TY - JOUR
T1 - Survey of culture, goldengate assay, universal biosensor assay, and 16s rRNA gene sequencing as alternative methods of bacterial pathogen detection
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 - Anowar Hossain, M.
AU - Breiman, Robert F.
AU - Glenn Morris, J.
AU - McDaniel, Timothy K.
AU - Parkhill, Julian
AU - Saha, Debasish
AU - Sampath, Rangarajan
AU - Colin Stine, O.
AU - Nataro, James P.
PY - 2013/10
Y1 - 2013/10
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.
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U2 - 10.1128/JCM.01342-13
DO - 10.1128/JCM.01342-13
M3 - Article
C2 - 23884998
AN - SCOPUS:84884770143
VL - 51
SP - 3263
EP - 3269
JO - Journal of Clinical Microbiology
JF - Journal of Clinical Microbiology
SN - 0095-1137
IS - 10
ER -