Detection of pathogens in water: from phylochips to qPCR to pyrosequencing

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.

Source-to-tap investigation of the occurrence of nontuberculous mycobacteria in a full-scale chloraminated drinking water system

Nontuberculous mycobacteria (NTM) in drinking water are a significant public health concern. However, an incomplete understanding of the factors that influence the occurrence of NTM in drinking water limits our ability to characterize risk and prevent infection. This study sought to evaluate the influence of season and water treatment, distribution, and stagnation on NTM in drinking water. Samples were collected source-to-tap in a full-scale, chloraminated drinking water system approximately monthly from December 2019 to November 2020. NTM were characterized using culture-dependent (plate culture with matrix-assisted laser desorption ionization-time-of-flight mass spectrometry [MALDI-TOF MS] isolate analysis) and culture-independent methods (quantitative PCR and genome-resolved metagenomics). Sampling locations included source waters, three locations within the treatment plant, and five buildings receiving water from the distribution system. Building plumbing samples consisted of first draw, 5-min flush, and full flush cold-water samples. As the study took place during the COVID-19 pandemic, the influence of reduced water usage in three of the five buildings was also investigated. The highest NTM densities source-to-tap were found in the summer first draw building water samples (107 gene copies/L), which also had the lowest monochloramine concentrations. Flushing was found to be effective for reducing NTM and restoring disinfectant residuals, though flush times necessary to improve water quality varied by building. Clinically relevant NTM species, including Mycobacterium avium, were recovered via plate culture, with increased occurrence observed in buildings with higher water age. Four of five NTM metagenome-assembled genomes were identified to the species level and matched identified isolates.IMPORTANCENTM infections are increasing in prevalence, difficult to treat, and associated with high morbidity and mortality rates. Our lack of understanding of the factors that influence NTM occurrence in drinking water limits our ability to prevent infections, accurately characterize risk, and focus remediation efforts. In this study, we comprehensively evaluated NTM in a full-scale drinking water system, showing that various steps in treatment and distribution influence NTM presence. Stagnant building water contained the highest NTM densities source-to-tap and was associated with low disinfectant residuals. We illustrated the differences in NTM detection and characterization obtained from culture-based and culture-independent methods, highlighting the complementarity between these approaches. We demonstrated that focusing NTM mitigation efforts in building plumbing systems, which have the highest NTM densities source-to-tap, has potential for immediate positive effects. We also identified steps during treatment that increase NTM levels, which provides beneficial information for utilities seeking to reduce NTM in finished water.

Establishment and evaluation of a qPCR method for the detection of pfmdr1 mutations in Plasmodium falciparum, the causal agent of fatal malaria

Drug resistance surveillance is a major integral part of malaria control programs. Molecular methods play a pivotal role in drug resistance detection and related molecular research. This study aimed to develop a rapid and accurate detection method for drug resistance of Plasmodium falciparum (P. falciparum). A quantitative real-time PCR (qPCR) assay has been developed that identifies the mutation at locus A256T in the P.falciparum multi-drug resistance(pfmdr1) gene producing amino acid change at position 86. The results of 198 samples detected by qPCR were consistent with nested PCR and sequencing, giving an accuracy of 94.3%. The sensitivity, specificity, positive and negative predictive value of qPCR were 85.7%, 97.6%, 90.0% and 96.4%, respectively. The results of qPCR are basically consistent with the nested PCR, which is expected to replace the nested PCR as a new molecular biological method for drug resistance detection, providing reliable technical support for global malaria prevention and control.

HPB-Chip: An accurate high-throughput qPCR-based tool for rapidly profiling waterborne human pathogenic bacteria in the environment

