Validation and application of high-throughput quantitative PCR for the simultaneous detection of microbial source tracking markers in environmental water

No single microbial source tracking (MST) marker can be applied to determine the sources of fecal pollution in all water types. This study aimed to validate a high-throughput quantitative polymerase chain reaction (HT-qPCR) method for the simultaneous detection of multiple MST markers. A total of 26 fecal-source samples that had been previously collected from human sewage (n = 6) and ruminant (n = 3), dog (n = 6), pig (n = 6), chicken (n = 3), and duck (n = 2) feces in the Kathmandu Valley, Nepal, were used to validate 10 host-specific MST markers, i.e., Bacteroidales (BacHum, gyrB, BacR, and Pig2Bac), mitochondrial DNA (mtDNA) (swine, bovine, and Dog-mtDNA), and viral (human adenovirus, porcine adenovirus, and chicken/turkey parvovirus) markers, via HT-qPCR. Only Dog-mtDNA showed 100 % accuracy. All the tested bacterial markers showed a sensitivity of 100 %. Nine of the 10 markers were further used to identify fecal contamination in groundwater sources (n = 54), tanker filling stations (n = 14), drinking water treatment plants (n = 5), and river water samples (n = 6). The human-specific Bacteroidales marker BacHum and ruminant-specific Bacteroidales marker BacR was detected at a high ratio in river water samples (83 % and 100 %, respectively). The results of HT-qPCR were in agreement with the standard qPCR. The comparable performances of HT-qPCR and standard qPCR as well as the successful detection of MST markers in the fecal-source and water samples demonstrated the potential applicability of these markers for detecting fecal contamination sources via HT-qPCR.

Drinking Water Quality and Public Health in the Kathmandu Valley, Nepal: Coliform Bacteria, Chemical Contaminants, and Health Status of Consumers

Residents of Nepal’s Kathmandu Valley draw drinking water from tube wells, dug wells, and stone spouts, all of which have been reported to have serious water quality issues. In this study, we analyzed drinking water samples from 35 tube wells, dug wells, stone spouts, and municipal tap water for bacterial and chemical contaminants, including total and fecal coliform, aluminum, arsenic, barium, beryllium, boron, cadmium, cobalt, chromium, copper, fluoride, iron, mercury, manganese, molybdenum, nickel, lead, antimony, selenium, thallium, uranium, vanadium, and zinc. We also asked a sampling of households who used these specific water sources to rate the taste of their water, list any waterborne diseases they were aware of, and share basic health information about household members. This survey provided us with information from 146 households and 603 individuals. We found widespread bacterial contamination of water sources, with 94% of sources having detectable total or fecal coliform. Nepal Drinking Water Quality Standards and World Health Organization (WHO) Drinking-Water Guidelines or health-based values were exceeded for aluminum (max = 0.53 mg/L), arsenic (max = 0.071 mg/L), iron (max = 7.22 mg/L), and manganese (max = 3.229 mg/L). The distribution of water sources with high arsenic, iron, and manganese appeared to be associated with floodplain deposits. Mixed effects logistic regression models were used to examine the interactions between social factors and water contaminants and their effects on household members’ health. Consumers of water sources with both high and low concentrations of manganese were less likely to have a positive attitude towards school than those whose water sources had moderate concentrations of manganese. Social factors, especially education, played a large role in predicting individual health outcomes. Household taste ratings of drinking water were not correlated with iron or manganese concentrations, suggesting that WHO’s reliance on aesthetic criteria for these contaminants instead of formal drinking-water guidelines may not be sufficient to protect public health.

Bacteriological Analysis of Household Water at the Source and Point of Consumption at Karwar, India

Access to safe drinking water is the key to promoting good health. At Karwar, the primary source of drinking water is well, but heavy rain, and deficiencies in underground drainage systems result in well water contamination. However, water handling practices followed at the point of consumption act as a better predictor of water contamination. To assess and compare the bacteriological quality of household water at the source and point of consumption. A prospective cross-sectional study was conducted at Karwar. Households owning private wells were selected by Simple Random Sampling. Semi-structured questionnaires were used to interview the households regarding socioeconomic status (SES), chlorination of well, purification method, and water handling practices. Presumptive coliform count and the differential coliform count were determined. Data thus obtained were analyzed using a Microsoft Excel. c2-test was used to see the association between variables. The present study included 30 households. All the samples taken from the well revealed contamination with E. coli. 80% of samples from the point of consumption revealed coliforms, among which 47% were confirmed with E. coli. RO/RO+UV were found to be relatively better performing than the filtration and boiling methods. Contamination of water at the point of consumption had a significant association with both purification and water retrieval methods. The samples taken from the point of consumption reflect better quality of water sampling than source water. The present study revealed post-collection contamination as major reason for compromising water quality despite improved water cleaning and purification techniques.

