Quantitative PCR for detection of Shigella improves ascertainment of Shigella burden in children with moderate-to-severe diarrhea in low-income countries

Brianna Lindsay, John B. Ochieng, Usman N. Ikumapayi, Aliou Toure, Dilruba Ahmed, Shan Li, Sandra Panchalingam, Myron M. Levine, Karen Kotloff, David A. Rasko, Carolyn R. Morris, Jane Juma, Barry S. Fields, Michel Dione, Dramane Malle, Stephen M. Becker, Eric R. Houpt, James P. Nataro, Halvor Sommerfelt, Mihai Pop & 5 others Joe Oundo, Martin Antonio, Anowar Hossain, Boubou Tamboura, O. Colin Stine

Research output: Contribution to journalArticle

Abstract

Estimates of the prevalence of Shigella spp. are limited by the suboptimal sensitivity of current diagnostic and surveillance methods. We used a quantitative PCR (qPCR) assay to detect Shigella in the stool samples of 3,533 children aged 4 ipaH copies per 100 ng of stool DNA for set 1 (n = 877). One hundred fifty-eight (18%) specimens yielded >2.9 × 104 ipaH copies. Ninety (10%) specimens were positive by traditional culture for Shigella. Individuals with ≥2.9 × 104 ipaH copies have 5.6-times-higher odds of having diarrhea than those with 4 ipaH copies (95% confidence interval, 3.7 to 8.5; P <0.0001). Nearly identical results were found using an independent set of samples. qPCR detected 155 additional MSD cases with high copy numbers of ipaH, a 90% increase from the 172 cases detected by culture in both samples. Among a subset (n = 2,874) comprising MSD cases and their age-, gender-, and location-matched controls, the fraction of MSD cases that were attributable to Shigella infection increased from 9.6% (n = 129) for culture to 17.6% (n = 262) for qPCR when employing our cutpoint. We suggest that qPCR with a cutpoint of approximately 1.4 × 104 ipaH copies be the new reference standard for the detection and diagnosis of shigellosis in children in low-income countries. The acceptance of this new standard would substantially increase the fraction of MSD cases that are attributable to Shigella.

Original languageEnglish (US)
Pages (from-to)1740-1746
Number of pages7
JournalJournal of Clinical Microbiology
Volume51
Issue number6
DOIs
StatePublished - Jun 2013
Externally publishedYes

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Shigella
Diarrhea
Polymerase Chain Reaction
Bacillary Dysentery
Confidence Intervals
DNA
Infection

ASJC Scopus subject areas

  • Microbiology (medical)

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Quantitative PCR for detection of Shigella improves ascertainment of Shigella burden in children with moderate-to-severe diarrhea in low-income countries. / Lindsay, Brianna; Ochieng, John B.; Ikumapayi, Usman N.; Toure, Aliou; Ahmed, Dilruba; Li, Shan; Panchalingam, Sandra; Levine, Myron M.; Kotloff, Karen; Rasko, David A.; Morris, Carolyn R.; Juma, Jane; Fields, Barry S.; Dione, Michel; Malle, Dramane; Becker, Stephen M.; Houpt, Eric R.; Nataro, James P.; Sommerfelt, Halvor; Pop, Mihai; Oundo, Joe; Antonio, Martin; Hossain, Anowar; Tamboura, Boubou; Stine, O. Colin.

In: Journal of Clinical Microbiology, Vol. 51, No. 6, 06.2013, p. 1740-1746.

Research output: Contribution to journalArticle

Lindsay, B, Ochieng, JB, Ikumapayi, UN, Toure, A, Ahmed, D, Li, S, Panchalingam, S, Levine, MM, Kotloff, K, Rasko, DA, Morris, CR, Juma, J, Fields, BS, Dione, M, Malle, D, Becker, SM, Houpt, ER, Nataro, JP, Sommerfelt, H, Pop, M, Oundo, J, Antonio, M, Hossain, A, Tamboura, B & Stine, OC 2013, 'Quantitative PCR for detection of Shigella improves ascertainment of Shigella burden in children with moderate-to-severe diarrhea in low-income countries', Journal of Clinical Microbiology, vol. 51, no. 6, pp. 1740-1746. https://doi.org/10.1128/JCM.02713-12
Lindsay, Brianna ; Ochieng, John B. ; Ikumapayi, Usman N. ; Toure, Aliou ; Ahmed, Dilruba ; Li, Shan ; Panchalingam, Sandra ; Levine, Myron M. ; Kotloff, Karen ; Rasko, David A. ; Morris, Carolyn R. ; Juma, Jane ; Fields, Barry S. ; Dione, Michel ; Malle, Dramane ; Becker, Stephen M. ; Houpt, Eric R. ; Nataro, James P. ; Sommerfelt, Halvor ; Pop, Mihai ; Oundo, Joe ; Antonio, Martin ; Hossain, Anowar ; Tamboura, Boubou ; Stine, O. Colin. / Quantitative PCR for detection of Shigella improves ascertainment of Shigella burden in children with moderate-to-severe diarrhea in low-income countries. In: Journal of Clinical Microbiology. 2013 ; Vol. 51, No. 6. pp. 1740-1746.
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T1 - Quantitative PCR for detection of Shigella improves ascertainment of Shigella burden in children with moderate-to-severe diarrhea in low-income countries

AU - Lindsay, Brianna

AU - Ochieng, John B.

AU - Ikumapayi, Usman N.

AU - Toure, Aliou

AU - Ahmed, Dilruba

AU - Li, Shan

AU - Panchalingam, Sandra

AU - Levine, Myron M.

AU - Kotloff, Karen

AU - Rasko, David A.

AU - Morris, Carolyn R.

AU - Juma, Jane

AU - Fields, Barry S.

AU - Dione, Michel

AU - Malle, Dramane

AU - Becker, Stephen M.

AU - Houpt, Eric R.

AU - Nataro, James P.

AU - Sommerfelt, Halvor

AU - Pop, Mihai

AU - Oundo, Joe

AU - Antonio, Martin

AU - Hossain, Anowar

AU - Tamboura, Boubou

AU - Stine, O. Colin

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N2 - Estimates of the prevalence of Shigella spp. are limited by the suboptimal sensitivity of current diagnostic and surveillance methods. We used a quantitative PCR (qPCR) assay to detect Shigella in the stool samples of 3,533 children aged 4 ipaH copies per 100 ng of stool DNA for set 1 (n = 877). One hundred fifty-eight (18%) specimens yielded >2.9 × 104 ipaH copies. Ninety (10%) specimens were positive by traditional culture for Shigella. Individuals with ≥2.9 × 104 ipaH copies have 5.6-times-higher odds of having diarrhea than those with 4 ipaH copies (95% confidence interval, 3.7 to 8.5; P <0.0001). Nearly identical results were found using an independent set of samples. qPCR detected 155 additional MSD cases with high copy numbers of ipaH, a 90% increase from the 172 cases detected by culture in both samples. Among a subset (n = 2,874) comprising MSD cases and their age-, gender-, and location-matched controls, the fraction of MSD cases that were attributable to Shigella infection increased from 9.6% (n = 129) for culture to 17.6% (n = 262) for qPCR when employing our cutpoint. We suggest that qPCR with a cutpoint of approximately 1.4 × 104 ipaH copies be the new reference standard for the detection and diagnosis of shigellosis in children in low-income countries. The acceptance of this new standard would substantially increase the fraction of MSD cases that are attributable to Shigella.

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