Waterborne pathogens are threatening public health globally, but profiling multiple human pathogenic bacteria (HPBs) in various polluted environments is still a challenge due to the absence of rapid, high-throughput and accurate quantification tools. This work developed a novel chip, termed the HPB-Chip, based on high-throughput quantitative polymerase chain reactions (HT-qPCR). The HPB-Chip with 33-nL reaction volume could simultaneously complete 10,752 amplification reactions, quantifying 27 HPBs in up to 192 samples with two technical replicates (including those for generating standard curves). Specific positive bands of target genes across different species and single peak melting curves demonstrated high specificity of the HPB-Chip. The mixed plasmid serial dilution test validated its high sensitivity with the limit of quantification (LoD) of averaged 82 copies per reaction for 25 target genes. PCR amplification efficiencies and R2 coefficients of standard curves of the HPB-Chip averaged 101 % and 0.996, respectively. Moreover, a strong positive correlation (Pearson' r: 0.961-0.994, P < 0.001) of HPB concentrations (log10 copies/L) between HPB-Chip and conventional qPCR demonstrated high accuracy of the HPB-Chip. Subsequently, the HPB-Chip has been successfully applied to absolutely quantify 27 HPBs in municipal and hospital wastewater treatment plants (WWTPs) after PMA treatment. A total of 17 HPBs were detected in the 6 full-scale WWTPs, with an additional 19 in the hospital WWTP. Remarkably, Acinetobacter baumannii, Legionella pneumophila, and Arcobacter butzler were present in the final effluent of each municipal WWTP. Overall, the HPB-Chip is an efficient and accurate high-throughput quantification tool to comprehensively and rapidly quantify 27 HPBs in the environment.

A narrative review of wastewater surveillance: pathogens of concern, applications, detection methods, and challenges

Introduction

The emergence and resurgence of pathogens have led to significant global health challenges. Wastewater surveillance has historically been used to track water-borne or fecal-orally transmitted pathogens, providing a sensitive means of monitoring pathogens within a community. This technique offers a comprehensive, real-time, and cost-effective approach to disease surveillance, especially for diseases that are difficult to monitor through individual clinical screenings.

Methods

This narrative review examines the current state of knowledge on wastewater surveillance, emphasizing important findings and techniques used to detect potential pathogens from wastewater. It includes a review of literature on the detection methods, the pathogens of concern, and the challenges faced in the surveillance process.

Results

Wastewater surveillance has proven to be a powerful tool for early warning and timely intervention of infectious diseases. It can detect pathogens shed by asymptomatic and pre-symptomatic individuals, providing an accurate population-level view of disease transmission. The review highlights the applications of wastewater surveillance in tracking key pathogens of concern, such as gastrointestinal pathogens, respiratory pathogens, and viruses like SARS-CoV-2.

Discussion

The review discusses the benefits of wastewater surveillance in public health, particularly its role in enhancing existing systems for infectious disease surveillance. It also addresses the challenges faced, such as the need for improved detection methods and the management of antimicrobial resistance. The potential for wastewater surveillance to inform public health mitigation strategies and outbreak response protocols is emphasized.

Conclusion

Wastewater surveillance is a valuable tool in the fight against infectious diseases. It offers a unique perspective on the spread and evolution of pathogens, aiding in the prevention and control of disease epidemics. This review underscores the importance of continued research and development in this field to overcome current challenges and maximize the potential of wastewater surveillance in public health.

The escalating threat of human-associated infectious bacteria in surface aquatic resources: Insights into prevalence, antibiotic resistance, survival mechanisms, detection, and prevention strategies

Anthropogenic activities and climate change profoundly impact water quality, leading to a concerning increase in the prevalence and abundance of bacterial pathogens across diverse aquatic environments. This rise has resulted in a growing challenge concerning the safety of water sources, particularly surface waters and marine environments. This comprehensive review delves into the multifaceted challenges presented by bacterial pathogens, emphasizing threads to human health within ground and surface waters, including marine ecosystems. The exploration encompasses the intricate survival mechanisms employed by bacterial pathogens and the proliferation of antimicrobial resistance, largely driven by human-generated antibiotic contamination in aquatic systems. The review further addresses prevalent pathogenic bacteria, elucidating associated risk factors, exploring their eco-physiology, and discussing the production of potent toxins. The spectrum of detection techniques, ranging from conventional to cutting-edge molecular approaches, is thoroughly examined to underscore their significance in identifying and understanding waterborne bacterial pathogens. A critical aspect highlighted in this review is the imperative for real-time monitoring of biomarkers associated with waterborne bacterial pathogens. This monitoring serves as an early warning system, facilitating the swift implementation of action plans to preserve and protect global water resources. In conclusion, this comprehensive review provides fresh insights and perspectives, emphasizing the paramount importance of preserving the quality of aquatic resources to safeguard human health on a global scale.

