Diagnostic Microbiologic Methods in the GEMS-1 Case/Control Study

Panchalingam, Sandra; Antonio, Martín; Hossain, Ahmed; Mandomando, Inácio; Ochieng, Ben; Oundo, Joseph; Ramamurthy, Thandavarayan; Tamboura, Boubou; Zaidi, Anita K. M.; Petri, William A.; Houpt, Eric R.; Murray, Patrick R.; Prado, Valeria; Vidal, Roberto; Steele, Duncan; Strockbine, Nancy; Sansonetti, Philippe J.; Glass, Roger I.; Robins-Browne, Roy M.; Tauschek, Marija; Svennerholm, A. M.; Kotloff, Karen L.; Levine, Myron M.; Nataro, James P.

doi:10.1093/cid/cis754

Cited by 177 publications

(210 citation statements)

References 15 publications

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“…Stool specimens were handled following the GEMS protocol (14). The specimens were collected in sterile containers, kept at 2 to 8°C while in transit, and examined within 24 h (Ͻ6 h between evacuation and placement into transport medium, which was made weekly, and Ͻ18 h before the transport swab inoculated the culture plates).…”

Section: Methodsmentioning

confidence: 99%

Quantitative PCR for Detection of Shigella Improves Ascertainment of Shigella Burden in Children with Moderate-to-Severe Diarrhea in Low-Income Countries

et al. 2013

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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 <59 months from the Gambia, Mali, Kenya, and Bangladesh, with or without moderate-to-severe diarrhea (MSD). We compared the results from conventional culture to those from qPCR for the Shigella ipaH gene. Using MSD as the reference standard, we determined the optimal cutpoint to be 2.9 ؋ 10 4 ipaH copies per 100 ng of stool DNA for set 1 (n ‫؍‬ 877). One hundred fifty-eight (18%) specimens yielded >2.9 ؋ 10 4 ipaH copies. Ninety (10%) specimens were positive by traditional culture for Shigella. Individuals with >2.9 ؋ 10 4 ipaH copies have 5.6-times-higher odds of having diarrhea than those with <2.9 ؋ 10 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 ؋ 10 4 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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Section: Methodsmentioning

confidence: 99%

Quantitative PCR for Detection of Shigella Improves Ascertainment of Shigella Burden in Children with Moderate-to-Severe Diarrhea in Low-Income Countries

et al. 2013

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“…were identified by PCR as previously described [10][11][12]. DEC, in particular enteroagreggative (EAEC), enterotoxigenic (ETEC) and enteropathogenic E. coli (EPEC) were identified by multiplex PCR as previously described [13].…”

Section: Pathogen Detectionmentioning

confidence: 99%

Etiology, epidemiology and clinical characteristics of acute diarrhea in hospitalized children in rural Peru

Cornejo-Tapia

Orellana-Peralta

Weilg

et al. 2017

J Infect Dev Ctries

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Introduction: Diarrhea remains one of the main causes of morbidity and mortality in children under five years of age especially in low-income countries. In Peru, epidemiological reports about enteropathogens related to acute diarrhea are scarce in rural areas. The aim of this study was to describe the etiology, epidemiology, and clinical characteristics of the principal causes of acute infectious diarrhea in in a northern rural region of Peru. Methodology: A prospective study was conducted from January 2011 to December 2012 to describe the main pathogens causing acute diarrhea using PCR assay. Results: A total of 117 children diagnosed with acute diarrhea were included in the study. A single etiological agent was identified in 41.03% of samples, being rotavirus followed by norovirus and Shigella. Co-infections containing virus and bacteria were found in 22.22% of samples. Vomiting was most commonly found symptoms in 58.97% cases followed by fever (54.70%). Malnutrition was detected in 14.53% of the children. Conclusions: High prevalence of rotavirus, as well as adenovirus and norovirus, was observed in the present study. Shigella was the most common bacteria found in acute diarrhea in the area. The implementation of a better surveillance system is mandatory in order to identify the principal etiologies of gastroenteritis in the rural areas of Peru and to develop of better prevention strategies and reduce diarrhea-associated mortalities.

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“…In GEMS, an extensive workup for a wide array of putative and established viral, bacterial, and protozoal diarrheal pathogens was undertaken on each case and control specimen at the local site laboratories, as described by Panchalingam and others. 11 These laboratories followed standard protocols, which were ensured by site supervisors and site visits by study personnel. Rigorous quality control and quality assurance procedures were implemented to ensure robustness of procedures.…”

Section: Methodsmentioning

confidence: 99%

Aeromonas-Associated Diarrhea in Children Under 5 Years: The GEMS Experience

Qamar

Nisar

Quadri

et al. 2016

The American Society of Tropical Medicine and Hygiene

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Abstract. We report the clinical findings, epidemiology, and risk factors for moderate-to-severe diarrhea (MSD) associated with Aeromonas species in children 0-59 months of age, from the Global Enteric Multicenter Study, conducted at three sites in south Asia and four sites in sub-Saharan Africa. Children with MSD were enrolled along with controls matched for age, gender, and neighborhood. Pooled, age-stratified conditional logistic regression models were applied to evaluate the association of Aeromonas infection controlling for coinfecting pathogens and sociodemographic variables. A pooled, age-stratified, multivariate logistic regression analysis was done to identify risk factors associated with Aeromonas positivity in MSD cases. A total of 12,110 cases and 17,291 matched controls were enrolled over a period of 48 months. Aeromonas was identified as a significant pathogen in 736 cases of MSD in Pakistan and Bangladesh (22.2%). Aeromonas remained a significant pathogen even after adjustment for the presence of other pathogens and sociodemographic factors. Odds ratio (OR) for Aeromonas were higher in the presence of Shigella (matched OR: 6.2, 95% confidence interval [CI]: 1.9-20.2). Cases of Aeromonas were likely to present with dysentery, particularly in the 0-11 months (OR: 1.4, 95% CI 1.0-2.0) and 12-23 months (OR: 1.8, 95% CI: 1.3-2.5) age group. The odds of Aeromonas increased with increasing degree of stunting, being highest for severe stunting (OR: 10

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Diagnostic Microbiologic Methods in the GEMS-1 Case/Control Study

Cited by 177 publications

References 15 publications

Quantitative PCR for Detection of Shigella Improves Ascertainment of Shigella Burden in Children with Moderate-to-Severe Diarrhea in Low-Income Countries

Quantitative PCR for Detection of Shigella Improves Ascertainment of Shigella Burden in Children with Moderate-to-Severe Diarrhea in Low-Income Countries

Etiology, epidemiology and clinical characteristics of acute diarrhea in hospitalized children in rural Peru

Aeromonas-Associated Diarrhea in Children Under 5 Years: The GEMS Experience

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