Application of quantitative PCR for the detection of microorganisms in water

Persistence of crAssBcn phages in conditions of natural inactivation and disinfection process and their potential role as human source tracking markers

Due to their abundance in the human gut, human specificity, and global distribution, some crAss-like phages, including the original p-crAssphage, have been proposed as indicators of human fecal pollution suitable for microbial source tracking (MST). The prevalence of crAss-like phages in water, and consequently their usefulness as MST indicators, is determined by their ability to survive various inactivation and disinfection processes. Recently, we isolated new crAss-like phages (named crAssBcn phages) capable of infecting Bacteroides intestinalis and exhibiting a wide geographical distribution. Here, we assessed the infectivity and DNA integrity of three crAssBcn phages (ΦCrAssBcn6, 10, and 15) and ΦCrAss001, the first crAss-like phage isolated, at different pHs and temperatures, after UV and chlorine treatments, and under natural conditions. Their bacterial host, B. intestinalis and a siphovirus Bacteroides-infecting phage GA17-A were used as controls. Infectious crAssBcn phages remained stable for a month at 4, 22, and 37 °C, and at pH 7, but inactivated when exposed to pH 3. Infective crAssBcn phages decreased by 5 log10 after treatment with 10 ppm of chlorine for 1 min and after UV treatment at a fluence of 5.94 mJ/cm2. However, heat treatment at 60 and 70 °C resulted in only a moderate decrease (<1 log10 and almost 3 log10 units of reduction, respectively). Experiments under natural conditions in outdoor mesocosms revealed that inactivation rates for crAssBcn phages, as for the other microorganisms, were higher in summer (up to 6 log10) than in winter (<4 log10), suggesting a higher incidence of inactivation factors, such as sunlight and temperature, in the warmer months. B. intestinalis was significantly more prone to inactivation than phages in most conditions except for the irradiation treatment. In contrast, crAssBcn phage DNA remained stable, with minimal reduction under most of the tested conditions, except in the summer mesocosm and UV assays.

qPCR-based phytoplankton abundance and chlorophyll a: A multi-year study in twelve large freshwater rivers across the United States

Phytoplankton overgrowth, which characterizes the eutrophication or trophic status of surface water bodies, threatens ecosystems and public health. Quantitative polymerase chain reaction (qPCR) is promising for assessing the abundance and community composition of phytoplankton. However, applications of qPCR to indicate eutrophication and trophic status, especially in lotic systems, have yet to be comprehensively evaluated. For the first time, this study correlates qPCR-based phytoplankton abundance with chlorophyll a (the most widely used indicator of eutrophication and trophic status) in multiple freshwater rivers. From early summer to late fall in 2017, 2018, and 2019, we evaluated phytoplankton, chlorophyll a, pheophytin a, and the Trophic Level Index (TLI) in twelve large freshwater rivers in three regions (western, midcontinent, and eastern) in the United States. qPCR-based phytoplankton abundance had positive allometric correlations with chlorophyll a concentration (adjusted R2 = 0.5437, p-value < 0.001), pheophytin a concentration (adjusted R2 = 0.3378, p-value <0.001), and TLI (adjusted R2 = 0.4789, p-value < 0.001). Thus, a greater phytoplankton abundance suggests a higher trophic status. This work also presents the numerical values of qPCR-based phytoplankton abundance defining the boundaries among trophic statuses (e.g., oligotrophic, mesotrophic, and eutrophic) of freshwater rivers. The sampling sites in the midcontinent rivers were more eutrophic because they had significantly higher chlorophyll a concentrations, pheophytin a concentrations, and TLI values than the sites in the western and eastern rivers. The higher phytoplankton abundance at the midcontinent sites confirmed their higher trophic status. By linking qPCR-based phytoplankton abundance to chlorophyll a, this study demonstrates that qPCR is a promising avenue to investigate the population dynamics of phytoplankton and the trophic status (or eutrophication) of freshwater rivers.

Prevalence of hepatitis A and E viruses in wastewater in Asian countries

Hepatitis A and E viruses (HAV and HEV, respectively) remain a significant global health concern despite advancements in healthcare and vaccination programs. Regular monitoring and vaccine efficacy of HAV are still lacking in different countries. This study aimed to investigate HAV and HEV prevalence in developed, developing, and least-developed Asian countries using wastewater as a surveillance tool. A total of 232 untreated wastewater samples were collected from six wastewater treatment plants, a sewage treatment plant, or an open drainage in six countries [Nepal (n = 51), Indonesia (n = 37), Thailand (n = 30), Vietnam (n = 27), the Philippines (n = 17), and Japan (n = 70)] between April and October 2022. Viruses in wastewater were concentrated by simple centrifugation or polyethylene glycol precipitation method, followed by viral RNA extraction and reverse transcription-quantitative polymerase chain reaction. HAV and HEV RNA were detected in the samples from Nepal (51 % for HAV and 2 % for HEV), Thailand (3 % for both viruses), and Japan (1 % for HAV and 24 % for HEV). Only HAV RNA was found in 11 % of the samples in Indonesia, whereas only HEV RNA was detected in Vietnam and the Philippines, with a positive ratio of 15 % and 12 %, respectively. These results highlighted the geographic variability in HAV and HEV prevalence, underscoring the need for localized public health strategies to address specific viral hepatitis challenges in each country.

Addressing underestimation of waterborne disease risks due to fecal indicator bacteria bound in aggregates

AIMS

This study aims to identify and address significant limitations in current culture-based regulatory methods used for monitoring microbiological water quality. Specifically, these methods' inability to distinguish between planktonic forms and aggregates containing higher bacterial loads and associated pathogens may lead to a severe underestimation of exposure risks, with critical public health implications.

METHODS AND RESULTS

We employed a novel methodology combining size fractionation with ALERT (Automatic Lab-in-a-vial E.coli Remote Tracking), an automated rapid method for comprehensive quantification of culturable fecal indicator bacteria (FIB). Our findings reveal a substantial and widespread presence of aggregate-bound indicator bacteria across various water matrices and geographical locations. Comprehensive bacterial counts consistently exceeded those obtained by traditional methods by significant multiples, such as an average of 3.4× at the Seine River 2024 Olympic venue, and occasionally up to 100× in irrigation canals and wastewater plant effluent. These results, supported by microscopic and molecular analyses, underscore a systematic bias in global water safety regulatory frameworks.

CONCLUSIONS

Our research demonstrates the inadequacy of traditional culture-based techniques in assessing microbiological risks posed by aggregate-bound FIB and associated pathogens, particularly in water matrices affected by FIB-rich fecal particles from recent sewer overflows or sediment, which can carry higher infectious risks. Incorporating comprehensive FIB analysis techniques, including molecular methods and rapid culture-based approaches as shown in this study, offers a promising and effective solution to these risk assessment limitations.

The effects of RT-qPCR standards on reproducibility and comparability in monitoring SARS-CoV-2 levels in wastewater

Reverse transcription-quantitative PCR (RT-qPCR) is widely used for monitoring viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), in wastewater. Various materials, including plasmid DNA, synthetic nucleic acids, PCR amplicons, genomic DNA, and cDNA, are currently used for SARS-CoV-2 quantification by generating standard curves. We assessed three common standards on quantifying SARS-CoV-2 RNA across nine wastewater treatment plants in Finland, as part of the national wastewater surveillance effort. We pairwise compared RT-qPCR results from 148 wastewater samples, using both IDT (#10006625, IDT, USA) and CODEX standards (#SC2-RNAC-1100, CODEX DNA), and 179 samples using both IDT and EURM019 standards (#EURM-019, European Commission, Joint Research Centre) in our assessment. Amongst the tested standards, the CODEX standard consistently yielded more stable results than either the IDT or EURM019 standards. We found that SARS-CoV-2 levels were higher with the IDT standard (4.36 Log10 GC/100 mL) compared to the CODEX standard (4.05 Log10 GC/100 mL). Similarly, quantification using the IDT standard was higher (5.27 Log10 GC/100 mL) than values obtained with the EURM019 (4.81 Log10 GC/100 mL). SARS-CoV-2 RNA quantified with IDT and CODEX standards exhibited stronger concordance (Spearman's correlation rho median of 0.79) compared to those quantified with IDT and EURM019 standards (rho median of 0.59). This study highlights the significant impact of standard material selection on SARS-CoV-2 RNA quantification, emphasizing the need for harmonization in standard material.