A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality

Nucleic acid based techniques, such as quantitative PCR (qPCR) and next generation sequencing (NGS), provide new insights into microbial water quality, but considerable uncertainty remains around their correct interpretation. We demonstrate, for different water sources in informal settlements in the Kathmandu Valley, Nepal, significant Spearman rank correlations between conventional and molecular microbiology methods that indicate faecal contamination. At family and genera level, 16S rRNA amplicon sequencing results obtained with the low-cost, portable next generation sequencer MinION from Oxford Nanopore Technologies had significant Spearman rank correlations with Illumina MiSeq sequencing results. However, method validation by amplicon sequencing of a MOCK microbial community revealed the need to ascertain MinION sequencing results for putative pathogens at species level with complementary qPCR assays. Vibrio cholerae hazards were poorly associated with plate count faecal coliforms, but flagged up by the MinION screening method, and confirmed by a qPCR assay. Plate counting methods remain important to assess viability of faecal coliforms in disinfected water sources. We outline a systematic approach for data collection and interpretation of such complementary results. In the Kathmandu Valley, there is high variability of water quality from different sources, including for treated water samples, illustrating the importance of disinfection at the point of use.

A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality

Nucleic acid based techniques, such as quantitative PCR (qPCR) and next generation sequencing (NGS), provide new insights into microbial water quality, but considerable uncertainty remains around their correct interpretation. We demonstrate, for different water sources in informal settlements in the Kathmandu Valley, Nepal, significant Spearman rank correlations between conventional and molecular microbiology methods that indicate faecal contamination. At family and genera level, 16S rRNA amplicon sequencing results obtained with the low-cost, portable next generation sequencer MinION from Oxford Nanopore Technologies had significant Spearman rank correlations with Illumina MiSeq sequencing results. However, method validation by amplicon sequencing of a MOCK microbial community revealed the need to ascertain MinION sequencing results for putative pathogens at species level with complementary qPCR assays. Vibrio cholerae hazards were poorly associated with plate count faecal coliforms, but flagged up by the MinION screening method, and confirmed by a qPCR assay. Plate counting methods remain important to assess viability of faecal coliforms in disinfected water sources. We outline a systematic approach for data collection and interpretation of such complementary results. In the Kathmandu Valley, there is high variability of water quality from different sources, including for treated water samples, illustrating the importance of disinfection at the point of use.

Intestinal parasitic infections among public and private schoolchildren of Kathmandu, Nepal: prevalence and associated risk factors

Objective

Intestinal parasitic infections (IPIs) are a major cause of morbidity among children in developing countries. Investigation about the etiological agents and socio-ecological pattern of the infection would help to design better preventive strategy. The previous studies reported high prevalence of IPIs among schoolchildren of Nepal. Though these data may be essential for the policymakers and researchers, in Kathmandu, the capital of Nepal it remains unexplored whether the types of school and socioeconomic status affect the IPIs or not. The present study is an extension of previous works to investigate causative agents and associated risk factors. We examined 508 stool samples of schoolchildren from two schools by formal-ether concentration technique and analyzed the data based on school types.

Results

The overall IPIs rate was 19.9% (n = 101) with the dominance of protozoans (78.4%) over helminths (21.6%). Giardia duodenalis (32.7%) and Ascaris lumbricoides (21.8%) were the most commonly detected protozoan and helminth species respectively. Prevalence of IPIs was higher among children from public school (26.1%) than private school (12.1%). Higher infection rates were found among farmer’s children (29.0%) and Dalit children (36.2%). These findings reveal the different prevalence of IPIs among public and private schoolchildren and suggest the need of effective preventive measures.

Development of a Quantitative PCR Assay for Arcobacter spp. and its Application to Environmental Water Samples

Arcobacter spp. are emerging pathogens associated with gastroenteritis in humans. The objective of this study was to develop a highly sensitive and broadly reactive quantitative PCR (qPCR) assay for Arcobacter spp. and to apply the developed assay to different water sources in the Kathmandu Valley, Nepal. Fifteen samples to be analyzed by next-generation sequencing were collected from 13 shallow dug wells, a deep tube well, and a river in the Kathmandu Valley in August 2015. Among the 86 potential pathogenic bacterial genera identified, Acinetobacter, Pseudomonas, Flavobacterium, and Arcobacter were detected with relatively high abundance in 15, 14, 12, and 8 samples, respectively. A primer pair was designed with maximal nucleotide homologies among Arcobacter spp. by comparing the sequences of 16S rRNA genes. These primers were highly specific to most of the known species of Arcobacter and quantified between 1.0×10¹ and 6.4×10⁶ copies reaction⁻¹ and sometimes detected as few as 3 copies reaction⁻¹. The qPCR assay was used to quantify Arcobacter spp. in bacterial DNA in not only the above 15 water samples, but also in 33 other samples collected from 15 shallow dug wells, 6 shallow tube wells, 5 stone spouts, 4 deep tube wells, and 3 springs. Thirteen (27%) out of 48 samples tested were positive for Arcobacter spp., with concentrations of 5.3–9.1 log copies 100 mL⁻¹. This qPCR assay represents a powerful new tool to assess the prevalence of Arcobacter spp. in environmental water samples.