Global diversity, coexistence and consequences of resistome in inland waters

Human activities have long impacted the health of Earth's rivers and lakes. These inland waters, crucial for our survival and productivity, have suffered from contamination which allows the formation and spread of antibiotic-resistant genes (ARGs) and consequently, ARG-carrying pathogens (APs). Yet, our global understanding of waterborne pathogen antibiotic resistance remains in its infancy. To shed light on this, our study examined 1240 metagenomic samples from both open and closed inland waters. We identified 22 types of ARGs, 19 types of mobile genetic elements (MGEs), and 14 types of virulence factors (VFs). Our findings showed that open waters have a higher average abundance and richness of ARGs, MGEs, and VFs, with more robust co-occurrence network compared to closed waters. Out of the samples studied, 321 APs were detected, representing a 43 % detection rate. Of these, the resistance gene 'bacA' was the most predominant. Notably, AP hotspots were identified in regions including East Asia, India, Western Europe, the eastern United States, and Brazil. Our research underscores how human activities profoundly influence the diversity and spread of resistome. It also emphasizes that both abiotic and biotic factors play pivotal roles in the emergence of ARG-carrying pathogens.

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.

Emerging Applications of Nanobiosensors in Pathogen Detection in Water and Food

Food and waterborne illnesses are still a major concern in health and food safety areas. Every year, almost 0.42 million and 2.2 million deaths related to food and waterborne illness are reported worldwide, respectively. In foodborne pathogens, bacteria such as Salmonella, Shiga-toxin producer Escherichia coli, Campylobacter, and Listeria monocytogenes are considered to be high-concern pathogens. High-concern waterborne pathogens are Vibrio cholerae, leptospirosis, Schistosoma mansoni, and Schistosima japonicum, among others. Despite the major efforts of food and water quality control to monitor the presence of these pathogens of concern in these kinds of sources, foodborne and waterborne illness occurrence is still high globally. For these reasons, the development of novel and faster pathogen-detection methods applicable to real-time surveillance strategies are required. Methods based on biosensor devices have emerged as novel tools for faster detection of food and water pathogens, in contrast to traditional methods that are usually time-consuming and are unsuitable for large-scale monitoring. Biosensor devices can be summarized as devices that use biochemical reactions with a biorecognition section (isolated enzymes, antibodies, tissues, genetic materials, or aptamers) to detect pathogens. In most cases, biosensors are based on the correlation of electrical, thermal, or optical signals in the presence of pathogen biomarkers. The application of nano and molecular technologies allows the identification of pathogens in a faster and high-sensibility manner, at extremely low-pathogen concentrations. In fact, the integration of gold, silver, iron, and magnetic nanoparticles (NP) in biosensors has demonstrated an improvement in their detection functionality. The present review summarizes the principal application of nanomaterials and biosensor-based devices for the detection of pathogens in food and water samples. Additionally, it highlights the improvement of biosensor devices through nanomaterials. Nanomaterials offer unique advantages for pathogen detection. The nanoscale and high specific surface area allows for more effective interaction with pathogenic agents, enhancing the sensitivity and selectivity of the biosensors. Finally, biosensors' capability to functionalize with specific molecules such as antibodies or nucleic acids facilitates the specific detection of the target pathogens.

Shift of human pathogen community composition and their potential human health risk after supply suspension in tap water

Water supply suspension-restoration can occur frequently due to the overhauling of civil infrastructure in developing countries and the shutdown of commercial buildings during the pandemic. For comprehensive insights into the effects of water supply suspension-restoration, this study characterized the variations of the pathogen community composition of the tap water and their infection risk under different water supply scenarios. Metagenomic sequencing revealed a significant change of the human pathogen profiles, among which the most dominant pathogen changed from Pseudomonas aeruginosa (4.91%) to Acinetobacter johnsonii (0.59%). Furthermore, absolute quantification of pathogens by propidium-monoazide-qPCR revealed that the abundance of the three typical pathogens (Pseudomonas aeruginosa, Mycobacterium avium and Salmonella sp.) showed an increase of 2.44 log to 3.60 log immediately after water supply suspension-restoration and did not return to the normal level even after 2-h supply restoration, except for Pseudomonas aeruginosa. Quantitative microbial risk assessment suggested the infection risks of the three pathogens arising from direct utilization of tap water under stable water supply, including dermal exposure and oral intake, were all above the threshold of 10^-4, and evidently increased after water supply suspension-restoration. This study warns us against the risk induced by the pathogens in tap water, especially after water supply suspension-restoration.

