Comparison of four DNA extraction and three preservation protocols for the molecular detection and quantification of soil-transmitted helminths in stool

Background

A DNA extraction and preservation protocol that yields sufficient and qualitative DNA is pivotal for the success of any nucleic acid amplification test (NAAT), but it still poses a challenge for soil-transmitted helminths (STHs), including Ascaris lumbricoides, Trichuris trichiura and the two hookworms (Necator americanus and Ancylostoma duodenale). In the present study, we assessed the impact of different DNA extraction and preservativation protocols on STH-specific DNA amplification from stool.

Methodology and principal findings

In a first experiment, DNA was extracted from 37 stool samples with variable egg counts for T. trichiura and N. americanus applying two commercial kits, both with and without a prior bead beating step. The DNA concentration of T. trichiura and N. americanus was estimated by means of qPCR. The results showed clear differences in DNA concentration across both DNA extraction kits, which varied across both STHs. They also indicated that adding a bead beating step substantially improved DNA recovery, particularly when the FECs were high. In a second experiment, 20 stool samples with variable egg counts for A. lumbricoides, T. trichiura and N. americanus were preserved in either 96% ethanol, 5% potassium dichromate or RNAlater and were stored at 4°C for 65, 245 and 425 days. DNA was extracted using the DNeasy Blood & Tissue kit with a bead beating step. Stool samples preserved in ethanol proved to yield higher DNA concentrations as FEC increased, although stool samples appeared to be stable over time in all preservatives.

Conclusions

The choice of DNA extraction kit significantly affects the outcome of NAATs. Given the clear benefit of bead beating and our validation of ethanol for (long-term) preservation, we recommend that these aspects of the protocol should be adopted by any stool sampling and DNA extraction protocol for downstream NAAT-based detection and quantification of STHs.

DNA-based tools are increasingly being used for the diagnosis of intestinal worm infections in both clinical and research laboratories. However, recovering DNA from intestinal worm eggs in stool remains a challenge since this DNA is protected by a very rigid egg shell. Furthermore, stool contains inhibitors that can affect test results and these should be removed during DNA extraction. Prior to DNA extraction, samples are often preserved, but the impact of the type of preservatives and the duration of preservation remains poorly studied. In the present study, we assessed the impact of four DNA extraction and three preservation protocols on the downstream performance of a DNA-based diagnostic tool for intestinal worms. We found significant differences in DNA recovery across the DNA and preservation protocols, but DNA from worm eggs in stool proved to be stable over time in all preservatives.

Isothermal diagnostic assays for the detection of soil-transmitted helminths based on the SmartAmp2 method

Background

Diagnosis of soil-transmitted helminths (STHs) has traditionally relied on stool microscopy, which has a number of critical deficiencies. Molecular diagnostics are powerful tools to identify closely related species, but the requirement for costly equipment makes their implementation difficult in low-resource or field settings. Rapid, sensitive and cost-effective diagnostic tools are crucial for accurate estimation of STH infection intensity in MDA programmes in which the goal is to reduce morbidity following repeated rounds of chemotherapy.

Results

In this study, colourimetric isothermal assays were developed using SmartAmp2 primer sets and reagents in loop-mediated amplification (LAMP) assays. Species-specific primer sets, designed on a specific target sequence in the β-tubulin gene, were used to identify Necator americanus, Trichuris trichiura and Ascaris lumbricoides. After initial optimization on control plasmids and genomic DNA from adult worms, assays were evaluated on field samples. Assays showed high sensitivity and demonstrated high tolerance to inhibitors in spiked faecal samples. Rapid and sensitive colourimetric assays were successfully developed to identify the STHs in field samples using hydroxy napthol blue (HNB) dye.

Conclusions

Rapid and simple colourimetric diagnostic assays, using the SmartAmp2 method, were developed, with the potential to be applied in the field for detection of STH infections and the estimation of response to treatment. However, further validation on large numbers of field samples is needed.

