Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection

Brianna Lindsay, Mihai Pop, Martin Antonio, Alan W Walker, Volker Mai, Dilruba Ahmed, Joseph Oundo, Boubou Tamboura, Sandra Panchalingam, Myron M Levine, Karen Kotloff, Shan Li, Laurence S Magder, Joseph N Paulson, Bo Liu, Usman Ikumapayi, Chinelo Ebruke, Michel Dione, Mitchell Adeyemi, Richard Rance & 32 others Mark D Stares, Maria Ukhanova, Bret Barnes, Ian Lewis, Firoz Ahmed, Meer Taifur Alam, Ruhul Amin, Sabbir Siddiqui, John B Ochieng, Emmanuel Ouma, Jane Juma, Eunice Mailu, Richard Omore, Ciara E O'Reilly, James Hannis, Sheri Manalili, Jonna Deleon, Irene Yasuda, Lawrence Blyn, Raymond Ranken, Feng Li, Roberta Housley, David J Ecker, M Anowar Hossain, Robert F Breiman, J Glenn Morris, Timothy K McDaniel, Julian Parkhill, Debasish Saha, Rangarajan Sampath, O Colin Stine, James P Nataro

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

Cultivation-based assays combined with PCR or enzyme-linked immunosorbent assay (ELISA)-based methods for finding virulence factors are standard methods for detecting bacterial pathogens in stools; however, with emerging molecular technologies, new methods have become available. The aim of this study was to compare four distinct detection technologies for the identification of pathogens in stools from children under 5 years of age in The Gambia, Mali, Kenya, and Bangladesh. The children were identified, using currently accepted clinical protocols, as either controls or cases with moderate to severe diarrhea. A total of 3,610 stool samples were tested by established clinical culture techniques: 3,179 DNA samples by the Universal Biosensor assay (Ibis Biosciences, Inc.), 1,466 DNA samples by the GoldenGate assay (Illumina), and 1,006 DNA samples by sequencing of 16S rRNA genes. Each method detected different proportions of samples testing positive for each of seven enteric pathogens, enteroaggregative Escherichia coli (EAEC), enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), Shigella spp., Campylobacter jejuni, Salmonella enterica, and Aeromonas spp. The comparisons among detection methods included the frequency of positive stool samples and kappa values for making pairwise comparisons. Overall, the standard culture methods detected Shigella spp., EPEC, ETEC, and EAEC in smaller proportions of the samples than either of the methods based on detection of the virulence genes from DNA in whole stools. The GoldenGate method revealed the greatest agreement with the other methods. The agreement among methods was higher in cases than in controls. The new molecular technologies have a high potential for highly sensitive identification of bacterial diarrheal pathogens.
Original languageEnglish
Pages (from-to)3263-3269
Number of pages7
JournalJournal of Clinical Microbiology
Volume51
Issue number10
Early online date24 Jul 2013
DOIs
Publication statusPublished - Oct 2013

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Biosensing Techniques
rRNA Genes
Enterotoxigenic Escherichia coli
Enteropathogenic Escherichia coli
Shigella
Technology
DNA
Surveys and Questionnaires
Gambia
Escherichia coli
Mali
Aeromonas
Culture Techniques
Campylobacter jejuni
Salmonella enterica
Bangladesh
Kenya
Virulence Factors
Clinical Protocols
DNA Sequence Analysis

Keywords

  • Adolescent
  • Adult
  • Africa
  • Bacteria
  • Bacterial Infections
  • Bacteriological Techniques
  • Bangladesh
  • Biosensing Techniques
  • Child
  • Child, Preschool
  • Diarrhea
  • Feces
  • Female
  • Humans
  • Infant
  • Infant, Newborn
  • Male
  • Middle Aged
  • Molecular Diagnostic Techniques
  • Young Adult

Cite this

Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection. / Lindsay, Brianna; Pop, Mihai; Antonio, Martin; Walker, Alan W; Mai, Volker; Ahmed, Dilruba; Oundo, Joseph; Tamboura, Boubou; Panchalingam, Sandra; Levine, Myron M; Kotloff, Karen; Li, Shan; Magder, Laurence S; Paulson, Joseph N; Liu, Bo; Ikumapayi, Usman; Ebruke, Chinelo; Dione, Michel; Adeyemi, Mitchell; Rance, Richard; Stares, Mark D; Ukhanova, Maria; Barnes, Bret; Lewis, Ian; Ahmed, Firoz; Alam, Meer Taifur; Amin, Ruhul; Siddiqui, Sabbir; Ochieng, John B; Ouma, Emmanuel; Juma, Jane; Mailu, Eunice; Omore, Richard; O'Reilly, Ciara E; Hannis, James; Manalili, Sheri; Deleon, Jonna; Yasuda, Irene; Blyn, Lawrence; Ranken, Raymond; Li, Feng; Housley, Roberta; Ecker, David J; Hossain, M Anowar; Breiman, Robert F; Morris, J Glenn; McDaniel, Timothy K; Parkhill, Julian; Saha, Debasish; Sampath, Rangarajan; Stine, O Colin; Nataro, James P.