Molecular characterization of Cryptosporidium and Giardia in environmental samples and faecal samples from biogas users in Bac Giang, Vietnam

Little is known about Cryptosporidium and Giardia in biogas waste and humans in Vietnam. There is a potential risk of infections during or after using the biogas system. The detected protozoan genotypes are zoonotic pathogens, and contamination of vegetables may relay through runoff to the surface waters and soil. The objective of this study was to understand the role of the environment in the epidemiology of human infections in Bac Giang province, Vietnam, with a focus on investigating the presence of Cryptosporidium spp. genotypes and Giardia assemblages among 239 environmental samples and 94 faecal samples of biogas users. PCR and sequencing analysis were used to identify the occurrence and genotypes of Cryptosporidium and Giardia in these samples. Results showed that 13/333 (3.9 %) and 9/333 (2.7 %) samples were positive for Cryptosporidium oocyst and Giardia cysts, respectively. Characterization revealed the presence of Cryptosporidium scrofarum, C. suis, C. meleagridis, C. bailey and Giardia intestinalis assemblage A and E. C. scrofarum and Giardia assemblage E were identified for the first time in humans in Bac Giang. The current information from the above investigations will be valuable for protozoan source tracking and control interventions against Cryptosporidium and Giardia infection associated with biogas wastes in Vietnam.

Microbiological quality of irrigation water for cultivation of fruits and vegetables: An overview of available guidelines, water testing strategies and some factors that influence compliance

Contaminated irrigation water is among many potential vehicles of human pathogens to food plants, constituting significant public health risks especially for the fresh produce category. This review discusses some available guidelines or regulations for microbiological safety of irrigation water, and provides a summary of some common methods used for characterizing microbial contamination. The goal of such exploration is to understand some of the considerations that influence formulation of water testing guidelines, describe priority microbial parameters particularly with respect to food safety risks, and attempt to determine what methods are most suitable for their screening. Furthermore, the review discusses factors that influence the potential for microbiologically polluted irrigation water to pose substantial risks of pathogenic contamination to produce items. Some of these factors include type of water source exploited, irrigation methods, other agro ecosystem features/practices, as well as pathogen traits such as die-off rates. Additionally, the review examines factors such as food safety knowledge, other farmer attitudes or inclinations, level of social exposure and financial circumstances that influence adherence to water testing guidelines and other safe water application practices. A thorough understanding of relevant risk metrics for the application and management of irrigation water is necessary for the development of water testing criteria. To determine sampling and analytical approach for water testing, factors such as agricultural practices (which differ among farms and regionally), as well as environmental factors that modulate how water quality may affect the microbiological safety of produce should be considered. Research and technological advancements that can improve testing approach and the determination of target levels for hazard characterization or description for the many different pollution contexts as well as farmer adherence to testing requirements, are desirable.

Metagenomic sequencing combined with flow cytometry facilitated a novel microbial risk assessment framework for bacterial pathogens in municipal wastewater without cultivation

A workflow that combined metagenomic sequencing with flow cytometry was developed. The absolute abundance of pathogens was accurately estimated in mock communities and real samples. Metagenome-assembled genomes binned from metagenomic data set is robust in phylogenetic analysis and virulence profiling.

Emerging Bioanalytical Devices and Platforms for Rapid Detection of Pathogens in Environmental Samples

The development of robust bioanalytical devices and biosensors for infectious pathogens is progressing well with the advent of new materials, concepts, and technology. The progress is also stepping towards developing high throughput screening technologies that can quickly identify, differentiate, and determine the concentration of harmful pathogens, facilitating the decision-making process for their elimination and therapeutic interventions in large-scale operations. Recently, much effort has been focused on upgrading these analytical devices to an intelligent technological platform by integrating them with modern communication systems, such as the internet of things (IoT) and machine learning (ML), to expand their application horizon. This review outlines the recent development and applications of bioanalytical devices and biosensors to detect pathogenic microbes in environmental samples. First, the nature of the recent outbreaks of pathogenic microbes such as foodborne, waterborne, and airborne pathogens and microbial toxins are discussed to understand the severity of the problems. Next, the discussion focuses on the detection systems chronologically, starting with the conventional methods, advanced techniques, and emerging technologies, such as biosensors and other portable devices and detection platforms for pathogens. Finally, the progress on multiplex assays, wearable devices, and integration of smartphone technologies to facilitate pathogen detection systems for wider applications are highlighted.