Electronic supplementary material

The online version of this article (10.1186/s13071-017-2420-1) contains supplementary material, which is available to authorized users.

Isothermal Diagnostic Assays for Monitoring Single Nucleotide Polymorphisms in Necator americanus Associated with Benzimidazole Drug Resistance

BACKGROUND

Soil-transmitted helminths (STHs) are the most prevalent intestinal helminths of humans, and a major cause of morbidity in tropical and subtropical countries. The benzimidazole (BZ) drugs albendazole (ABZ) and mebendazole (MBZ) are used for treatment of human STH infections and this use is increasing dramatically with massive drug donations. Frequent and prolonged use of these drugs could lead to the emergence of anthelmintic resistance as has occurred in nematodes of livestock. Previous molecular assays for putative resistance mutations have been based mainly on PCR amplification and sequencing. However, these techniques are complicated and time consuming and not suitable for resource-constrained situations. A simple, rapid and sensitive genotyping method is required to monitor for possible developing resistance to BZ drugs.

METHODS

To address this problem, single nucleotide polymorphism (SNP) detection assays were developed based on the Smart amplification method (SmartAmp2) to target codons 167, 198, and 200 in the β-tubulin isotype 1 gene for the hookworm Necator americanus.

FINDINGS

Diagnostic assays were developed and applied to analyze hookworm samples by both SmartAmp2 and conventional sequencing methods and the results showed high concordance. Additionally, fecal samples spiked with N. americanus larvae were assessed and the results showed that the Aac polymerase used has high tolerance to inhibitors in fecal samples.

CONCLUSION

The N. americanus SmartAmp2 SNP detection assay is a new genotyping tool that is rapid, sensitive, highly specific and efficient with the potential to be used as a field tool for monitoring SNPs associated with BZ resistance. However, further validation on large numbers of field samples is required.

Effect of repeated doses of dexamethasone on the incidence and severity of respiratory distress syndrome in multifetal gestation between 24 and 34 weeks

The objective of the study was to evaluate the effects of antenatal corticosteroid therapy in multiple pregnancy on the incidence and severity of respiratory distress syndrome (RDS). Twenty-two women with twin, 12 with triplet and 2 with quadruplet pregnancies and an emergency group of 20 mothers with twin pregnancies, who only had one course of dexamethasone, were compared with controls. Corticosteroid therapy was associated with a reduction in moderate to severe RDS in all groups (twins p < 0.01, triplets and quadruplets p < 0.008) and the emergency group with dexamethasone therapy (p < 0.036) when compared to their individual controls. Dexamethasone reduced the duration of stay in the neonatal intensive care unit of the emergency twin group (p < 0.01). Neonatal birth weights were significantly less in all groups treated with repeated doses in comparison to the controls.

Retinopathy of prematurity: mutations in the Norrie disease gene and the risk of progression to advanced stages

BACKGROUND

Retinopathy of prematurity (ROP) is a retinal vascular disease that occurs in infants with short gestational age and low birth weight and may lead to retinal detachment and blindness. Missense mutations in the Norrie disease (ND) gene have been associated with the risk of progression to advanced stages in cases of ROP from the US and also in clinically similar ND and familial exudative vitreoretinopathy.

METHODS

We have screened two ND gene mutations, namely A105T and Val60Glu, by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and allele-specific PCR methods, respectively, in 210 Kuwaiti premature newborns to replicate these findings in a different ethnic group.

RESULTS

In the Kuwaiti premature newborn cohort, 115 of 210 babies had no eye problems and served as controls, while 95 were cases of ROP. In 71 of 95 ROP cases, the disease regressed spontaneously on or before stage 3, while in 24 of 95 ROP cases the disease progressed to advanced stages 4 and 5. In case of missense mutation (A105T), the AA genotype was detected in 96% of controls compared with 87% of ROP cases (NS); similarly no significant difference was found between spontaneously regressed ROP cases and those who progressed to advanced stages. For the Val60Glu mutation, no significant association was detected between the genotype and progression of ROP to advanced stages.

