate and does not identify common blood culture contaminants such as <i>Micrococcus</i>, <i>Corynebacterium</i>, and <i>Bacillus</i>.</p><p>Conclusions</p><p>The BC-GP test is a multiplex test capable of detecting most leading causes of Gram-positive bacterial blood stream infections as well as genetic markers of methicillin and vancomycin resistance directly from positive blood cultures.</p><p><i>Please see later in the article for the Editors' Summary</i></p></div>", "links"=>[], "tags"=>["microbiology", "Bacterial pathogens", "Gram positive", "Medical microbiology", "Microbial pathogens", "Diagnostic medicine", "pathology", "Clinical pathology", "Clinical microbiology", "Test evaluation", "gram-positive", "determinants", "automated", "microarray-based", "nucleic"], "article_id"=>737644, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Blake W. Buchan", "Christine C. Ginocchio", "Ryhana Manii", "Robert Cavagnolo", "Preeti Pancholi", "Lettie Swyers", "Richard B. Thomson Jr", "Christopher Anderson", "Karen Kaul", "Nathan A. Ledeboer"], "doi"=>["https://dx.doi.org/10.1371/journal.pmed.1001478.s001", "https://dx.doi.org/10.1371/journal.pmed.1001478.s002", "https://dx.doi.org/10.1371/journal.pmed.1001478.s003", "https://dx.doi.org/10.1371/journal.pmed.1001478.s004"], "stats"=>{"downloads"=>35, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multiplex_Identification_of_Gram_Positive_Bacteria_and_Resistance_Determinants_Directly_from_Positive_Blood_Culture_Broths_Evaluation_of_an_Automated_Microarray_Based_Nucleic_Acid_Test_/737644", "title"=>"Multiplex Identification of Gram-Positive Bacteria and Resistance Determinants Directly from Positive Blood Culture Broths: Evaluation of an Automated Microarray-Based Nucleic Acid Test", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-07-02 03:34:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1108865"], "description"=>"a<p>Total number of cultures with reported result.</p>b<p>95% confidence interval.</p><p>FN, false negative; FP, false positive; TN, true negative; TP, true positive.</p>", "links"=>[], "tags"=>["microbiology", "Bacterial pathogens", "Gram positive", "Medical microbiology", "Microbial pathogens", "Diagnostic medicine", "pathology", "Clinical pathology", "Clinical microbiology", "Test evaluation", "prospectively", "monomicrobial", "cultures", "verigene", "bc-gp"], "article_id"=>737641, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Blake W. Buchan", "Christine C. Ginocchio", "Ryhana Manii", "Robert Cavagnolo", "Preeti Pancholi", "Lettie Swyers", "Richard B. Thomson Jr", "Christopher Anderson", "Karen Kaul", "Nathan A. Ledeboer"], "doi"=>"https://dx.doi.org/10.1371/journal.pmed.1001478.t003", "stats"=>{"downloads"=>4, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detection_of_E_faecalis_E_faecium_and_Listeria_in_prospectively_collected_monomicrobial_blood_cultures_by_Verigene_BC_GP_n_8202_8202_1_157_/737641", "title"=>"Detection of <i>E. faecalis</i>, <i>E. faecium</i>, and <i>Listeria</i> in prospectively collected monomicrobial blood cultures by Verigene BC-GP (<i>n = </i>1,157).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-02 03:34:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1108863"], "description"=>"a<p>Coagulase negative <i>Staphylococcus</i> species, not including <i>S. epidermidis</i> and <i>S. lugdunensis</i>.</p>b<p>Contrived culture.</p>c<p><i>E. faecalis</i> or <i>E. faecium</i>.</p>d<p><i>Gram-negative rod</i>.</p>e<p><i>Bacillus</i> spp. not <i>anthracis</i>.</p>", "links"=>[], "tags"=>["microbiology", "Bacterial pathogens", "Gram positive", "Medical microbiology", "Microbial pathogens", "Diagnostic medicine", "pathology", "Clinical pathology", "Clinical microbiology", "Test evaluation", "gram-positive", "determinants", "polymicrobial", "cultures", "verigene", "bc-gp"], "article_id"=>737639, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Blake W. Buchan", "Christine C. Ginocchio", "Ryhana Manii", "Robert Cavagnolo", "Preeti Pancholi", "Lettie Swyers", "Richard B. Thomson Jr", "Christopher Anderson", "Karen Kaul", "Nathan A. Ledeboer"], "doi"=>"https://dx.doi.org/10.1371/journal.pmed.1001478.t005", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detection_of_Gram_positive_identification_and_resistance_determinants_from_polymicrobial_blood_cultures_by_Verigene_BC_GP_n_8202_8202_95_/737639", "title"=>"Detection of Gram-positive identification and resistance determinants from polymicrobial blood cultures by Verigene BC-GP (<i>n = </i>95).