Water Quality and Microbiological Contamination across the Fish Marketing Chain: A Case Study in the Peruvian Amazon (Lagoon Yarinacocha)

The contamination of the surface water of lagoons is a common problem in developing countries, and can affect fishing activities. A case study was conducted on water quality and microbiological contamination of the fishing marketing chain in the Peruvian Amazon (Laguna de Yarinacocha). The microbiological, physical–chemical and parasitological parameters of the surface water were evaluated in three points of the lagoon near the landing stage; and microbiological parameters of facilities, handlers and three species of fish (Prochilodus nigricans, Mylossoma duriventre and Siluriforme spp.). In the water, there were coliform counts ≥ 23 (Most probable number—MPN)/100 mL, Escherichia coli ≥ 3.6 MPN/100 mL, and Pseudomona spp. up to 2.2 MPN/100 mL; high turbidity and variable amounts of parasites. In facilities and handlers, high levels of coliforms, mainly Escherichia coli, and Staphylococcus aureus and Escherichia coli, were found in M. duriventre meat. A poor quality of the surface water of the lagoon is concluded that compromises part of the fishing marketing chain, mainly facilities and manipulators. Furthermore, the levels of Staphylococcus aureus and Escherichia coli in fish meat show poor handling practices and possible risk of contamination by water sources.

Microeukaryotic gut parasites in wastewater treatment plants: diversity, activity, and removal

BACKGROUND

During wastewater treatment, the wastewater microbiome facilitates the degradation of organic matter, reduction of nutrients, and removal of gut parasites. While the latter function is essential to minimize public health risks, the range of parasites involved and how they are removed is still poorly understood.

RESULTS

Using shotgun metagenomic (DNA) and metatranscriptomic (RNA) sequencing data from ten wastewater treatment plants in Switzerland, we were able to assess the entire wastewater microbiome, including the often neglected microeukaryotes (protists). In the latter group, we found a surprising richness and relative abundance of active parasites, particularly in the inflow. Using network analysis, we tracked these taxa across the various treatment compartments and linked their removal to trophic interactions.

CONCLUSIONS

Our results indicate that the combination of DNA and RNA data is essential for assessing the full spectrum of taxa present in wastewater. In particular, we shed light on an important but poorly understood function of wastewater treatment - parasite removal. Video Abstract.

Acanthamoeba species isolated from marine water in Malaysia exhibit distinct genotypes and variable physiological properties

The present study identifies the Acanthamoeba genotypes and their pathogenic potential in five marine waters in Malaysia. Fifty water samples were collected between January and May 2019. Physical parameters of water quality were measured in situ, whereas chemical and microbiological analyses were conducted in the laboratory. All samples had undergone filtration using nitrocellulose membrane and were tested for Acanthamoeba using cultivation and polymerase chain reaction by targeting the 18S ribosomal RNA gene. The pathogenic potential of all positive isolates was identified using physiological tolerance tests. Thirty-six (72.0%) samples were positive for Acanthamoeba. Total coliforms (p = 0.013) and pH level (p = 0.023) displayed significant correlation with Acanthamoeba presence. Phylogenetic analysis showed that 27 samples belonged to genotype T4, four (T11), two (T18) and one from each genotype T5, T15 and T20. Thermo- and osmo-tolerance tests signified that three (8.3%) Acanthamoeba strains displayed highly pathogenic attributes. This study is the first investigation in Malaysia describing Acanthamoeba detection in marine water with molecular techniques and genotyping. The study outcomes revealed that the marine water in Malaysia could be an integral source of Acanthamoeba strains potentially pathogenic in humans. Thus, the potential risk of this water should be monitored routinely in each region.

Legionella: A Promising Supplementary Indicator of Microbial Drinking Water Quality in Municipal Engineered Water Systems