CONCLUSIONS

Unlike data from the US, our findings from a Kuwaiti cohort of ROP cases and controls suggest a lack of association between the two ND gene mutations (A105T and Val60Glu) and ROP and the risk of progression of the disease to advanced stages.

Retinopathy of prematurity in infants with birth weight above 1500 grams

OBJECTIVE

To identify the rate and prognosis of retinopathy of prematurity (ROP) among newborn infants of birthweight of above 1500 grams, and the possible risk factors associated with the disease.

DESIGN

A prospective cohort study.

SETTING

Neonatal unit at Maternity Hospital, Kuwait city, Kuwait.

METHODS

All low birth weight infants were examined for the presence of ROP in the period between January 1996 to December 1997. Prospective collection of data on babies who were above 1500 grams was done to find an association between the disease in these babies and some of the maternal and neonatal risk factors.

RESULTS

A total of 68 babies of birth weight above 1500 grams were screened for ROP out of which 13 (19.1%) had different stages of the disease. None of the patients had threshold disease requiring surgery. Among the risk factors chosen, oxygen therapy, presence of hypotension at birth and the non-use of surfactant were the only risk factors to be associated with disease. However, with logistic regression analysis, none of these were independently associated with ROP.

CONCLUSION

ROP may occur in newborn infants of larger birthweight but with good prognosis, and oxygen therapy seems to predispose to the disease.

Threshold stage of retinopathy of prematurity: maternal and neonatal risk factors

BACKGROUND

The aim of this study was to review the maternal and neonatal risk factors associated with retinopathy of prematurity (ROP) and the threshold stage of the disease.

PATIENTS AND METHODS

In this prospective cohort study, all preterm infants of less than 1501 g birth weight were screened for ROP between January 1996 and December 1997 at the neonatal unit of the Maternity Hospital in Kuwait. The rate of the threshold stage of ROP, as well as risk factors associated with the disease, were identified.

RESULTS

A total of 234 babies were screened for ROP, of which 151 (64.5%) developed the disease and 34 (14.5%) had the threshold stage of ROP. Several factors were found to be associated with ROP and threshold ROP. Stepwise regression analysis revealed that low birth weight (P<0.002) and exposure to high oxygen concentration (P<0.0001) were independently associated with ROP. In addition, low birth weight (P<0.006), high oxygen concentration (P<0.003), and culture-proven sepsis (P<0.04) were found to be independent predictors of threshold ROP.

CONCLUSION

Apart from low birth weight and exposure to high oxygen therapy, which are well-documented risk factors of ROP, septicemia was also found to be associated with the threshold stage of ROP.

Missense mutations in norrie disease gene are not associated with advanced stages of retinopathy of prematurity in Kuwaiti arabs

Retinopathy of prematurity (ROP) is a disease characterized by retinal neovascularization, possibly leading to retinal detachment and finally blindness. In a proportion of ROP cases, the disease progresses to advanced stages despite rigorous intervention. Missense mutations of the Norrie disease (ND) gene have been associated with progression of the disease in ROP cases from the USA. We have investigated the presence of ND gene mutations in 102 premature newborns of Kuwaiti Arab origin to replicate this finding in a different population/racial group. 56 (55%) of these newborns had normal eyes and served as controls. In 35 (34%) cases, the ROP regressed spontaneously during stage 1-3. In 11 (11%) cases, ROP progressed to advanced stages. A PCR-RFLP method was used to detect the mutations in exon 3 of the ND gene and confirmed the DNA sequence by direct sequencing of the PCR product. The [R121W] mutation of the ND gene was not detected in the premature newborns screened from our Kuwaiti population/group. For the second mutation [L108P], a genotype (PP) was present in 98% of the premature newborns screened and only in 1 of 56 normal infants was the (LL) genotype detected. Our population is genetically homogenous in that genotype (PP) was detected at codon 108 in almost all controls and ROP cases. We did not find an association between the presence or absence of missense mutations of the ND gene and the risk of severe ROP.