Microfluidic quantification of multiple enteric and opportunistic bacterial pathogens in roof-harvested rainwater tank samples

Decision support system for community managed rainwater harvesting: A case study in the salinity-prone coastal region of Bangladesh

Climate change-induced saline intrusion into both surface and groundwater, extreme weather events, and unregulated water usage are serious threats to the drinking water supply in coastal areas worldwide, especially in least-developed countries. This research developed a data-driven decision-making methodology to evaluate the performance of rainwater harvesting (RWH) systems in the saline-prone southwestern coastal region of Bangladesh. Twenty-five community managed RWH systems, recently piloted in two major coastal districts, were considered the case study to develop and validate this evaluation tool. The evaluation methodology integrates daily water models, lifetime cost analysis, Geographic Information System (GIS)-based parameters supported by the Analytical Hierarchy Process (AHP), and field observation. While the meteorological parameters as well as the hydrological and economic performance were found to be highly suitable, 36 % of the systems showed moderate performance, as challenges remain in ensuring proper operation and maintenance practices at the community level. However, 40 % of the systems showed high performance, with two systems showing very high suitability, which suggests community managed RWH systems as a sustainable adaptation for coastal water supply.

Spread of antibiotic resistance genes to Antarctica by migratory birds

Recent studies have highlighted the presence of antibiotic resistance genes (ARGs) in Antarctica, which are typically indicative of human activity. However, these studies have concentrated in the Antarctic Peninsula region, and relatively less is known about ARG prevalence in East Antarctica, where human activity levels are lower compared to the Antarctic Peninsula. In addition, the mechanisms of ARG transmission to Antarctica through natural or anthropogenic pathways remain unclear. In this study, we analyzed the fecal samples of Adélie penguins and South polar skuas by using high-throughput sequencing and microfluidic quantitative PCR to detect potential pathogens and ARGs at their breeding colonies near Syowa Station in East Antarctica. These results revealed the presence of several potential pathogens in the fecal matter of both bird species. However, the HF183 marker, which indicates human fecal contamination, was absent in all samples, as well as seawater sampled near the breeding colonies. This suggests that the human fecal contamination was negligible in our study area. In addition to pathogens, we found a significant number of ARGs and metal resistance genes in the feces of both Adélie penguins and South polar skuas, with higher detection rates in skuas than in penguins. To better understand how these birds acquire and transmit these genes, we analyzed the migratory patterns of Adélie penguins and South polar skuas by geolocator tracking. We found that the skuas migrate to the tropical and subtropical regions of the Indian Ocean during the austral winter. On the other hand, Adélie penguins exhibited a more localized migration pattern, mainly staying within Antarctic waters. Because the Indian Ocean is considered one of the major reservoirs of ARGs, South polar skuas might be exposed to ARGs during their winter migration and transfer these genes to Antarctica.

Meta-analysis of microbial source tracking for the identification of fecal contamination in aquatic environments based on data-mining

Microbial source tracking (MST) technology represents an innovative approach employed to trace fecal contamination in environmental water systems. The performance of primers may be affected by amplification techniques, target primer categories, and regional differences. To investigate the influence of these factors on primer recognition performance, a meta-analysis was conducted on the application of MST in water environments using three databases: Web of Science, Scopus, and PubMed (n = 2291). After data screening, 46 studies were included in the final analysis. The investigation encompassed Polymerase Chain Reaction (PCR)/quantitative PCR (qPCR) methodologies, dye-based (SYBR)/probe-based (TaqMan) techniques, and geographical differences of a human host-specific (HF183) primer and other 21 additional primers. The results indicated that the primers analyzed were capable of differentiating host specificity to a certain degree. Nonetheless, by comparing sensitivity and specificity outcomes, it was observed that virus-based primers exhibited superior specificity and recognition capacity, as well as a stronger correlation with human pathogenicity in water environments compared to bacteria-based primers. This finding highlights an important direction for future advancements. Moreover, within the same category, qPCR did not demonstrate significant benefits over conventional PCR amplification methods. In comparing dye-based and probe-based techniques, it was revealed that the probe-based method's advantage lay primarily in specificity, which may be associated with the increased propensity of dye-based methods to produce false positives. Furthermore, the heterogeneity of the HF183 primer was not detected in China, Canada, and Singapore respectively, indicating a low likelihood of regional differences. The variation among the 21 other primers may be attributable to regional differences, sample sources, detection techniques, or alternative factors. Finally, we identified that economic factors, climatic conditions, and geographical distribution significantly influence primer performance.