Opportunistic pathogens (OPs) are natural inhabitants and the predominant disease causative biotic agents in municipal engineered water systems (EWSs). In EWSs, OPs occur at high frequencies and concentrations, cause drinking-water-related disease outbreaks, and are a major factor threatening public health. Therefore, the prevalence of OPs in EWSs represents microbial drinking water quality. Closely or routinely monitoring the dynamics of OPs in municipal EWSs is thus critical to ensuring drinking water quality and protecting public health. Monitoring the dynamics of conventional (fecal) indicators (e.g., total coliforms, fecal coliforms, and Escherichia coli) is the customary or even exclusive means of assessing microbial drinking water quality. However, those indicators infer only fecal contamination due to treatment (e.g., disinfection within water utilities) failure and EWS infrastructure issues (e.g., water main breaks and infiltration), whereas OPs are not contaminants in drinking water. In addition, those indicators appear in EWSs at low concentrations (often absent in well-maintained EWSs) and are uncorrelated with OPs. For instance, conventional indicators decay, while OPs regrow with increasing hydraulic residence time. As a result, conventional indicators are poor indicators of OPs (the major aspect of microbial drinking water quality) in EWSs. An additional or supplementary indicator that can well infer the prevalence of OPs in EWSs is highly needed. This systematic review argues that Legionella as a dominant OP-containing genus and natural inhabitant in EWSs is a promising candidate for such a supplementary indicator. Through comprehensively comparing the behavior (i.e., occurrence, growth and regrowth, spatiotemporal variations in concentrations, resistance to disinfectant residuals, and responses to physicochemical water quality parameters) of major OPs (e.g., Legionella especially L. pneumophila, Mycobacterium, and Pseudomonas especially P. aeruginosa), this review proves that Legionella is a promising supplementary indicator for the prevalence of OPs in EWSs while other OPs lack this indication feature. Legionella as a dominant natural inhabitant in EWSs occurs frequently, has a high concentration, and correlates with more microbial and physicochemical water quality parameters than other common OPs. Legionella and OPs in EWSs share multiple key features such as high disinfectant resistance, biofilm formation, proliferation within amoebae, and significant spatiotemporal variations in concentrations. Therefore, the presence and concentration of Legionella well indicate the presence and concentrations of OPs (especially L. pneumophila) and microbial drinking water quality in EWSs. In addition, Legionella concentration indicates the efficacies of disinfectant residuals in EWSs. Furthermore, with the development of modern Legionella quantification methods (especially quantitative polymerase chain reactions), monitoring Legionella in ESWs is becoming easier, more affordable, and less labor-intensive. Those features make Legionella a proper supplementary indicator for microbial drinking water quality (especially the prevalence of OPs) in EWSs. Water authorities may use Legionella and conventional indicators in combination to more comprehensively assess microbial drinking water quality in municipal EWSs. Future work should further explore the indication role of Legionella in EWSs and propose drinking water Legionella concentration limits that indicate serious public health effects and require enhanced treatment (e.g., booster disinfection).

Spatiotemporal Quantification of Plasmodiophora brassicae Inoculum in Relation to Clubroot Development Under Inoculated and Naturally Infested Field Conditions

Clubroot caused by Plasmodiophora brassicae is a destructive disease of cruciferous plants worldwide. A quantitative PCR (qPCR) system specific to P. brassicae was developed. Analysis of the qPCR sensitivity indicated that the lower limit of detection was 1 × 10¹ resting spores/ml, 1 × 10² spores/g of soil, and 1 × 10³ spores/g of roots and seeds. The regression curves generated from the qPCR data of different samples had a parallel relationship. The difference between the theoretical and actual concentrations was lowest at 1 × 10⁵ spores/g of sample, compared with other concentrations. The P. brassicae biomass in soil and plant root tissues after inoculated with different spore concentrations was correlated. A correlation analysis confirmed that the clubroot incidence and disease index at 6 weeks after inoculation increased as the spore concentration increased. Under field conditions, the natural inoculum density of the P. brassicae population decreased at the early stage and then increased, with P. brassicae mainly being detected at a soil depth of 0 to 50 cm. The horizontal distribution of P. brassicae varied in the field with occurrences of hot spots. This study established a qPCR-based method for quantitative detection of clubroot. The developed assay is useful for monitoring the spatiotemporal dynamics of P. brassicae in the field. It may also be applicable for clubroot forecasting as a part of proactive disease management.

Wildlife pathogen detection: evaluation of alternative DNA extraction protocols

Accurate detection of wildlife pathogens is critical in wildlife disease research. False negatives or positives can have catastrophic consequences for conservation and disease-mitigation decisions. Quantitative polymerase chain reaction is commonly used for molecular detection of wildlife pathogens. The reliability of this method depends on the effective extraction of the pathogen's DNA from host samples. A wildlife disease that has been in the centre of conservationist's attention is the amphibian disease Chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd). Here, we compare the efficiency of a spin column extraction kit (QIAGEN), commonly used in Bd DNA extraction, to an alternative spin column kit (BIOKÈ) used in extractions from other types of samples, which is considerably cheaper but not typically used for Bd DNA extraction. Additionally, we explore the effect of an enzymatic pre-treatment on detection efficiency. Both methods showed similar efficiency when extracting Bd DNA from zoospores from laboratory-created cell-cultures, as well as higher efficiency when combined with the enzymatic pre-treatment. Our results indicate that selecting the optimal method for DNA extraction is essential to ensure minimal false negatives and reduce project costs.