A pH ultra-sensitive hydrated iridium oxyhydroxide films electrochemical sensor for label-free detection of Vibrio parahaemolyticus

Vibrio parahaemolyticus (V. parahaemolyticus) is a major foodborne pathogen, which can cause serious foodborne illnesses like diarrhoea. Rapid on-site detection of foodborne pathogens is an ideal way to respond to foodborne illnesses. Herein, we provide an electrochemical sensor for rapid on-site detection. This sensor utilized a pH-sensitive metal-oxide material for the concurrent isothermal amplification and label-free detection of nucleic acids. Based on a pH-sensitive hydrated iridium oxide oxyhydroxide film (HIROF), the electrode transforms the hydrogen ion compound generated during nucleic acid amplification into potential, so as to achieve a real-time detection. The results can be transmitted to a smartphone via Bluetooth. Moreover, HIROF was applied in nucleic acid device detection, with a super-Nernst sensitivity of 77.6 mV/pH in the pH range of 6.0-8.5, and the sensitivity showed the best results so far. Detection of V. parahaemolyticus by this novel method showed a detection limit of 1.0 × 103 CFU/mL, while the time consumption was only 30 min, outperforming real-time fluorescence loop-mediated isothermal amplification (LAMP). Therefore, the characteristics of compact, portable, and fast make the sensor more widely used in on-site detection.

Advancing Pathogen Identification: The Role of Digital PCR in Enhancing Diagnostic Power in Different Settings

Digital polymerase chain reaction (dPCR) has emerged as a groundbreaking technology in molecular biology and diagnostics, offering exceptional precision and sensitivity in nucleic acid detection and quantification. This review highlights the core principles and transformative potential of dPCR, particularly in infectious disease diagnostics and environmental surveillance. Emphasizing its evolution from traditional PCR, dPCR provides accurate absolute quantification of target nucleic acids through advanced partitioning techniques. The review addresses the significant impact of dPCR in sepsis diagnosis and management, showcasing its superior sensitivity and specificity in early pathogen detection and identification of drug-resistant genes. Despite its advantages, challenges such as optimization of experimental conditions, standardization of data analysis workflows, and high costs are discussed. Furthermore, we compare various commercially available dPCR platforms, detailing their features and applications in clinical and research settings. Additionally, the review explores dPCR's role in water microbiology, particularly in wastewater surveillance and monitoring of waterborne pathogens, underscoring its importance in public health protection. In conclusion, future prospects of dPCR, including methodological optimization, integration with innovative technologies, and expansion into new sectors like metagenomics, are explored.

Next-generation microbiological testing in intraabdominal infections with PCR technology

PURPOSE

Intraabdominal infections (IAI) are increasing worldwide and are a major contributor to morbidity and mortality. Among IAI, the number of multi-drug resistant organisms (MDRO) is increasing globally. We tested the Unyvero A50® for intraabdominal infections, compared the detected microorganisms and antibiotic resistance, and compared the results with those of routine microbiology.

METHODS

We prospectively compared samples obtained from surgical patients using PCR-based Unyvero IAI cartridges against routine microbiology for the detection of microorganisms. Additionally, we identified clinical parameters that correlated with the microbiological findings. Data were analyzed using the t-test and Mann-Whitney U test.

RESULTS

Sixty-two samples were analyzed. The PCR system identified more microorganisms, mostly Bacteroides species, Escherichia coli, and Enterococcus spp. For bacterial resistance, the PCR system results were fully concordant with those of routine microbiology, resulting in a sensitivity, specificity, and positive and negative predictive value (PPV, NPV) of 100%. The sensitivity, specificity, PPV, and NPV for the detection of microorganisms were 74%, 58%, 60%, and 72%, respectively. CRP levels were significantly higher in patients with detectable microorganisms. We identified more microorganisms and bacterial resistance in hospital-acquired intra-abdominal infections by using the PCR system.

DISCUSSION

IAI warrants early identification of the microorganisms involved and their resistance to allow for adequate antibiotic therapy. PCR systems enable physicians to rapidly adjust their antibiotic treatment. Conventional microbiological culture and testing remain essential for determining the minimal growth inhibition concentrations for antibiotic therapy.

Biomineral deposits and coatings on stone monuments as biodeterioration fingerprints

Biominerals deposition processes, also called biomineralisation, are intimately related to biodeterioration on stone surfaces. They include complex processes not always completely well understood. The study of biominerals implies the identification of organisms, their molecular mechanisms, and organism/rock/atmosphere interactions. Sampling restrictions of monument stones difficult the biominerals study and the in situ demonstrating of biodeterioration processes. Multidisciplinary works are required to understand the whole process. Thus, studies in heritage buildings have taken advantage of previous knowledge acquired thanks to laboratory experiments, investigations carried out on rock outcrops and within caves from some years ago. With the extrapolation of such knowledge to heritage buildings and the advances in laboratory techniques, there has been a huge increase of knowledge regarding biomineralisation and biodeterioration processes in stone monuments during the last 20 years. These advances have opened new debates about the implications on conservation interventions, and the organism's role in stone conservation and decay. This is a review of the existing studies of biominerals formation, biodeterioration on laboratory experiments, rocks, caves, and their application to building stones of monuments.

Comparison of quantitative PCR and digital PCR assays for quantitative detection of infectious bronchitis virus (IBV) genome

The quantitative polymerase chain reaction (qPCR) technique is an extensively used molecular tool for the detection and quantification of viral genome load. However, since the qPCR assay is a relative quantification method that relies on an external calibration curve it has a lower assay precision and sensitivity. The digital PCR (dPCR) technique is a good alternative to the qPCR assay as it offers highly precise and direct quantification of viral genome load in samples. In this study, performance characteristics such as the quantification range, sensitivity, precision, and specificity of the dPCR technique was compared to qPCR technique for the detection and quantification of IBV genome loads in serial dilutions of IBV positive plasmid DNA, and IBV infected chicken tissue and swab samples. The quantification range of the qPCR assay was wider than that of the dPCR assay, however dPCR had a higher sensitivity compared to qPCR. The precision of quantification of DNA in plasmid samples in terms of repeatability and reproducibility of results was higher when using the dPCR assay compared to qPCR assay. The quantification results of IBV genome load in infected samples by the qPCR and dPCR assays displayed a high correlation. Hence, our findings suggest that dPCR could be used in avian virology research for improved precision and sensitivity in detection and quantification of viral genome loads.

Rapid detection method of bacterial pathogens in surface waters and a new risk indicator for water pathogenic pollution

In this study, a accurate, rapid quantitative PCR method for the simultaneous detection of 4 kinds of pathogenic bacteria in water was established, and the distribution of pathogenic bacteria in surface waters with different levels of pollution (Yulin region, China) was detected. The results showed that the detection accuracy was 94%; the detection limit was 2.7 in bacterial cells. Salmonella enterica subsp. enterica serovar typhimurium and Salmonella dysenteria were always present in water when the universal primer for pathogenic bacteria abundance detection was greater than 104 copies 100 mL-1. When the detection value is lower than 104 copy 100 mL-1, the bacteria in the water are rarely pathogenic bacteria, so the detection value of 104 copy 100 mL-1 can be used as a new indicator of waterborne pathogen pollution.

