@article{e2952ca614204252a1a803e89fdf3f01,
title = "Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection",
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.",
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",
author = "Brianna Lindsay and Mihai Pop and Martin Antonio and Walker, {Alan W} and Volker Mai and Dilruba Ahmed and Joseph Oundo and Boubou Tamboura and Sandra Panchalingam and Levine, {Myron M} and Karen Kotloff and Shan Li and Magder, {Laurence S} and Paulson, {Joseph N} and Bo Liu and Usman Ikumapayi and Chinelo Ebruke and Michel Dione and Mitchell Adeyemi and Richard Rance and Stares, {Mark D} and Maria Ukhanova and Bret Barnes and Ian Lewis and Firoz Ahmed and Alam, {Meer Taifur} and Ruhul Amin and Sabbir Siddiqui and Ochieng, {John B} and Emmanuel Ouma and Jane Juma and Eunice Mailu and Richard Omore and O'Reilly, {Ciara E} and James Hannis and Sheri Manalili and Jonna Deleon and Irene Yasuda and Lawrence Blyn and Raymond Ranken and Feng Li and Roberta Housley and Ecker, {David J} and Hossain, {M Anowar} and Breiman, {Robert F} and Morris, {J Glenn} and McDaniel, {Timothy K} and Julian Parkhill and Debasish Saha and Rangarajan Sampath and Stine, {O Colin} and Nataro, {James P}",
year = "2013",
month = oct,
doi = "10.1128/JCM.01342-13",
language = "English",
volume = "51",
pages = "3263--3269",
journal = "Journal of Clinical Microbiology",
issn = "0095-1137",
publisher = "American Society for Microbiology",
number = "10",
}