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-02 03:34:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1108864"], "description"=>"a<p>Total number of cultures with reported result.</p>b<p>95% confidence interval.</p>c<p><i>mecA</i> is reported only for cultures with positive <i>S. aureus</i> or <i>S. epidermidis</i> species targets. Inferred based upon resistance to cefoxitin using disk diffusion method.</p>d<p><i>mecA</i> specific PCR was positive for eight of 14 isolates. Final specificity of 97.5%.</p>e<p><i>mecA</i> specific PCR was negative for four of five isolates. Final sensitivity of 99.7%.</p>f<p>vanA and vanB are reported only for cultures with positive <i>E. feacium</i> or <i>E. faecalis</i> targets.</p>g<p><i>vanB</i> was not detected in any prospectively collected cultures.</p><p>FN, false negative; FP, false positive; TN, true negative; TP, true positive.</p>", "links"=>[], "tags"=>["microbiology", "Bacterial pathogens", "Gram positive", "Medical microbiology", "Microbial pathogens", "Diagnostic medicine", "pathology", "Clinical pathology", "Clinical microbiology", "Test evaluation", "determinants", "prospectively", "monomicrobial", "cultures", "verigene", "bc-gp"], "article_id"=>737640, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Blake W. Buchan", "Christine C. Ginocchio", "Ryhana Manii", "Robert Cavagnolo", "Preeti Pancholi", "Lettie Swyers", "Richard B. Thomson Jr", "Christopher Anderson", "Karen Kaul", "Nathan A. Ledeboer"], "doi"=>"https://dx.doi.org/10.1371/journal.pmed.1001478.t004", "stats"=>{"downloads"=>5, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detection_of_resistance_determinants_mecA_vanA_and_vanB_in_prospectively_collected_monomicrobial_blood_cultures_by_Verigene_BC_GP_n_8202_8202_599_S_aureus_S_epidermidis_n_8202_8202_81_E_faecalis_E_faecium_/737640", "title"=>"Detection of resistance determinants <i>mecA, vanA, and vanB</i> in prospectively collected monomicrobial blood cultures by Verigene BC-GP (<i>n = </i>599 <i>S. aureus/S. epidermidis</i>, <i>n = </i>81 <i>E. faecalis/E. faecium</i>).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-02 03:34:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1108862"], "description"=>"a<p>Total number of cultures with reported result.</p>b<p>95% confidence interval.</p>c<p><i>mecA</i> is reported only for cultures with positive <i>S. aureus</i> or <i>S. epidermidis</i> species targets.</p>d<p><i>vanA</i> and <i>vanB</i> are reported only for cultures with positive <i>E. feacium</i> or <i>E. faecalis</i> targets.</p><p>FN, false negative; FP, false positive; TN, true negative; TP, true positive.</p>", "links"=>[], "tags"=>["microbiology", "Bacterial pathogens", "Gram positive", "Medical microbiology", "Microbial pathogens", "Diagnostic medicine", "pathology", "Clinical pathology", "Clinical microbiology", "Test evaluation", "gram", "determinants", "contrived", "cultures", "verigene", "bc-gp"], "article_id"=>737638, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Blake W. Buchan", "Christine C. Ginocchio", "Ryhana Manii", "Robert Cavagnolo", "Preeti Pancholi", "Lettie Swyers", "Richard B. Thomson Jr", "Christopher Anderson", "Karen Kaul", "Nathan A. Ledeboer"], "doi"=>"https://dx.doi.org/10.1371/journal.pmed.1001478.t006", "stats"=>{"downloads"=>3, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detection_of_Gram_positive_identification_and_resistance_determinants_from_contrived_blood_cultures_by_Verigene_BC_GP_n_8202_8202_387_/737638", "title"=>"Detection of Gram positive identification and resistance determinants from contrived blood cultures by Verigene BC-GP (<i>n = </i>387).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-02 03:34:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1108867"], "description"=>"a<p>Total number of cultures with reported result.</p>b<p>95% confidence interval.</p>c<p>Nucleic acid sequencing confirmed the identification of <i>S. epidermidis</i> in five of ten cultures.