In: Journal of Clinical Microbiology, Vol. 51, No. 10, 10.2013, p. 3263-3269.

Research output: Contribution to journalArticle

Lindsay, B, Pop, M, Antonio, M, Walker, AW, Mai, V, Ahmed, D, Oundo, J, Tamboura, B, Panchalingam, S, Levine, MM, Kotloff, K, Li, S, Magder, LS, Paulson, JN, Liu, B, Ikumapayi, U, Ebruke, C, Dione, M, Adeyemi, M, Rance, R, Stares, MD, Ukhanova, M, Barnes, B, Lewis, I, Ahmed, F, Alam, MT, Amin, R, Siddiqui, S, Ochieng, JB, Ouma, E, Juma, J, Mailu, E, Omore, R, O'Reilly, CE, Hannis, J, Manalili, S, Deleon, J, Yasuda, I, Blyn, L, Ranken, R, Li, F, Housley, R, Ecker, DJ, Hossain, MA, Breiman, RF, Morris, JG, McDaniel, TK, Parkhill, J, Saha, D, Sampath, R, Stine, OC & Nataro, JP 2013, 'Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection' Journal of Clinical Microbiology, vol. 51, no. 10, pp. 3263-3269. https://doi.org/10.1128/JCM.01342-13
Lindsay, Brianna ; Pop, Mihai ; Antonio, Martin ; Walker, Alan W ; Mai, Volker ; Ahmed, Dilruba ; Oundo, Joseph ; Tamboura, Boubou ; Panchalingam, Sandra ; Levine, Myron M ; Kotloff, Karen ; Li, Shan ; Magder, Laurence S ; Paulson, Joseph N ; Liu, Bo ; Ikumapayi, Usman ; Ebruke, Chinelo ; Dione, Michel ; Adeyemi, Mitchell ; Rance, Richard ; Stares, Mark D ; Ukhanova, Maria ; Barnes, Bret ; Lewis, Ian ; Ahmed, Firoz ; Alam, Meer Taifur ; Amin, Ruhul ; Siddiqui, Sabbir ; Ochieng, John B ; Ouma, Emmanuel ; Juma, Jane ; Mailu, Eunice ; Omore, Richard ; O'Reilly, Ciara E ; Hannis, James ; Manalili, Sheri ; Deleon, Jonna ; Yasuda, Irene ; Blyn, Lawrence ; Ranken, Raymond ; Li, Feng ; Housley, Roberta ; Ecker, David J ; Hossain, M Anowar ; Breiman, Robert F ; Morris, J Glenn ; McDaniel, Timothy K ; Parkhill, Julian ; Saha, Debasish ; Sampath, Rangarajan ; Stine, O Colin ; Nataro, James P. / Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection. In: Journal of Clinical Microbiology. 2013 ; Vol. 51, No. 10. pp. 3263-3269.
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abstract = "Cultivation-based assays combined with PCR or enzyme-linked immunosorbent assay (ELISA)-based methods for finding virulence factors are standard methods for detecting bacterial pathogens in stools; however, with emerging molecular technologies, new methods have become available. The aim of this study was to compare four distinct detection technologies for the identification of pathogens in stools from children under 5 years of age in The Gambia, Mali, Kenya, and Bangladesh. The children were identified, using currently accepted clinical protocols, as either controls or cases with moderate to severe diarrhea. A total of 3,610 stool samples were tested by established clinical culture techniques: 3,179 DNA samples by the Universal Biosensor assay (Ibis Biosciences, Inc.), 1,466 DNA samples by the GoldenGate assay (Illumina), and 1,006 DNA samples by sequencing of 16S rRNA genes. Each method detected different proportions of samples testing positive for each of seven enteric pathogens, enteroaggregative Escherichia coli (EAEC), enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), Shigella spp., Campylobacter jejuni, Salmonella enterica, and Aeromonas spp. The comparisons among detection methods included the frequency of positive stool samples and kappa values for making pairwise comparisons. Overall, the standard culture methods detected Shigella spp., EPEC, ETEC, and EAEC in smaller proportions of the samples than either of the methods based on detection of the virulence genes from DNA in whole stools. The GoldenGate method revealed the greatest agreement with the other methods. The agreement among methods was higher in cases than in controls. The new molecular technologies have a high potential for highly sensitive identification of bacterial diarrheal pathogens.",
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AU - Lindsay, Brianna