Next-generation sequencing identification of pathogenic bacterial genes and their relationship with fecal indicator bacteria in different water sources in the Kathmandu Valley, Nepal

Bacteriological analysis of drinking water leads to detection of only conventional fecal indicator bacteria. This study aimed to explore and characterize bacterial diversity, to understand the extent of pathogenic bacterial contamination, and to examine the relationship between pathogenic bacteria and fecal indicator bacteria in different water sources in the Kathmandu Valley, Nepal. Sixteen water samples were collected from shallow dug wells (n=12), a deep tube well (n=1), a spring (n=1), and rivers (n=2) in September 2014 for 16S rRNA gene next-generation sequencing. A total of 525 genera were identified, of which 81 genera were classified as possible pathogenic bacteria. Acinetobacter, Arcobacter, and Clostridium were detected with a relatively higher abundance (>0.1% of total bacterial genes) in 16, 13, and 5 of the 16 samples, respectively, and the highest abundance ratio of Acinetobacter (85.14%) was obtained in the deep tube well sample. Furthermore, the bla_OXA23-like genes of Acinetobacter were detected using SYBR Green-based quantitative PCR in 13 (35%) of 37 water samples, including the 16 samples that were analyzed for next-generation sequencing, with concentrations ranging 5.3-7.5logcopies/100mL. There was no sufficient correlation found between fecal indicator bacteria, such as Escherichia coli and total coliforms, and potential pathogenic bacteria, as well as the bla_OXA23-like gene of Acinetobacter. These results suggest the limitation of using conventional fecal indicator bacteria in evaluating the pathogenic bacteria contamination of different water sources in the Kathmandu Valley.

Prevalence of enteropathogens in children under 15 years of age with special reference to parasites in Kathmandu, Nepal; a cross sectional study

In developing countries like Nepal, gastrointestinal infections due to various parasites are common causes of morbidity and mortality in children. Present study was carried out from June 2013 to December 2013, among the children (<15 years of age) of Kathmandu Valley. Stool samples were collected from total 600 children (350 from four public schools and slum areas of Kathmandu valley and 250 from pediatric department of Tribhuvan University Teaching Hospital). The main objectives of this study were to investigate the intestinal parasitic infections in children below 15 years of age and their risk factors. However, some bacterial pathogens were also investigated. The overall prevalence of parasitic infections was 29.5 %. The rate of parasitic infections in children from community (39.43 %) was higher than that from hospital (15.6 %; p < 0.05). Giardia lamblia was the most common protozoan found to be causing infections in children and among helminths Ascaris lumbricoides was the most common worm isolated. Higher rates of parasitic infections were found in children of illiterate parents (38.17 %), children using untreated drinking water (49.77 %) and children having habit of consuming raw vegetables (31.50 %; p < 0.05). The present study indicated that the rate of infections due to enteropathogenic parasites was high among children of Nepal.

Decreasing prevalence of intestinal parasitic infections among school-aged children in Nepal: a systematic review and meta-analysis

BACKGROUND

In the last two decades there have been several studies describing the prevalence of intestinal parasites in Nepal; however, there is a lack of surveillance data in the country.

METHODS

We searched literature in PubMed, MEDLINE, EMBASE, Google Scholar and local peer-reviewed journals published from 1990 to 2015 for studies describing prevalence of intestinal parasites among school-aged children. We conducted meta-regression to understand the trend over time and pooled the prevalence using 'metaprop' command in STATA 12.1.

RESULTS

Thirty-one studies examining 12 080 fecal specimens were included. The prevalence of intestinal parasitic infections showed a significantly decreasing trend (OR 0.56; 95% CI 0.43-0.73 for each consecutive 5 years) and was similar in males and females. The pooled prevalence in years 1996-2000, 2001-2005, 2006-2010 and 2011-2015 was 61.1% (95% CI 51.47-70.26), 53.2% (95% CI 20.94-83.99), 32.7% (95% CI 26.57-39.21) and 20.4% (95% CI 15.04-26.25), respectively. The proportion of helminths among total intestinal parasites was higher in rural areas 57.6% (95% CI 43.54-71.61), and proportion of protozoa among total intestinal parasites was higher in urban areas 68.4% (95% CI 63.23-73.62). Poly-parasitism was observed in 7.7% (95% CI 5.57-9.73) of children.