Multiplexed colorimetric detection of SARS-CoV-2 and other pathogens in wastewater on a 3D printed integrated microfluidic chip

Severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic has become a global public health emergency. The detection of SARS-CoV-2 and human enteric pathogens in wastewater can provide an early warning of disease outbreak. Herein, a sensitive, multiplexed, colorimetric detection (termed "SMCD") method was established for pathogen detection in wastewater samples. The SMCD method integrated on-chip nucleic acid extraction, two-stage isothermal amplification, and colorimetric detection on a 3D printed microfluidic chip. The colorimetric signal during nucleic acid amplification was recorded in real-time and analyzed by a programmed smartphone without the need for complicated equipment. By combining two-stage isothermal amplification assay into the integrated microfluidic platform, we detected SARS-CoV-2 and human enteric pathogens with sensitivities of 100 genome equivalent (GE)/mL and 500 colony-forming units (CFU)/mL, respectively, in wastewater within one hour. Additionally, we realized smart, connected, on-site detection with a reporting framework embedded in a portable detection platform, which exhibited potential for rapid spatiotemporal epidemiologic data collection regarding the environmental dynamics, transmission, and persistence of infectious diseases.

Water volume influences antibiotic resistomes and microbiomes during fish corpse decomposition

Corpse decomposition may cause serious pollution (e.g., releasing antibiotic resistance genes) to the water environment, thereby threatening public health. However, whether antibiotic resistance genes (ARGs) and microbiomes are affected by different water volumes during carcass decomposition remains unknown. Here, we investigated the effects of large/small water volumes on microbial communities and ARGs during fish cadaver decomposition by 16S rRNA high-throughput sequencing and high-throughput quantitative PCR. The results showed that the large water volume almost eliminated the effects of corpse decomposition on pH, total organic carbon (TOC), and total nitrogen (TN). When the water volume enlarged by 62.5 fold, the relative abundances of some ARGs resisting tetracycline and sulfonamide during carcass decomposition decreased by 217 fold on average, while there was also a mean 5267 fold increase of vancomycin resistance genes. Compared with the control group, the enriched types of ARGs varied between the large and small volume. Water volume, mobile genetic elements, and carcass decomposition were the most important factors affecting ARG profiles. Many opportunistic pathogens (like Bacteroides and Comamonas) were enriched in the corpse group. Bacteroides and Comamonas may be potential hosts of ARGs, indicating the potential for the spread of ARGs to humans by water pathogenic bacteria. This research highlights that the "dilution effect" can contribute to eliminating this adverse effect during corpse decomposition to a certain extent. It may provide references for environmental governance and public health.

Monitoring of diverse enteric pathogens across environmental and host reservoirs with TaqMan array cards and standard qPCR: a methodological comparison study

BACKGROUND

Multiple bacteria, viruses, protists, and helminths cause enteric infections that greatly impact human health and wellbeing. These enteropathogens are transmited via several pathways through human, animal, and environmental reservoirs. Individual qPCR assays have been extensively used to detect enteropathogens within these types of samples, whereas the TaqMan array card (TAC), which allows simultaneous detection of multiple enteropathogens, has only previously been validated in human clinical samples.

METHODS

In this methodological comparison study, we compared the performance of a custom 48-singleplex TAC relative to standard qPCR. We established the sensitivity and specificity of each method for the detection of eight enteric targets, by using spiked samples with varying levels of PCR inhibition. We then tested the prevalence and abundance of pathogens in wastewater from Melbourne (Australia), and human, animal, and environmental samples from informal settlements in Suva, Fiji using both TAC and qPCR.

FINDINGS

Both methods exhibited similarly h specificity (TAC 100%, qPCR 94%), sensitivity (TAC 92%, qPCR 100%), and quantitation accuracy (TAC 91%, qPCR 99%) in non-inhibited sample matrices with spiked gene fragments. PCR inhibitors substantially affected detection via TAC, though this issue was alleviated by ten-fold sample dilution. Among samples from informal settlements, the two techniques performed similarly for detection (89% agreement) and quantitation (R2 0·82) for the eight enteropathogen targets. The TAC additionally included 38 other enteric targets, enabling detection of diverse faecal pathogens and extensive environmental contamination that would be prohibitively labour intensive to assay by standard qPCR.

