Urban versus rural prevalence of intestinal parasites using multi-parallel qPCR in Colombia

Bryan, Patricia; Romero, Marcela; Sánchez, Miryan M; Torres, Giovanny; Gómez, Wilber; Restrepo, Marcos I.; Restrepo, Alejandro; Mejia, Rojelio

doi:10.1101/2020.09.20.20197616

Cited by 3 publications

References 12 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

Confirmation of multi-parallel quantitative real-time PCR as the gold standard for detecting soil-transmitted helminths in stool

Papaiakovou

Pilotte

Dunn

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

Due to its simplicity and cost-effectiveness, microscopy has seen extensive field-use as the diagnostic standard for the detection of soil-transmitted helminths (STH) in stool samples. However, the sensitivity of microscopy-based detection is inadequate in reduced-transmission settings where worm burden is oftentimes low. Equally problematic, eggs of closely related species oftentimes have indistinguishable morphologies, leading to species misidentification. In light of these shortcomings, the purpose of this study was to demonstrate multi-parallel quantitative real-time PCR (qPCR) as the new “gold standard” for STH detection. Accordingly, stool samples from non-endemic participants were spiked with limited numbers of eggs or larvae (1 to 40) of five different species of STH. DNA extracts were tested using two unique multi-parallel real-time PCR-based diagnostic methods. These methods employed different target sequences (ribosomal internal transcribed spacer, or highly repetitive non-coding regions), to evaluate the detection of DNA from as little as one egg per sample. There was a statistically significant kendall correlation between egg/larvae counts and qPCR from both methods for Trichuris trichiura (0.86 and 0.872 for NHM and Baylor assays) and a strong correlation (0.602 and 0.631 for NHM and Baylor assays, respectively) for Ascaris lumbricoides. Less strong but still significant was the Kendall Tau-b value for A. duodenale (0.408 for both) and for S. stercoralis (0.483 and 0.653, respectively). In addition, using field stool samples from rural Argentina both assays had fair to moderate kappa agreement (0.329-0.454), except for Strongyloides stercoralis (0.121) that both assays had slight agreement. In spite of the small cohort of samples, both qPCR assays, targeting of two independent genomic regions, provided reproducible results and we believe that, low cost multi-parallel quantitative real-time PCR-based diagnostics should supplant microscopy as the new gold standard for stool-based detection of soil transmitted helminths in public-health and community settings.

show abstract

Confirmation of multi-parallel quantitative real-time PCR as the gold standard for detecting soil-transmitted helminths in stool

Papaiakovou

Pilotte

Dunn

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

Intestinal microbiota changes due toGiardia intestinalisinfections in a longitudinal Ecuadorian birth cohort and impact on cobalamin biosynthesis

Damania,

Arévalo-Cortés,

Lopez

et al. 2024

Preprint

View full text Add to dashboard Cite

Background Giardia intestinalis is a protozoal parasite infecting the gastrointestinal tract worldwide. Chronic infections/reinfections are common, with adverse nutritional consequences for critical growth during the first five years of life. Vitamin B12 (cobalamin) is absorbed primarily in the ileum of the small intestine, where Giardia trophozoites attach and replicate. Bacteria activate bioavailable vitamin B12, which is essential for human DNA synthesis and development. A disturbance in cobalamin biosynthesis caused by giardiasis may contribute to impairment of childhood development and growth. Methodology/Principal Findings We performed a longitudinal analysis on 61 Ecuadorian children using multi-parallel real-time quantitative PCR and whole genome sequencing. Children had increased Giardia DNA burden from ages 3 to 5 (p = 0.0012) and 7.58 times more frequent Giardia infections (1.31 to 34.33, P = 0.0176). There was an increased alpha diversity/ Giardia fg/µl in three-year-olds compared to age-matched non-infected (30.20 vs 4.37, p = 0.050), but decreased alpha diversity/ Giardia fg/µl in five-year-olds compared to age-matched non-infected children (0.21 vs 4.31, p = 0.021). Alpha diversity/ Giardia fg/µl was also decreased in samples collected longitudinally from the same children at five compared to 3 years (p = 0.031). Cobalt transport protein (CbiN) (FDR < 0.003) and IPR011822 (Cobalamin-dependent methionine synthase) sequences were decreased in infected children (p < 0.002) and among those with greatest Giardia burdens (p < 0.001). Conclusion/Significance Giardia intestinalis infection may affect bacterial diversity in the ileum where vitamin B12 is activated, as suggested by a reduced proportion of Cobalt transport protein component (CbiN) gene sequences in the gut microbiome of infected children. These findings are potentially important to our understanding of how Giardia infections may affect childhood growth.

show abstract

Epidemiological and Molecular Characterization of Blastocystis Infection in Children Attending Daycare Centers in Medellín, Colombia

Osorio-Pulgarin

Higuera

Beltrán-Alzate

et al. 2021

Biology

View full text Add to dashboard Cite

Background: The present study aims to perform an epidemiological and molecular characterization of Blastocystis infection in a child population attending daycare centers of Medellín, Colombia. Methods: A total of 265 children aged 0–5 years were enrolled in five children’s centers in urban sectors of Medellín, northwestern Colombia. Stool samples were taken to identify intestinal parasites by direct examination, Ritchie–Frick concentration, and molecular identification of Blastocystis by conventional PCR and subtype (ST) identification by PCR barcoding with subsequent phylogenetic reconstruction. Kappa index was calculated to evaluate the agreement between microscopy and PCR for the diagnosis of Blastocystis. Results: The prevalence of intestinal protozoa was 36.6% (97/265), with Blastocystis as the most frequent parasitic protozoan at 15.8% (42/265), followed by Giardia intestinalis at 15.5% (41/265) and Endolimax nana at 15.1% (40/265). The prevalence of Blastocystis by PCR was 53.2% (141/265), the subtypes identified were ST3 at 30.5% (18/59), ST2 at 23.7% (14/59), ST1 at 20.3% (12/59), and with less frequency, ST4 at 5.1% (3/59), ST6 at 1.7% (1/59) and ST16 at 15.3% (9/59) allele 162. Conclusion: This study provides the first genetic characterization of Blastocystis subtypes circulating in a population of Medellín, Colombia, and also updates the epidemiology of Blastocystis subtypes in the world with the first identification of ST16 in humans.

show abstract

Urban versus rural prevalence of intestinal parasites using multi-parallel qPCR in Colombia

Cited by 3 publications

References 12 publications

Confirmation of multi-parallel quantitative real-time PCR as the gold standard for detecting soil-transmitted helminths in stool

Confirmation of multi-parallel quantitative real-time PCR as the gold standard for detecting soil-transmitted helminths in stool

Intestinal microbiota changes due toGiardia intestinalisinfections in a longitudinal Ecuadorian birth cohort and impact on cobalamin biosynthesis

Epidemiological and Molecular Characterization of Blastocystis Infection in Children Attending Daycare Centers in Medellín, Colombia

Contact Info

Product

Resources

About