Performance evaluation of a low-throughput qPCR-based Legionella assay for utility as an onsite industrial water system monitoring method

Legionella is a bacterial genus found in natural aquatic environments, as well as domestic and industrial water systems. Legionella presents potential human health risks when aerosolized and inhaled by at-risk individuals and is commonly monitored at locations with likelihood of proliferation and human exposure. Legionella monitoring is widely performed using culture-based testing, which faces limitations including turnaround time and interferences. Molecular biology methodologies, including quantitative polymerase chain reaction (qPCR), are being explored to supplement or replace culture-based testing because of faster turnaround and lower detection limits, allowing for more rapid water remediation measures. In this study, three methods were compared by testing industrial water samples: culture-based testing by a certified lab, high throughput qPCR testing (HT qPCR), and field deployable low throughput qPCR testing (LT qPCR). The qPCR test methods reported more positive results than culture testing, indicating improved sensitivity and specificity. The LT qPCR test is portable with quick turnaround times, and can be leveraged for environmental surveillance, process optimization, monitoring, and onsite case investigations. The LT qPCR test had high negative predictive value and would be a useful tool for negative screening of Legionella samples from high-risk environments and/or outbreak investigations to streamline samples for culture testing.

ONE-SENTENCE SUMMARY

This study compared three test methods for Legionella to evaluate performance of a low throughput quantitative polymerase chain reaction (LT qPCR) test for Legionella that can be used onsite; the study found that the high throughput (HT) and LT qPCR tests used in this study gave more positive results than culture testing, and the results indicated a similar negative predictive value for the HT and LT qPCR tests, supporting that the LT qPCR method could be useful for negative screening of Legionella samples in industrial water systems onsite.

Molecular detection of waterborne pathogens in infants' drinking water and their relationship with water quality determinants in eastern Ethiopia: loop-mediated isothermal amplification (LAMP)-based study

Cryptosporidium, Shigella, toxin-producing Escherichia coli, and rotavirus were reported to be the most responsible for severe and fatal diarrhea among infants. This study aimed to investigate the presence of these pathogens in infants' drinking water samples and analyzing using water quality determinants in eastern Ethiopia. A molecular (LAMP)-based cross-sectional study design was employed. A total of 410 and 37 water samples were tested from infant point-of-use at household and corresponding water source, respectively, from June 2020 to May, 2021. Cryptosporidium, Shigella, toxin-producing E. coli, and rotavirus were detected in 28.5, 30.0, 26.3, and 32.2%, of water samples tested from infant point-of-use, respectively. About 13.2% of the water samples were positive for all (four) pathogens together. Cryptosporidium, Shigella, toxin-producing E. coli, and rotavirus were detected in 27.0, 32.4, 29.7, and 37.8%, of water samples tested from water sources, respectively. Positive significant correlation was observed between infant point-of-consumption and water sources from which it is drawn toward the presence of each targeted pathogen. Unimproved water source showed a strong significant association with the presence of Cryptosporidium, Shigella and toxin-producing E. coli. Therefore, efforts should be made in development of improved water sources, source protection safety and health education to caretakers of infants.

Optimization of RT-PCR methods for enterovirus detection in groundwater

Enteroviruses (EVs), which belong to the Picornaviridae family, infect individuals asymptomatically or cause mild symptoms (fever, runny nose, cough, skin rash, sneezing, mouth blister). Severe cases can cause various diseases, such as acute hemorrhagic conjunctivitis, aseptic meningitis, or myocarditis, especially in infants. These viruses can be transmitted via the fecal-oral route via contaminated water. In this study, we established a polymerase chain reaction (PCR) method for detecting EVs in water sample using Coxsackievirus B5 (CV-B5) and Echovirus 30 (E-30), which belong to species B of the four species of EVs (EV-A to D). Several methods have been investigated and compared for the detection of EVs, including real-time reverse transcription (RT) polymerase chain reaction and conventional RT-PCR. The most sensitive primer sets were selected, and the PCR conditions were modified to increase sensitivity. We also quantified the detection limits of real-time and conventional RT-PCR. The detection limits of conventional RT-PCR were detected in 105-106 copy/mL for CV-B5 and 106-107 copy/mL for E-30, respectively. This optimized method for detecting EVs is expected to contribute substantially to the investigation of EV outbreaks in water samples.

Water, Water Everywhere, but Every Drop Unique: Challenges in the Science to Understand the Role of Contaminants of Emerging Concern in the Management of Drinking Water Supplies

The protection and management of water resources continues to be challenged by multiple and ongoing factors such as shifts in demographic, social, economic, and public health requirements. Physical limitations placed on access to potable supplies include natural and human-caused factors such as aquifer depletion, aging infrastructure, saltwater intrusion, floods, and drought. These factors, although varying in magnitude, spatial extent, and timing, can exacerbate the potential for contaminants of concern (CECs) to be present in sources of drinking water, infrastructure, premise plumbing and associated tap water. This monograph examines how current and emerging scientific efforts and technologies increase our understanding of the range of CECs and drinking water issues facing current and future populations. It is not intended to be read in one sitting, but is instead a starting point for scientists wanting to learn more about the issues surrounding CECs. This text discusses the topical evolution CECs over time (Section 1), improvements in measuring chemical and microbial CECs, through both analysis of concentration and toxicity (Section 2) and modeling CEC exposure and fate (Section 3), forms of treatment effective at removing chemical and microbial CECs (Section 4), and potential for human health impacts from exposure to CECs (Section 5). The paper concludes with how changes to water quantity, both scarcity and surpluses, could affect water quality (Section 6). Taken together, these sections document the past 25 years of CEC research and the regulatory response to these contaminants, the current work to identify and monitor CECs and mitigate exposure, and the challenges facing the future.

Investigating the Relationship between Surface Water Pollution and Onsite Wastewater Treatment Systems

Onsite wastewater treatment systems (OWTSs) are important nonpoint sources (NPSs) of pollution to consider in watershed management. However, limited OWTS data availability makes it challenging to account for them as an NPS of water pollution. In this study, we succeeded in obtaining OWTS permits and integrated them with environmental data to model the pollution potential from OWTSs at the watershed scale using GIS-based multicriteria decision analysis. Then, in situ water quality parameters─Escherichia coli (E. coli), total nitrogen, total phosphorus, temperature, and pH─were measured along the main tributary at base-flow conditions. Three general linear models were developed to relate E. coli to water quality parameters and OWTS pollution indicators. It was found that the model with the OWTS pollution potential had the lowest corrected Akaike information criterion (AICc) value (35.01) compared to the models that included classified OWTS pollution potential input criteria (AICc = 36.76) and land cover (AICc = 36.74). These results demonstrate that OWTSs are a significant contributor to surface water pollution, and future efforts should be made to improve access to OWTS data (i.e., location and age) to account for these systems as an NPS of water pollution.

Tools to Enumerate and Predict Distribution Patterns of Environmental Vibrio vulnificus and Vibrio parahaemolyticus

Vibrio vulnificus (Vv) and Vibrio parahaemolyticus (Vp) are water- and foodborne bacteria that can cause several distinct human diseases, collectively called vibriosis. The success of oyster aquaculture is negatively impacted by high Vibrio abundances. Myriad environmental factors affect the distribution of pathogenic Vibrio, including temperature, salinity, eutrophication, extreme weather events, and plankton loads, including harmful algal blooms. In this paper, we synthesize the current understanding of ecological drivers of Vv and Vp and provide a summary of various tools used to enumerate Vv and Vp in a variety of environments and environmental samples. We also highlight the limitations and benefits of each of the measurement tools and propose example alternative tools for more specific enumeration of pathogenic Vv and Vp. Improvement of molecular methods can tighten better predictive models that are potentially important for mitigation in more controlled environments such as aquaculture.

