Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection
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Published:2013-10
Issue:10
Volume:51
Page:3263-3269
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ISSN:0095-1137
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Container-title:Journal of Clinical Microbiology
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language:en
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Short-container-title:J Clin Microbiol
Author:
Lindsay Brianna1, Pop Mihai2, Antonio Martin3, Walker Alan W.4, Mai Volker5, Ahmed Dilruba6, Oundo Joseph7, Tamboura Boubou8, Panchalingam Sandra1, Levine Myron M.1, Kotloff Karen1, Li Shan1, Magder Laurence S.1, Paulson Joseph N.2, Liu Bo2, Ikumapayi Usman3, Ebruke Chinelo3, Dione Michel3, Adeyemi Mitchell3, Rance Richard4, Stares Mark D.4, Ukhanova Maria5, Barnes Bret9, Lewis Ian9, Ahmed Firoz6, Alam Meer Taifur6, Amin Ruhul6, Siddiqui Sabbir6, Ochieng John B.7, Ouma Emmanuel7, Juma Jane7, Mailu Eunice7, Omore Richard7, O'Reilly Ciara E.10, Hannis James11, Manalili Sheri11, DeLeon Jonna11, Yasuda Irene11, Blyn Lawrence11, Ranken Raymond11, Li Feng11, Housley Roberta11, Ecker David J.11, Hossain M. Anowar6, Breiman Robert F.7, Morris J. Glenn5, McDaniel Timothy K.9, Parkhill Julian4, Saha Debasish3, Sampath Rangarajan11, Stine O. Colin1, Nataro James P.12
Affiliation:
1. University of Maryland, School of Medicine, Baltimore, Maryland, USA 2. University of Maryland, College Park, Maryland, USA 3. Medical Research Council Unit, Serrekunda, The Gambia 4. Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom 5. University of Florida, Gainesville, Florida, USA 6. International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh 7. CDC/Kenya Medical Research Institute Research Station, Kisumu, Kenya 8. Center for Vaccine Development, Bamako, Mali 9. Illumina, San Diego, California, USA 10. Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA 11. Ibis, San Diego, California, USA 12. University of Virginia, Charlottesville, Virginia, USA
Abstract
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.
Publisher
American Society for Microbiology
Subject
Microbiology (medical)
Cited by
22 articles.
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