AU - Pop, Mihai

AU - Antonio, Martin

AU - Walker, Alan W

AU - Mai, Volker

AU - Ahmed, Dilruba

AU - Oundo, Joseph

AU - Tamboura, Boubou

AU - Panchalingam, Sandra

AU - Levine, Myron M

AU - Kotloff, Karen

AU - Li, Shan

AU - Magder, Laurence S

AU - Paulson, Joseph N

AU - Liu, Bo

AU - Ikumapayi, Usman

AU - Ebruke, Chinelo

AU - Dione, Michel

AU - Adeyemi, Mitchell

AU - Rance, Richard

AU - Stares, Mark D

AU - Ukhanova, Maria

AU - Barnes, Bret

AU - Lewis, Ian

AU - Ahmed, Firoz

AU - Alam, Meer Taifur

AU - Amin, Ruhul

AU - Siddiqui, Sabbir

AU - Ochieng, John B

AU - Ouma, Emmanuel

AU - Juma, Jane

AU - Mailu, Eunice

AU - Omore, Richard

AU - O'Reilly, Ciara E

AU - Hannis, James

AU - Manalili, Sheri

AU - Deleon, Jonna

AU - Yasuda, Irene

AU - Blyn, Lawrence

AU - Ranken, Raymond

AU - Li, Feng

AU - Housley, Roberta

AU - Ecker, David J

AU - Hossain, M Anowar

AU - Breiman, Robert F

AU - Morris, J Glenn

AU - McDaniel, Timothy K

AU - Parkhill, Julian

AU - Saha, Debasish

AU - Sampath, Rangarajan

AU - Stine, O Colin

AU - Nataro, James P

PY - 2013/10

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N2 - Cultivation-based assays combined with PCR or enzyme-linked immunosorbent assay (ELISA)-based methods for finding virulence factors are standard methods for detecting bacterial pathogens in stools; however, with emerging molecular technologies, new methods have become available. The aim of this study was to compare four distinct detection technologies for the identification of pathogens in stools from children under 5 years of age in The Gambia, Mali, Kenya, and Bangladesh. The children were identified, using currently accepted clinical protocols, as either controls or cases with moderate to severe diarrhea. A total of 3,610 stool samples were tested by established clinical culture techniques: 3,179 DNA samples by the Universal Biosensor assay (Ibis Biosciences, Inc.), 1,466 DNA samples by the GoldenGate assay (Illumina), and 1,006 DNA samples by sequencing of 16S rRNA genes. Each method detected different proportions of samples testing positive for each of seven enteric pathogens, enteroaggregative Escherichia coli (EAEC), enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), Shigella spp., Campylobacter jejuni, Salmonella enterica, and Aeromonas spp. The comparisons among detection methods included the frequency of positive stool samples and kappa values for making pairwise comparisons. Overall, the standard culture methods detected Shigella spp., EPEC, ETEC, and EAEC in smaller proportions of the samples than either of the methods based on detection of the virulence genes from DNA in whole stools. The GoldenGate method revealed the greatest agreement with the other methods. The agreement among methods was higher in cases than in controls. The new molecular technologies have a high potential for highly sensitive identification of bacterial diarrheal pathogens.

AB - Cultivation-based assays combined with PCR or enzyme-linked immunosorbent assay (ELISA)-based methods for finding virulence factors are standard methods for detecting bacterial pathogens in stools; however, with emerging molecular technologies, new methods have become available. The aim of this study was to compare four distinct detection technologies for the identification of pathogens in stools from children under 5 years of age in The Gambia, Mali, Kenya, and Bangladesh. The children were identified, using currently accepted clinical protocols, as either controls or cases with moderate to severe diarrhea. A total of 3,610 stool samples were tested by established clinical culture techniques: 3,179 DNA samples by the Universal Biosensor assay (Ibis Biosciences, Inc.), 1,466 DNA samples by the GoldenGate assay (Illumina), and 1,006 DNA samples by sequencing of 16S rRNA genes. Each method detected different proportions of samples testing positive for each of seven enteric pathogens, enteroaggregative Escherichia coli (EAEC), enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), Shigella spp., Campylobacter jejuni, Salmonella enterica, and Aeromonas spp. The comparisons among detection methods included the frequency of positive stool samples and kappa values for making pairwise comparisons. Overall, the standard culture methods detected Shigella spp., EPEC, ETEC, and EAEC in smaller proportions of the samples than either of the methods based on detection of the virulence genes from DNA in whole stools. The GoldenGate method revealed the greatest agreement with the other methods. The agreement among methods was higher in cases than in controls. The new molecular technologies have a high potential for highly sensitive identification of bacterial diarrheal pathogens.

KW - Adolescent

KW - Adult

KW - Africa

KW - Bacteria

KW - Bacterial Infections

KW - Bacteriological Techniques

KW - Bangladesh

KW - Biosensing Techniques

KW - Child

KW - Child, Preschool

KW - Diarrhea

KW - Feces

KW - Female

KW - Humans

KW - Infant

KW - Infant, Newborn

KW - Male

KW - Middle Aged

KW - Molecular Diagnostic Techniques

KW - Young Adult

U2 - 10.1128/JCM.01342-13

DO - 10.1128/JCM.01342-13

M3 - Article

VL - 51

SP - 3263

EP - 3269

JO - Journal of Clinical Microbiology

JF - Journal of Clinical Microbiology

SN - 0095-1137

IS - 10

ER -