</p>d<p>Nucleic acid sequencing confirmed the identification of <i>S. epidermidis</i> in six of ten cultures.</p><p>FN, false negative; FP, false positive; TN, true negative; TP, true positive.</p>", "links"=>[], "tags"=>["microbiology", "Bacterial pathogens", "Gram positive", "Medical microbiology", "Microbial pathogens", "Diagnostic medicine", "pathology", "Clinical pathology", "Clinical microbiology", "Test evaluation", "prospectively", "monomicrobial", "cultures", "verigene", "bc-gp"], "article_id"=>737643, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Blake W. Buchan", "Christine C. Ginocchio", "Ryhana Manii", "Robert Cavagnolo", "Preeti Pancholi", "Lettie Swyers", "Richard B. Thomson Jr", "Christopher Anderson", "Karen Kaul", "Nathan A. Ledeboer"], "doi"=>"https://dx.doi.org/10.1371/journal.pmed.1001478.t001", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detection_of_Staphylococcus_spp_in_prospectively_collected_monomicrobial_blood_cultures_by_Verigene_BC_GP_n_8202_8202_1_157_/737643", "title"=>"Detection of <i>Staphylococcus</i> spp. in prospectively collected monomicrobial blood cultures by Verigene BC-GP (<i>n = </i>1,157).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-02 03:34:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1108866"], "description"=>"a<p>Total number of cultures with reported result.</p>b<p>95% confidence interval.</p><p>FN, false negative; FP, false positive; TN, true negative; TP, true positive.</p>", "links"=>[], "tags"=>["microbiology", "Bacterial pathogens", "Gram positive", "Medical microbiology", "Microbial pathogens", "Diagnostic medicine", "pathology", "Clinical pathology", "Clinical microbiology", "Test evaluation", "prospectively", "monomicrobial", "cultures", "verigene", "bc-gp"], "article_id"=>737642, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Blake W. Buchan", "Christine C. Ginocchio", "Ryhana Manii", "Robert Cavagnolo", "Preeti Pancholi", "Lettie Swyers", "Richard B. Thomson Jr", "Christopher Anderson", "Karen Kaul", "Nathan A. Ledeboer"], "doi"=>"https://dx.doi.org/10.1371/journal.pmed.1001478.t002", "stats"=>{"downloads"=>1, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detection_of_Streptococcus_spp_in_prospectively_collected_monomicrobial_blood_cultures_by_Verigene_BC_GP_n_8202_8202_1_157_/737642", "title"=>"Detection of <i>Streptococcus</i> spp. in prospectively collected monomicrobial blood cultures by Verigene BC-GP (<i>n = </i>1,157).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-02 03:34:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1108861"], "description"=>"a<p>Difference in time between BC-GP result and final culture-based identification and susceptibility results.</p>b<p>Includes 26 <i>S. epidermidis</i>.</p>c<p>Three cultures reported as “Not Detected” by BC-GP.</p>d<p>Based on eight cultures that met criteria for full identification and susceptibility testing. Average time to “CoNS” identification only was 27.5 h (range 14 h to 48 h) earlier using BC-GP, <i>n = </i>35.</p>e<p>One culture reported as <i>S. pneumoniae</i> by BC-GP.</p>f<p>Based on six cultures that met criteria for full identification and susceptibility testing.</p>g<p>Culture reported as “<i>Staphylococcus</i> spp.” by BC-GP.</p>", "links"=>[], "tags"=>["microbiology", "Bacterial pathogens", "Gram positive", "Medical microbiology", "Microbial pathogens", "Diagnostic medicine", "pathology", "Clinical pathology", "Clinical microbiology", "Test evaluation", "antimicrobial", "susceptibility"], "article_id"=>737637, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Blake W. Buchan", "Christine C. Ginocchio", "Ryhana Manii", "Robert Cavagnolo", "Preeti Pancholi", "Lettie Swyers", "Richard B. Thomson Jr", "Christopher Anderson", "Karen Kaul", "Nathan A. Ledeboer"], "doi"=>"https://dx.doi.org/10.1371/journal.pmed.1001478.t007", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Difference_in_time_to_final_identification_and_antimicrobial_susceptibility_report_n_8202_8202_107_/737637", "title"=>"Difference in time to final identification and antimicrobial susceptibility report (<i>n = </i>107).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-02 03:34:27"}

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Relative Metric

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