Mayaro virus detection by integrating sample preparation with isothermal amplification in portable devices

Mayaro virus (MAYV) is an emerging mosquito-borne alphavirus that causes clinical symptoms similar to those caused by Chikungunya virus (CHIKV), Dengue virus (DENV), and Zika virus (ZIKV). To differentiate MAYV from these viruses diagnostically, we have developed a portable device that integrates sample preparation with real-time, reverse-transcription, loop-mediated isothermal amplification (rRT-LAMP). First, we designed a rRT-LAMP assay targeting MAYV's non-structural protein (NS1) gene and determined the limit of detection of at least 10 viral genome equivalents per reaction. The assay was specific for MAYV, without cross-reactions with CHIKV, DENV, or ZIKV. The rRT-LAMP assay was integrated with a sample preparation device (SPD) wherein virus lysis and RNA enrichment/purification were carried out on the spot, without requiring pipetting, while subsequent real-time amplification device (RAD) enables virus detection at the point of care (POC). The functions of our platform were demonstrated using purified MAYV RNA or blood samples containing viable viruses. We have used the devices for detection of MAYV in as short as 13 min, with limit of detection to as low as 10 GEs/reaction.

Paper-Based Radial Flow Assay Integrated to Portable Isothermal Amplification Chip Platform for Colorimetric Detection of Target DNA

A novel integrated detection system that introduces a paper-chip-based molecular detection strategy into a polydimethylsiloxane (PDMS) microchip and temperature control system was developed for on-site colorimetric detection of DNA. For the paper chip-based detection strategy, a padlock probe DNA (PLP)-mediated rolling circle amplification (RCA) reaction for signal amplification and a radial flow assay according to the Au-probe labeling strategy for visualization were optimized and applied for DNA detection. In the PDMS chip, the reactions for ligation of target-dependent PLP, RCA, and labeling were performed one-step under isothermal temperature in a single chamber, and one drop of the final reaction solution was loaded onto the paper chip to form a radial colorimetric signal. To create an optimal analysis environment, not only the optimization of molecular reactions for DNA detection but also the chamber shape of the PDMS chip and temperature control system were successfully verified. Our results indicate that a detection limit of 14.7 nM of DNA was achieved, and non-specific DNAs with a single-base mismatch at the target DNA were selectively discriminated. This integrated detection system can be applied not only for single nucleotide polymorphism identification, but also for pathogen gene detection. The adoption of inexpensive paper and PDMS chips allows the fabrication of cost-effective detection systems. Moreover, it is very suitable for operation in various resource-limited locations by adopting a highly portable and user-friendly detection method that minimizes the use of large and expensive equipment.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13206-023-00101-7.

A multi-functional reagent suitable for 1-step rapid DNA intercalation fluorescence-based screening of total bacteria in drinking water

The prerequisites for rapid screening of total bacteria in drinking water are low detection limit and convenience. Inspired by commercial adenosine 5'-triphosphate (ATP) based total bacterial detection kits, we pursued likewise convenience but with much lower detection limit. Existing intercalation fluorescence-based techniques employ multiple reagents to permeate the cell membrane and intercalate dye into the DNA in discrete sequential steps. A simple multi-functional reagent is proposed to do the same within one step. Surfactants (TritonX and SDS), and intercalating dyes (SYBR green, SYBR gold) were examined for their mutual compatibility and augmented with EDTA. Evaluation was performed with Gram negative Escherichia coli K12 (E. coli K12) and Gram positive Bacillus subtilis (B. subtilis) at serial dilution ratios from 10^-6 to 10^-2. Comparison was made with absorbance (600 nm) measurements and a commercial ATP kit. Using charge integrated photodetection, the proposed 1-step reagent achieved an LOD (1.00 × 10^-6, B. subtilis) that is two orders of magnitude lower than that of ATP kit (LOD = 1.06× 10^-4). This means it could detect minute quantity of total bacteria that is otherwise undetected by the ATP kit.

Wastewater surveillance of antibiotic-resistant bacterial pathogens: A systematic review

Infectious diseases caused by antibiotic-resistant bacterial (ARB) pathogens are a serious threat to human and animal health. The active surveillance of ARB using an integrated one-health approach can help to reduce the emergence and spread of ARB, reduce the associated economic impact, and guide antimicrobial stewardship programs. Wastewater surveillance (WWS) of ARB provides composite samples for a total population, with easy access to the mixed community microbiome. This concept is emerging rapidly, but the clinical utility, sensitivity, and uniformity of WWS of ARB remain poorly understood especially in relation to clinical evidence in sewershed communities. Here, we systematically searched the literature to identify studies that have compared findings from WWS of ARB and antibiotic resistance genes (ARG) with clinical evidence in parallel, thereby evaluating how likely WWS of ARB and ARG can relate to the clinical cases in communities. Initially, 2,235 articles were obtained using the primary search keywords, and 1,219 articles remained after de-duplication. Among these, 35 articles fulfilled the search criteria, and an additional 13 relevant articles were included by searching references in the primary literature. Among the 48 included papers, 34 studies used a culture-based method, followed by 11 metagenomics, and three PCR-based methods. A total of 28 out of 48 included studies were conducted at the single sewershed level, eight studies involved several countries, seven studies were conducted at national or regional scales, and five at hospital levels. Our review revealed that the performance of WWS of ARB pathogens has been evaluated more frequently for Escherichia coli, Enterococcus spp., and other members of the family Enterobacteriaceae, but has not been uniformly tested for all ARB pathogens. Many wastewater-based ARB studies comparing the findings with clinical evidence were conducted to evaluate the public health risk but not to relate with clinical evidence and to evaluate the performance of WWS of ARB. Indeed, relating WWS of ARB with clinical evidence in a sewershed is not straightforward, as the source of ARB in wastewater cannot be only from symptomatic human individuals but can also be from asymptomatic carriers as well as from animal sources. Further, the varying fates of each bacterial species and ARG within the sewerage make the aim of connecting WWS of ARB with clinical evidence more complicated. Therefore, future studies evaluating the performance of many AMR pathogens and their genes for WWS one by one can make the process simpler and the interpretation of results easier.

Potential Pathogenicity of Aeromonas spp. Recovered in River Water, Soil, and Vegetation from a Natural Recreational Area

The genus Aeromonas is widely distributed in aquatic environments and is recognized as a potential human pathogen. Some Aeromonas species are able to cause a wide spectrum of diseases, mainly gastroenteritis, skin and soft-tissue infections, bacteremia, and sepsis. Currently, untreated river water is used for irrigation and recreational purposes. In this study, the Aeromonas spp. present in a river recreational environment was investigated by quantifying its presence in water, soil, and vegetation using three techniques: qPCR, plate counting in selective ADA medium, and Most Probable Number, in parallel. The presence of clones in the three types of samples was elucidated through genotyping with the ERIC-PCR technique, whereas the identification of the isolated Aeromonas was carried out by sequencing the rpoD gene. Finally, the pathogenic potential of some of the strains was explored by studying the presence and expression of virulence genes characteristic of the genus, their antimicrobial susceptibility profile, as well as the quantification of their cell damage and intracellular survival in an in vitro macrophages infection model. The results showed the presence of Aeromonas in all samples with the three quantification methods, with Aeromonas popoffii being the most prevalent species. The presence of strains with the same genotype (ERIC-PCR) was also confirmed in different samples. Some of the strains showed a high level of cell damage and intracellular bacterial survival, as well as the presence of various virulence factors. Furthermore, these strains showed resistance to some of the antibiotics tested and used therapeutically in both humans and animals. These results indicate that the presence of Aeromonas in this environment may represent a biosanitary risk that could be a public health problem.