Evaluation of Sensitivity and Cost-Effectiveness of Molecular Methods for the Co-detection of Waterborne Pathogens in India

Waterborne microbial diseases are regarded as a major public health concern, particularly in nations with poor sanitation, a lack of social awareness, and problems linked with low socioeconomic status. Waterborne pathogen identification using traditional culture methods is time-consuming and labor-intensive. As a result, there is a growing demand for quick pathogen detection technologies. High sensitivity, specificity, and rapidity are all advantages of using molecular techniques like polymerase chain reaction (PCR) in such instances. In this study, we designed multiplex PCR and quantitative real-time PCR (qPCR) assays for the co-detection and enumeration of waterborne pathogens such as Aeromonas hydrophila, Pseudomonas aeruginosa, Salmonella enterica, Yersinia enterocolitica, Escherichia coli, Vibrio cholerae, and Shigella spp. Specific primers were selected against the virulence and species-specific genes of the seven target pathogens. For all seven target organisms, the detection limits for conventional culture methods were in the range of 10³-10⁴ cells/ml. While employing multiplex PCR method in this study, Pseudomonas aeruginosa and Shigella spp. have a detection sensitivity of 10¹ cells/ml, Vibrio cholerae and Aeromonas hydrophila have a detection sensitivity of 10² cells/ml, whereas Salmonella enterica, E. coli, and Yersinia enterocolitica have a detection sensitivity of only 10³ cells/ml. According to our cost-benefit analysis, these molecular technologies are less expensive, with unit analysis costs of ₹52 and ₹173 for qPCR and multiplex PCR, respectively. Furthermore, all of the target genes had a detection limit of 1 cell/ml in qPCR. Because of their speed, sensitivity, specificity, and cost-effectiveness, these multiplex and qPCR assays could be employed for successful co-detection of aquatic pathogens.

Microbial Indicators of Fecal Pollution: Recent Progress and Challenges in Assessing Water Quality

PURPOSE OF REVIEW

Fecal contamination of water is a major public health concern. This review summarizes recent developments and advancements in water quality indicators of fecal contamination.

RECENT FINDINGS

This review highlights a number of trends. First, fecal indicators continue to be a valuable tool to assess water quality and have expanded to include indicators able to detect sources of fecal contamination in water. Second, molecular methods, particularly PCR-based methods, have advanced considerably in their selected targets and rigor, but have added complexity that may prohibit adoption for routine monitoring activities at this time. Third, risk modeling is beginning to better connect indicators and human health risks, with the accuracy of assessments currently tied to the timing and conditions where risk is measured. Research has advanced although challenges remain for the effective use of both traditional and alternative fecal indicators for risk characterization, source attribution and apportionment, and impact evaluation.

Membrane-sensitive bacterial DNA extractions and absolute quantitation of recovery efficiencies

Absolute quantification of waterborne pathogens is mandatory for microbiological risk assessment (MRA). Determination of the DNA recovery efficiency is an essential step before the quantitative molecular measurements, which has been largely ignored. In this study, we compared the DNA recovery efficiency and quality of five extraction methods, including two modified phenol-chloroform-based extractions with mechanical shearing and three commercial kits for the extraction of DNA from indigenous mixed-bacteria culture of river water. All of the methods gave relatively satisfying results from the pelleted sample through centrifugation. However, the commercial kits provided surprisingly low DNA yields for membrane-filtered samples because of DNA trapping and/or absorption on the membrane. Integrating with enzymatic lysis, bath sonication, phenol extraction, and alcohol precipitation achieved highest DNA yields and an acceptable DNA integrity for quantitative PCR. A plasmid containing the human GADPH gene fragment was demonstrated to be a suitable spiking control for determining the absolute DNA recovery efficiency. The unexpectedly low efficiencies of commercial kit extractions imply the significant underestimation of pathogenic bacteria in previous studies, which should gain enough concern in the area of pathogen monitoring in the future.