CONCLUSION

We observed a significantly decreasing trend in prevalence of intestinal parasitic infections among school-aged children in Nepal over the last two decades.

Trends in prevalence of soil-transmitted helminth and major intestinal protozoan infections among school-aged children in Nepal

OBJECTIVES

To assess the trends in prevalence of soil-transmitted helminths (STHs), Entamoeba histolytica and Giardia lamblia among school-aged children in Nepal between 1990 and 2015.

METHODS

Systematic literature search in PubMed, MEDLINE, EMBASE, Google Scholar and local peer-reviewed journals for papers published between 1990 and December 2015. We conducted metaregression and meta-analyses to pool studies where applicable.

RESULTS

Thirty-nine studies that examined a total of 14 729 stool specimens were included in the meta-analyses. The metaregression of prevalence of hookworms, roundworm, and whipworm showed a significantly decreasing trend over time. In or after 2004, the pooled prevalence of hookworm infections was 1.53% (95% CI, 0.73-2.59), of roundworm 4.31% (95% CI, 2.52-6.53) and of whipworm 2.89% (95% CI, 1.33-4.97) vs. 16.54% (95% CI, 7.64-27.97) for hookworm, 25.20% (95% CI, 13.59-38.97) for roundworm and 11.54% (95% CI 4.25-21.76) for whipworm in 1993-2003. E. histolytica and G. lamblia had stable prevalence since early 1990s, with a pooled prevalences of 4.12% (95% CI, 2.73-5.77) and 9.40% (95% CI, 7.15-11.92), respectively. The prevalence of G. lamblia was significantly higher in urban areas.

CONCLUSIONS

We observed a sharp decrease in prevalence of STHs among school-aged children in Nepal in the past decade with prevalences dropping below 5% for STHs with no variation in prevalence in rural and urban areas. However, the prevalence of E. histolytica and G. lamblia remained stable over time. These results suggest that school-based deworming programmes rolled out during the study period had an observable impact on prevalence of STHs.

Risk of diarrhoea from shallow groundwater contaminated with enteropathogens in the Kathmandu Valley, Nepal

Shallow groundwater is the main water source among many alternatives in the Kathmandu Valley, Nepal, which has a rapidly growing population and intermittent piped water supply. Although human pathogens are detected in groundwater, its health effects are unclear. We estimated risk of diarrhoea from shallow groundwater use using quantitative microbial risk assessment. Escherichia coli, Giardia cyst and Cryptosporidium oocyst levels were analysed in dug and tube wells samples. E. coli concentrations were converted to those of enteropathogenic E. coli (EPEC). Risks from EPEC in dug wells and from Cryptosporidium and Giardia in both dug and tube wells were higher than the acceptable limit (<10⁻⁴ infections/person-year) for both drinking and bathing exposures. Risk from protozoan enteropathogens increased the total risk 10,000 times, indicating that ignoring protozoans could lead to serious risk underestimation. Bathing exposure considerably increased risk, indicating that it is an important pathway. Point-of-use (POU) water treatment decreased the risk six-fold and decreased risk overestimation. Because removal efficiency of POU water treatment has the largest impact on total risk, increasing the coverage and efficiency of POU water treatment could be a practical risk management strategy in the Kathmandu Valley and similar settings.

Contrasting influence of geology on E. coli and arsenic in aquifers of Bangladesh

Arsenic in groundwater has been a concern in South and Southeast Asia for more than a decade. We explore here the possibility that hydrogeologic factors recently shown to influence the distribution of arsenic might also affect the level of contamination of shallow (<20 m) wells with microbial pathogens. A total of 96 shallow tube wells in two nearby villages of Bangladesh were surveyed during the wet and dry seasons, along with 55 deeper wells in neighboring villages. One of the two villages is located in a particularly sandy environment where recharge is rapid and shallow wells contain little arsenic. Shallow aquifers in the other village are capped with an impermeable clay layer, recharge is an order of magnitude slower, and arsenic levels are high. The fecal indicator E. coli was detected in 43% of shallow wells, compared with 12% of deeper wells. More shallow wells contained E. coli during the wet season (61%) than during the dry season (9%). In the wet season, a higher proportion of shallow wells in the village with low arsenic levels (72%) contained E. coli compared with the village having high arsenic levels (43%). Differences in arsenic and E. coli distributions between the two sites are likely due to the differences in permeability of near-surface sediments although differences in average well-depth between the two villages (9 ± 4 vs. 15 ± 3 m) may play a role as well. Hydrogeologic conditions that favor high levels of fecal contamination but low levels of arsenic in shallow groundwater should be taken into account during arsenic mitigation throughout South and Southeast Asia.