Application of digital PCR for public health-related water quality monitoring

Digital polymerase chain reaction (dPCR) is emerging as a reliable platform for quantifying microorganisms in the field of water microbiology. This paper reviews the fundamental principles of dPCR and its application for health-related water microbiology. The relevant literature indicates increasing adoption of dPCR for measuring fecal indicator bacteria, microbial source tracking marker genes, and pathogens in various aquatic environments. The adoption of dPCR has accelerated recently due to increasing use for wastewater surveillance of Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2) - the virus that causes Coronavirus Disease 2019 (COVID-19). The collective experience in the scientific literature indicates that well-optimized dPCR assays can quantify genetic material from microorganisms without the need for a calibration curve and often with superior analytical performance (i.e., greater sensitivity, precision, and reproducibility) than quantitative polymerase chain reaction (qPCR). Nonetheless, dPCR should not be viewed as a panacea for the fundamental uncertainties and limitations associated with measuring microorganisms in water microbiology. With dPCR platforms, the sample analysis cost and processing time are typically greater than qPCR. However, if improved analytical performance (i.e., sensitivity and accuracy) is critical, dPCR can be an alternative option for quantifying microorganisms, including pathogens, in aquatic environments.

Perspective Chapter: Microfluidic Technologies for On-Site Detection and Quantification of Infectious Diseases - The Experience with SARS-CoV-2/COVID-19

Over the last 2 years, the economic and infrastructural damage incurred by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has exposed several limitations in the world’s preparedness for a pandemic-level virus. Conventional diagnostic techniques that were key in minimizing the potential transmission of SARS-CoV-2 were limited in their overall effectiveness as on-site diagnostic devices due to systematic inefficiencies. The most prevalent of said inefficiencies include their large turnaround times, operational costs, the need for laboratory equipment, and skilled personnel to conduct the test. This left many people in the early stages of the pandemic without the means to test themselves readily and reliably while minimizing further transmission. This unmet demand created a vacuum in the healthcare system, as well as in industry, that drove innovation in several types of diagnostic platforms, including microfluidic and non-microfluidic devices. In this chapter, we will explore how integrated microfluidic technologies have facilitated the improvements of previously existing diagnostic platforms for fast and accurate on-site detection of infectious diseases.

Effects of the Newly Isolated T4-like Phage on Transmission of Plasmid-Borne Antibiotic Resistance Genes via Generalized Transduction

Bacteriophages are the most abundant biological entities on earth and may play an important role in the transmission of antibiotic resistance genes (ARG) from host bacteria. Although the specialized transduction mediated by the temperate phage targeting a specific insertion site is widely explored, the carrying characteristics of “transducing particles” for different ARG subtypes in the process of generalized transduction remains largely unclear. Here, we isolated a new T4-like lytic phage targeting transconjugant Escherichia coli C600 that contained plasmid pHNAH67 (KX246266) and encoded 11 different ARG subtypes. We found that phage AH67C600_Q9 can misload plasmid-borne ARGs and package host DNA randomly. Moreover, for any specific ARG subtype, the carrying frequency was negatively correlated with the multiplicity of infection (MOI). Further, whole genome sequencing (WGS) identified that only 0.338% (4/1183) of the contigs of an entire purified phage population contained ARG sequences; these were floR, sul2, aph(4)-Ia, and fosA. The low coverage indicated that long-read sequencing methods are needed to explore the mechanism of ARG transmission during generalized transduction.

Detection of cholera toxin with surface plasmon field-enhanced fluorescent spectroscopy

In this work, a biosensor based on surface plasmon field-enhanced florescence spectroscopy (SPFS) method was successfully constructed to detect the truncated form of cholera toxin, that is, its beta subunit (CTX-B). CTX-B is a relatively small molecule (12 kDa) and it was chosen as model analyte for the detection of protein toxins originated from waterborne pathogens. Recognition layer was prepared on gold-coated LaSFN9 glasses modified with 11-mercaptoundecanoic acid (11-MUA). Biotin-conjugated anti-CTX-B polyclonal antibody (B-Ab) was immobilized on streptavidin (SA) layer constructed on the 11-MUA-modified surface. CTX-B amount was determined with direct assay using B-Ab in surface plasmon resonance (SPR) mode and with sandwich assay in SPFS mode using Cy5-conjugated anti-CTX-B polyclonal antibody. Minimum detected CTX-B concentrations were 10 and 0.01 μg/ml with SPR and SPFS, respectively, showing the sensitivity of the SPFS system over the conventional one. The detection was done in 2-6 h, which was faster than both culture and polymerase chain reaction (PCR)-based methods. Stability tests were performed with SA-coated sensors (excluding B-Ab). In this form, the layer was stable after 30 days of storage in phosphate-buffered saline (PBS; 0.01 M, pH = 7.4) at +4°C. B-Ab layer was formed immediately on them before each measurement.

CtNorm: Real time PCR cycle of threshold (Ct) normalization algorithm

In relative quantification with Real Time PCR (qRT-PCR,), accurate analysis requires equal amplification efficiency for both genes (Gene of interest and reference gene) and equal threshold values for all the samples. In this quantification method the expression level in treated samples will be calculated in comparison to the control group. We conducted the present study to design an algorithm for converting the data obtained from different runs containing identical standard samples into one run with the same amplification efficiency and threshold value. For this purpose, two formulas were designed; one to convert the amplification efficiency of the each run to 100%, and the other one for converting data from different runs into one run. Utilizing these two formulas, an algorithm was developed and named CtNorm. The online version of CtNorm algorithm is available at http://ctnorm.sums.ac.ir/. We used qRT-PCR technique to validate the accuracy of the designed algorithm for the normalization of four different human internal control genes. Normalizing the Ct values obtained from separate runs with the CtNorm algorithm has eliminated the differences and the average of the Ct values has become similar to the condition in which all the samples were amplified in a single run. The CtNorm algorithm could be utilized for equalizing the Ct values of several qRT-PCR runs with the same standard samples. The algorithm has also the ability to convert the amplification efficiency to 100% which is useful in absolute and relative quantification.

Evaluation of molecular techniques to visceral leishmaniasis detection in asymptomatic patients: a systematic review

INTRODUCTION

Visceral leishmaniasis (VL) is a systemic and neglected parasitic disease. Its main symptoms are fever, splenomegaly with or without hepatomegaly, and anemia, however, most individuals remain asymptomatic. Due to the lack of a gold standard and the limitations of current diagnostic techniques, where parasitology is ethically unfeasible for individuals without symptoms and serological tests do not differentiate between past and present disease, molecular methodologies are the most suitable.

AREAS COVERED

We performed a systematic review analyzing the molecular techniques based on PCR used, so far, to detect asymptomatic cases of VL in humans. Structured searches were carried out on PubMed, LILACS, Scopus, and Web of Science databases without time and language restrictions. Two reviewers evaluated the studies, performed data extraction, and quality assessment by assigning scores.

EXPERT OPINION

qPCR using RNA targets can be used in the diagnosis of asymptomatic cases of human VL, due to its characteristics. We recommend further studies to analyze the methodology, mainly observing the use of different rRNA targets. Therefore, we hope that this technique contributed to the construction of public policies that address the diagnosis and handling of asymptomatic patients.