Fecal indicator bacteria, fecal source tracking markers, and pathogens detected in two Hudson River tributaries

Volunteer monitoring in the Hudson River watershed since 2012 has identified that the Wallkill River and Rondout Creek tributary complex have elevated concentrations of the fecal indicator bacteria, enterococci. Concentrations of enterococci do not provide insight into the sources of pollution and are imperfect indicators of health risks. In 2017, the regular monthly volunteer monitoring campaign for culturable enterococci at 24 sites on the Wallkill and Rondout expanded to include: (1) culturable measurements of E. coli and quantification of E. coli and Enterococcus specific markers vis nanoscale qPCR, (2) microbial source tracking (MST) assays (avian, human, bovine, and equine) via real time PCR and nanoscale qPCR, and 3) quantification of 12 gastrointestinal pathogens including viruses, bacteria, and protozoa via nanoscale qPCR. Three human associated MST markers (HumM2, HF183, and B. theta) corroborated that human pollution was present in Rondout Creek and widespread in the Wallkill River. The presence of B. theta was associated with increased concentrations of culturable E. coli. Genes for adenovirus 40 and 41 conserved region, rotavirus A NSP3, E. coli eae and stx1, and Giardia lamblia 18S rRNA were detected in >45% of samples. Abundance of rotavirus A NSP3 genes was significantly correlated to the bovine marker gene, CowM3, though wild bird sources cannot be ruled out. This is the first study to investigate potential fecal pollution sources and pathogen concentrations in Hudson tributaries during the months of peak recreational use.

Evaluation of harvested rainwater quality at primary schools of southwest coastal Bangladesh

Rainwater is a typical source of drinking water in the coastal areas of Bangladesh given the acute scarcity of drinking water. This study assessed potability of harvested rainwater of primary schools in southwest coastal Bangladesh. Water samples collected from 23 primary schools of Mongla sub-district under Bagerhat district were evaluated for indicator bacteria (total coliform (TC) and E. coli) and physico-chemical parameters (pH, electrical conductivity, turbidity, total dissolved solid, Fe, Zn, Pb, and Cd). Median concentrations of TC and E. coli in the harvested rainwater samples were respectively 3000 cfu/100 ml and 6 cfu/100 ml. However, concentrations of these indicator bacteria were lower at the consumption points which received a prior treatment. Concentration of Pb exceeded the maximum allowable limit for drinking water indicated by WHO and Bangladesh drinking water guideline value in 92% and 61% of the samples respectively, and the mean concentration was 0.08 mg/l (8 times higher than the WHO guideline value). The Pb contamination possibly occurred from the painting on roof railing and roof stair room. Therefore, consumption of harvested rainwater at primary schools may cause substantial health risk for the school-going children.

Improved simultaneous quantification of multiple waterborne pathogens and fecal indicator bacteria with the use of a sample process control

Quantitative polymerase chain reaction (qPCR) is now commonly used to detect fecal indicator bacteria (FIB) as well as pathogens in water samples. However, DNA loss during sample processing can cause underestimation of target genes. In this study, we created a sample process control strain (SPC) by genetically engineering a non-pathogenic, Gram-negative bacterium Pseudogulbenkiania sp. strain NH8B. The SPC strain, named NH8B-1D2, has a kanamycin-resistance gene inserted to one of the 23S rRNA genes. To specifically quantify the SPC strain, a new TaqMan qPCR assay was developed. To obtain the relationship between the DNA recovery efficiencies of various pathogens and those of the SPC strain, known amount of E. coli O157:H7, Salmonella Typhimurium, Campylobacter jejuni, or Listeria monocytogenes cells were co-spiked with the SPC strain to environmental water samples. The DNA recovery efficiencies were calculated by comparing the quantity of bacterial cells inoculated to water samples prior to filtration and DNA extraction, and those measured by qPCR. We then obtained the ratios in the recovery efficiencies between pathogens and SPC strain (RR_PATH/SPC). The RR_PATH/SPC values obtained using Oono pond water collected in Japan were used as a pathogen-specific constant to estimate the accurate concentrations of pathogens in water samples collected from Mississippi River in Minnesota. Estimated pathogen concentrations were not significantly different from the inoculated pathogen concentration, suggesting our normalization approach is useful to estimate the accurate concentrations of pathogens in environmental water samples. The qPCR assay targeting the SPC strains and FIB were incorporated into the microfluidic qPCR chip format (PBQ chip ver. 2); therefore, we can simultaneously quantify multiple pathogens, FIB, and the SPC strain in high throughput from many water samples. This new tool can be useful for water quality monitoring and risk assessment.