A thermoelectrically stabilized aluminium acoustic trap combined with attenuated total reflection infrared spectroscopy for detection of Escherichia coli in water

Acoustic trapping is a non-contact particle manipulation method that holds great potential for performing automated assays. We demonstrate an aluminium acoustic trap in combination with attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR) for detection of E. coli in water. The thermal conductivity of aluminium was exploited to thermo-electrically heat and hold the acoustic trap at the desired assay temperature of 37 °C. Systematic characterisation and optimisation of the acoustic trap allowed high flow rates while maintaining high acoustic trapping performance. The ATR element serves not only as a reflector for ultrasound standing wave generation but also as a sensing interface. The enzyme conversion induced by alkaline phosphatase-labelled bacteria was directly monitored in the acoustic trap using ATR-FTIR spectroscopy. Sequential injection analysis allowed automated liquid handling, including non-contact bacteria retention, washing and enzyme-substrate exchange within the acoustic trap. The presented method was able to detect E. coli concentrations as low as 1.95 × 106 bacteria per mL in 197 min. The demonstrated ultrasound assisted assay paves the way to fully automated bacteria detection devices based on acoustic trapping combined with ATR-FTIR spectroscopy.

Reactive Quantum Dot-Based FRET Systems for Target-Catalyzed Detection of RNA

Oligonucleotide-templated reactions (OTRs) between two reactive hybridization probes allow for the detection of a DNA or RNA of interest by exploiting the target molecule as a catalyst of chemical reactions. The product of such a reaction commonly exhibits distinct fluorescence properties and can be detected by the means of fluorescence spectroscopy. The vast majority of OTR systems utilize organic dyes as fluorescent reporters. However, the use of brighter emitters, such as semiconductor quantum dots (QDs), has potential to improve the sensitivity of detection by providing brighter signals and permitting the use of probes at very low concentrations. Here we report an RNA-templated reaction between two fluorescently labeled peptide nucleic acid (PNA)-based probes, which proceeds on the surface of a QD. The QD-bound PNA probe bears a cysteine functionality, while the other PNA is functionalized with an organic dye as a thioester. OTR between these probes proceeds through a transfer of the organic dye to the QD and can be conveniently monitored via fluorescence resonance energy transfer (FRET) from the QD to the Cy5. The reaction was performed in a conventional fluorescence microplate reader and permits the detection of RNA in the picomolar range.

Optimizing a Suspension Culture Method with a Decreased Cost to Detect Enteroviruses in Water to Increase Surveillance Access

Enteroviruses are a public health threat due to the high incidence of infections and potential for serious illness or death. Some laboratories in high-income countries detect enteroviruses in water by integrating cell culture and PCR (ICC/PCR). This combined method carries a high financial burden, due in part to specialized cell culture equipment. Therefore, we expanded upon a pilot study to reduce the cost by using common laboratory polypropylene tubes to create a cell culture in suspension. We optimized the protocol by determining minimal incubation periods post-infection as a function of the initial virus concentration. Cells in suspension and traditional monolayers were inoculated with poliovirus and incubated in 8-hour intervals up to 48 hours prior to extraction. Quantitative PCR (qPCR) was used to detect viral nucleic acid targets. Treated and raw water samples were seeded with virus and the suspension ICC/qPCR protocol used to ascertain whether the protocol performed similar to directly seeding cells. No variation in virus detection occurred using the suspension ICC/qPCR or monolayer ICC/qPCR (p = 0.95). In surface water samples, viral nucleic acid was successfully detected, with no significant increase after 32 h (p > 0.05). Suspension ICC/qPCR is as effective as monolayer ICC/qPCR in detecting enteroviruses in surface waters. Materials used in the suspension ICC/qPCR have a lower monetary cost than traditional cell culture materials without loss of sensitivity. More accessible testing of waters for enterovirus contamination through cost reduction has the potential to reduce human exposure and disease.

Validation of an eDNA-based method for the detection of wildlife pathogens in water

Monitoring the occurrence and density of parasites and pathogens can identify high infection-risk areas and facilitates disease control and eradication measures. Environmental DNA (eDNA) techniques are increasingly used for pathogen detection due to their relative ease of application. Since many factors affect the reliability and efficacy of eDNA-based detection, rigorous validation and assessment of method limitations is a crucial first step. We evaluated an eDNA detection method using in situ filtration of large-volume water samples, developed to detect and quantify aquatic wildlife parasites by quantitative PCR (qPCR). We assessed method reliability using Batrachochytrium dendrobatidis, a pathogenic fungus of amphibians and the myxozoan Tetracapsuloides bryosalmonae, causative agent of salmonid proliferative kidney disease, in a controlled experimental setup. Different amounts of parasite spores were added to tanks containing either clean tap water or water from a semi-natural mesocosm community. Overall detection rates were higher than 80%, but detection was not consistent among replicate samples. Within-tank variation in detection emphasises the need for increased site-level replication when dealing with parasites and pathogens. Estimated parasite DNA concentrations in water samples were highly variable, and a significant increase with higher spore concentrations was observed only for B. dendrobatidis. Despite evidence for PCR inhibition in DNA extractions from mesocosm water samples, the type of water did not affect detection rates significantly. Direct spiking controls revealed that the filtration step reduced detection sensitivity. Our study identifies sensitive quantification and sufficient replication as major remaining challenges for the eDNA-based methods for detection of parasites in water.

Deep-amplicon sequencing (DAS) analysis to determine the presence of pathogenic Helicobacter species in wastewater reused for irrigation

Wastewater has become one of the most important and least expensive water for the agriculture sector, as well as an alternative to the overexploitation of water resources. However, inappropriate treatment before its reuse can result in a negative impact on the environment, such as the presence of pathogens. This poses an increased risk for environmental safety, which can subsequently lead to an increased risk for human health. Among all the emerging wastewater pathogens, bacteria of the genus Helicobacter are some of the most disturbing ones, since they are directly related to gastric illness and hepatobiliary and gastric cancer. Therefore, the aim of this study was to determine the presence of potentially pathogenic Helicobacter spp. in treated wastewater intended for irrigation. We used a next generation sequencing approach, based on Illumina sequencing in combination with culture and other molecular techniques (qPCR, FISH and DVC-FISH), to analyze 16 wastewater samples, with and without an enrichment step. By culture, one of the direct samples was positive for H. pylori. FISH and DVC-FISH techniques allowed for detecting viable Helicobacter spp., including H. pylori, in seven out of eight samples of wastewater from the tertiary effluents, while qPCR analysis yielded only three positive results. When wastewater microbiome was analyzed, Helicobacter genus was detected in 7 samples. The different molecular techniques used in the present study provided evidence, for the first time, of the presence of species belonging to the genus Helicobacter such as H. pylori, H. hepaticus, H. pullorum and H. suis in wastewater samples, even after disinfection treatment.

Reverse transcriptase enzyme and priming strategy affect quantification and diversity of environmental transcripts

Reverse-transcriptase-quantitative PCR (RT-Q-PCR) and RT-PCR amplicon sequencing, provide a convenient, target-specific, high-sensitivity approach for gene expression studies and are widely used in environmental microbiology. Yet, the effectiveness and reproducibility of the reverse transcription step has not been evaluated. Therefore, we tested a combination of four commercial reverse transcriptases with two priming techniques to faithfully transcribe 16S rRNA and amoA transcripts from marine sediments. Both enzyme and priming strategy greatly affected quantification of the exact same target with differences of up to 600-fold. Furthermore, the choice of RT system significantly changed the communities recovered. For 16S rRNA, both enzyme and priming had a significant effect with enzyme having a stronger impact than priming. Inversely, for amoA only the change in priming strategy resulted in significant differences between the same samples. Specifically, more OTUs and better coverage of amoA transcripts diversity were obtained with GS priming indicating this approach was better at recovering the diversity of amoA transcripts. Moreover, sequencing of RNA mock communities revealed that, even though transcript α diversities (i.e., OTU counts within a sample) can be biased by the RT, the comparison of β diversities (i.e., differences in OTU counts between samples) is reliable as those biases are reproducible between environments.

Amperometric genosensor for culture independent bacterial count

Bacterial plate count for general assessment of water quality requires lengthy bacterial culturing. We report here a new DNA induced current genosensor for culture independent total bacteria determination. Since the amount of bacterial DNA is correlated to the number of bacteria, the genosensor measures the amount of bacterial DNA to determine bacterial count. The approach relies on bacteria lysis to release DNA which can react with molybdate to form redox molybdophosphate and measured electrochemically. Analysis of E. coli and S. aureus demonstrated that the DNA generated current is highly correlated with the level of bacteria lysis which was confirmed by spectrometric measurement. Culture independent measurement of S. aureus bacterial load suggests limit of detection is 21.9 CFU/mL, with linear range from 3×10² to 3×10⁷ CFU/mL and correlation coefficient of 0.992. For E. coli analysis, the detection limit is 25.1 CFU/mL with the same linear range. The use of electrochemical microbial DNA quantitation for culture independent bacterial count is a new approach, the genosensor measurement is rapid (within 1 h) and has potential use for analysis of broad-spectrum bacteria for various applications.

Microbial Biodeterioration of Cultural Heritage: Events, Colonization, and Analyses

Geochemical cycles result in the chemical, physical, and mineralogical modification of rocks, eventually leading to formation of soil. However, when the stones and rocks are a part of historic buildings and monuments, the effects are deleterious. In addition, microorganisms also colonize these monuments over a period of time, resulting in formation of biofilms; their metabolites lead to physical weakening and discoloration of stone eventually. This process, known as biodeterioration, leads to a significant loss of cultural heritage. For formulating effective conservation strategies to prevent biodeterioration and restore monuments, it is important to know which microorganisms are colonizing the substrate and the different energy sources they consume to sustain themselves. With this view in scope, this review focuses on studies that have attempted to understand the process of biodeterioration, the mechanisms by which they colonize and affect the monuments, the techniques used for assessment of biodeterioration, and conservation strategies that aim to preserve the original integrity of the monuments. This review also includes the "omics" technologies that have started playing a large role in elucidating the nature of microorganisms, and how they can play a role in hastening the formulation of effective conservation strategies.

Profiling Bacterial Diversity and Potential Pathogens in Wastewater Treatment Plants Using High-Throughput Sequencing Analysis

Next-generation sequencing provides new insights into the diversity and structure of bacterial communities, as well as the fate of pathogens in wastewater treatment systems. In this study, the bacterial community structure and the presence of pathogenic bacteria in three wastewater treatment plants across Gauteng province in South Africa were studied. The physicochemical results indicated that the quality of wastewater varies considerably from one plant to the others. Proteobacteria, Actinobacteria, Firmicutes, and Chloroflexi were the dominant phyla across the three wastewater treatment plants, while Alphaproteobacteria, Actinobacteria, Bacilli, and Clostridia were the dominant classes. The dominant bacterial functions were highly associated with carbohydrate, energy, and amino acid metabolism. In addition, potential pathogenic bacterial members identified from the influent/effluent samples included Roseomonas, Bacillus, Pseudomonas, Clostridium, Mycobacterium, Methylobacterium, and Aeromonas. The results of linear discriminant analysis (LDA) effect size analysis also confirmed that these bacterial pathogens were significantly abundant in the wastewater treatment systems. Further, the results of this study highlighted that the presence of bacterial pathogens in treated effluent pose a potential contamination risk, transmitted through soil, agriculture, water, or sediments. There is thus a need for continuous monitoring of potential pathogens in wastewater treatment plants (WWTPs) in order to minimize public health risk.

Understanding the viral load during the synthesis and after rebinding of virus imprinted particles via real-time quantitative PCR

In the present study, virus imprinted particles have been synthesized for recognizing and specifically binding viruses. These materials may be used for biomimetic sensing schemes and for selective removal of virus particles. Virus imprinting procedures require careful optimization of the synthesis route for obtaining selective and efficiently binding imprinted materials. A remaining limitation has been a facile method for the quantification of the viral load during the imprinting process. Herein, human adenovirus (AdV) was selected as a model virus facilitating the development and application of a rapid virus quantification method based on a molecular biological approach. A real-time quantitative polymerase chain reaction, a.k.a., the qPCR method was developed for monitoring the AdV viral load during the synthesis of AdV imprinted particles, and subsequent rebinding studies. The developed analytical strategy allows the direct, rapid, and sensitive quantification of human adenovirus type 5 concentrations during synthesis and application of AdV imprinted polymers (AdV-MIPs) with a broad dynamic range suitable for both application scenarios. In addition, it was demonstrated by gel electrophoresis analysis that viruses indeed bind to the beads even after several washing steps.

Evaluation of Bacterial Contamination as an Indicator of Viral Contamination in a Sedimentary Aquifer in Uruguay

In Uruguay, groundwater is frequently used for agricultural activities, as well as for human consumption in urban and rural areas. As in many countries worldwide, drinking water microbiological quality is evaluated only according to bacteriological standards and virological analyses are not mentioned in the legislation. In this work, the incidence of human viral (Rotavirus A, Norovirus GII, and human Adenovirus) and bacterial (total and thermotolerant coliform and Pseudomonas aeruginosa) contamination in groundwater in the Salto district, Uruguay, as well as the possible correlation between these groups of microorganisms, was studied. From a total of 134 groundwater samples, 42 (32.1%) were positive for Rotavirus, only 1 (0.7%) for both Rotavirus and Adenovirus, and 96 (72.6%) samples were positive for bacterial indicators. Results also show that Rotavirus presence was not associated with changes in chemical composition of the aquifer water. Bacteriological indicators were not adequate to predict the presence of viruses in individual groundwater samples (well scale), but a deeper spatial-temporal analysis showed that they are promising candidates to assess the viral contamination degree at aquifer scale, since from the number of wells with bacterial contamination the number of wells with viral contamination could be estimated.

Development of Escherichia coli-based gene expression profiling of sewage sludge leachates

AIMS

The impact of municipal waste on pathogenic micro-organisms released into the environment is a public health concern. This study aims to evaluate the effects of sewage sludge and antibiotic contaminants on stress response, virulence and antibiotic resistance in a pathogenic Escherichia coli.

METHODS AND RESULTS

The effects of sewage sludge leachates on uropathogenic E. coli CFT073 were determined by monitoring the expression of 45 genes associated with antibiotic/metal resistance, stress response and virulence using RT-qPCR. The E. coli gene expression was validated using subinhibitory concentrations of tetracycline and ciprofloxacin. E. coli exposed to sewage sludge or sewage sludge+fly ash leachates altered the expression of five antibiotic and metal resistance, three stress response and two virulence-associated genes. When antibiotics were combined with sludge or sludge+fly ash the antibiotic-associated gene expression was altered.

CONCLUSIONS

E. coli treated with two sludge leachates had distinct gene expression patterns that were altered when the sludge leachates were combined with tetracycline, although to a lesser extent with ciprofloxacin.

SIGNIFICANCE AND IMPACT OF THE STUDY

The E. coli multigene expression analysis is a potential new tool for assessing the effects of pollutants on pathogenic microbes in environmental waters for improved risk assessment.

Performance evaluation of Bacteroidales genetic markers for human and animal microbial source tracking in tropical agricultural watersheds

Microbial source tracking (MST) DNA-based assays have been used to successfully solve fecal pollution problems in many countries, particularly in developed nations. However, their application in developing countries has been limited but continues to increase. In this study, sixteen endpoint and quantitative PCR (qPCR) assays targeting universal and human-, swine-, and cattle-specific Bacteroidales gene markers were modified for endpoint PCR, evaluated for their performance with sewage and fecal samples from the Tha Chin watershed and subsequently validated with samples from the Chao Phraya watershed, Thailand. Sample sizes of 81 composite samples (from over 1620 individual samples) of farm animals of each type as well as 19 human sewage samples from the Tha Chin watershed were calculated using a stratified random sampling design to achieve a 90% confidence interval and an expected prevalence (i.e., desired assay's sensitivity) of 0.80. The best universal and human-, swine-, and cattle-specific fecal markers were BacUni EP, HF183/BFDrev EP, Pig-2-Bac EP, and Bac3 assays, respectively. The detection limits for these assays ranged from 30 to 3000 plasmid copies per PCR. The positive predictive values were high in universal and swine- and cattle-specific markers (85-100%), while the positive predictive value of the human-specific assay was 52.2%. The negative predictive values in all assays were relatively high (90.8-100%). A suite of PCR assays in Thailand was established for potential MST use in environmental waters, which supports the worldwide applicability of Bacteroidales gene markers. This study also emphasizes the importance of using a proper sample size in assessing the performance of MST markers in a new geographic region.

Microplate Chemiluminescent Assay for DNA Detection Using Apoperoxidase-Oligonucleotide as Capture Conjugate and HRP-Streptavidin Signaling System

A covalent conjugate of horseradish apoperoxidase and amino-containing oligonucleotide was synthesized for the first time. Using the obtained conjugate as a capture reagent chemiluminescent microtiter plate-based assay for detection of 35-mer fragment of hepatitis B virus (HBV) DNA (proof-of-concept analyte) was developed. To detect the target DNA, a signaling system consisted of biotinylated reporter oligonucleotide and HRP-streptavidin conjugate was used. The high sensitivity of the assay was due to the enhanced chemiluminescence reaction, where 3-(10&prime;-phenothiazinyl)propane-1-sulfonate/N-morpholinopyridine pair was used as an enhancer. Under the optimized conditions the limit of detection and a working range of the assay were 3 pM and 6⁻100 pM, respectively. The assay sensitivity was 1.6 &times; 10⁵ RLU/pM of target. The coefficient of variation (CV) for determination of HBV DNA within the working range was lower than 6%.

Ultrasensitive DNA detection based on target-triggered rolling circle amplification and fluorescent poly(thymine)-templated copper nanoparticles

We describe a novel strategy for the ultrasensitive detection of target DNA based on rolling circle amplification (RCA) coupled with fluorescent poly(thymine)-templated copper nanoparticles (poly T-CuNPs). In the presence of target DNA, a padlock DNA probe that consists of two regions: a target DNA-specific region and a poly(adenine) region, is circularized by the ligation reaction, and the subsequent RCA reaction is promoted to generate long, concatemeric, single-stranded DNA (ssDNA) with a lot of repetitive poly T sequences. As a result, a large number of poly T-CuNPs are formed, exhibiting a highly fluorescent signal. However, in the absence of target DNA or in the presence of non-specific target DNA, the padlock DNA probe is not circularized and the subsequent RCA is not executed, leading to no production of fluorescent poly T-CuNPs. With this simple strategy, we successfully analyzed the target DNA with the ultralow detection limit of 7.79 aM, a value that is 3 or 7 orders of magnitude lower than those of previous RCA-based fluorescent DNA detection strategies. In addition, the developed system was demonstrated to selectively discriminate non-specific target DNAs with one-base mismatch, suggesting potential application in the accurate diagnosis of single nucleotide polymorphisms or mutations.

Fate of potential indicator antimicrobial resistance genes (ARGs) and bacterial community diversity in simulated manure-soil microcosms

The aim of this study was to investigate the fate of nine potential indicator antimicrobial resistance genes (ARGs) (sul1, sul2, tetB, tetM, ermB, ermF, fexA, cfr, intI1) and the diversity of bacterial communities in response to poultry manure applications to arable soil over a 90 day period. Quantitative real time PCR and Illumina high-throughput sequencing of 16S rDNA gene were used to quantify and trace ARG fate. The levels of all genes dramatically decreased over time and intI1, sul1, sul2 and tetM always had the greatest abundance and lowest dissipation rates. This indicated that more effort should be focused on the ARG elimination from manure rather than waiting for subsequent attenuation in the environment. Our sequencing results documented dramatic changes in the microbial community structure and diversity during these experiments. In poultry manure groups, Bacteroidetes and Actinobacteria were the two dominant phyla while Acidobacteria dominated the control groups. Moreover, the relative abundance of genera Corynebacterium, Pseudomonas, Ochrobactrum, Actinomadura and Bacillus, which contained potential opportunistic pathogens, changed over time suggesting that poultry manure not only strongly influenced bacterial community composition, but also selected specific bacterial communities. This study provides a glimpse of ARG fates and bacterial community diversity in soil after the application of poultry manure.

Monolith Chromatography as Sample Preparation Step in Virome Studies of Water Samples

Viruses exist in aquatic media and many of them use this media as transmission route. Next-generation sequencing (NGS) technologies have opened new doors in virus research, allowing also to reveal a hidden diversity of viral species in aquatic environments. Not surprisingly, many of the newly discovered viruses are found in environmental fresh and marine waters. One of the problems in virome research can be the low amount of viral nucleic acids present in the sample in contrast to the background ones (host, eukaryotic, prokaryotic, environmental). Therefore, virus enrichment prior to NGS is necessary in many cases. In water samples, an added problem resides in the low concentration of viruses typically present in aquatic media. Different concentration strategies have been used to overcome such limitations. CIM monoliths are a new generation of chromatographic supports that due to their particular structural characteristics are very efficient in concentration and purification of viruses. In this chapter, we describe the use of CIM monolithic chromatography for sample preparation step in NGS studies targeting viruses in fresh or marine water. The step-by-step protocol will include a case study where CIM concentration was used to study the virome of a wastewater sample using NGS.

Separation of Small DNAs by Gel Electrophoresis in a Fused Silica Capillary Coated with a Negatively Charged Copolymer

Active development of compact analytical instruments suitable for point-of-care testing (POCT) requires optimization of existing methods. To aid the development of capillary gel electrophoresis instruments for POCT, we attempted to separate polymerase chain reaction products (small DNAs) using a short, fused silica capillary coated with an acrylamide (AM)/acrylic acid (AA) copolymer (poly(AM-co-AA)). To realize the high capability of this capillary to separate small DNAs, the magnitude of electroosmotic flow (EOF) was controlled by varying the content of negatively charged AA in the copolymer, which significantly affected the separation ability. At an AA content ≥3.75 mol %, sample DNAs could not be injected into the copolymer-coated capillary owing to strong EOF, whereas a 100 bp DNA ladder sample was successfully separated at an AA content of ≤3.5 mol %, showing that even slight AA content variations impact DNA flow. EOF values measured using a neutral coumarin 334 solution suddenly decreased at an AA content of 3.5 mol % relative to those at an AA content of ≥3.75 mol %. Theoretical plate values revealed that an AA content of 2.75 mol % was optimal for separating ladder DNAs with sizes ≥600 bp. Hence, EOF control achieved by varying the amount of negatively charged AA in the poly(AM-co-AA) coating can promote further development of short capillaries for POCT applications.