INTERPRETATION

The two techniques produced similar results across diverse sample types, with qPCR prioritising greater sensitivity and quantitation accuracy, and TAC trading small reductions in these for a cost-effective larger enteropathogen panel enabling a greater number of enteric pathogens to be analysed concurrently, which is beneficial given the abundance and variety of enteric pathogens in environments such as urban informal settlements. The ability to monitor multiple enteric pathogens across diverse reservoirs could allow better resolution of pathogen exposure pathways, and the design and monitoring of interventions to reduce pathogen load.

FUNDING

Wellcome Trust Our Planet, Our Health programme.

Highlighting the promise of qPCR-based environmental monitoring: response of the ribosomal RNA:DNA ratio of calanoid copepods to toxic cyanobacteria

Calanoid copepods are integral to aquatic food webs and may drive the bioaccumulation of toxins and heavy metals, spread of infectious diseases, and occurrence of toxic cyanobacterial harmful algal blooms (HABs) in freshwater aquatic systems. However, interrelationships between copepod and cyanobacterial population dynamics and ecophysiology remain unclear. Insights into these relationships are important to aquatic resource management, as they may help guide mitigation efforts. We developed a calanoid copepod qPCR assay to investigate how copepod abundance and physiological status relate to the abundance of cyanobacteria and the concentration of total microcystin in a HAB-prone freshwater multi-use eutrophic lake. Through in silico and in vitro validation of primers and analyses of time series, we demonstrate that our assay can be used as a reliable tool for environmental monitoring. Importantly, copepod RNA:DNA ratios on and shortly after the day when microcystin concentration was at its highest within the lake were not significantly lower (or higher) than before or after this period, suggesting that copepods may have been tolerant of microcystin levels observed and capable of perpetuating bloom events by consuming competitors of toxic cyanobacteria.

A novel bioluminescent approach to the loop-mediated isothermal amplification-based detection of Lactobacillus salivarius in feed samples

Coupling loop-mediated isothermal amplification (LAMP) with a bioluminescent assay in real-time (LAMP-BART) is a strategy that can be readily leveraged to detect bacteria in particular samples of interest without the need for costly or complicated equipments. However, this approach exhibits poor sensitivity, and it additionally amplifies all target DNA including that derived from non-viable cells. Herein, we sought to overcome these traditional pyrophosphate bioluminescent assay limitations by utilizing 2-deoxyadenosine-5-(α-thio) -triphosphate (dATPαS) in place of dATP when conducting LAMP, thereby markedly reducing and stabilizing overall background signal levels, resulting in a detection limit of 3 CFU/μL. We were additionally able to ouple this LAMP-BART with propidium monoazide (PMAxx™) as a means of eliminating false-positive signals derived from nonviable cells. Herein, we detail the development of this PMAxx™-LAMP-BART assay and its use for the detection of live Lactobacillus salivarius. Our developed approach exhibited 100% specificity, with a 3 CFU/μL limit of detection (LOD) pure culture. In the application of feed, the LOD was 10³ CFU per 10 g of spiked dry dog food and 10² CFU per 10 g of spiked chicken feed without enrichment. Traditional culture methods and a MALDI Biotyper were also used to confirm the accuracy of our novel assay system.

An assessment of the persistence of putative pathogenic bacteria in chloraminated water distribution systems

This study investigated how a chloramine loss and nitrifying conditions influenced putative pathogenic bacterial diversity in bulk water and biofilm of a laboratory- and a full-scale chloraminated water distribution systems. Fifty-four reference databases containing full-length 16S rRNA gene sequences obtained from the National Centre for Biotechnology Information database were prepared to represent fifty-four pathogenic bacterial species listed in the World Health Organisation and Australian Drinking Water Quality Guidelines. When 16S rRNA gene sequences of all samples were screened against the fifty-four reference pathogenic databases, a total of thirty-one putative pathogenic bacteria were detected in both laboratory- and full-scale systems where total chlorine residuals ranged between 0.03 - 2.2 mg/L. Pathogenic bacterial species Mycolicibacterium fortuitum and Pseudomonas aeruginosa were noted in all laboratory (i.e. in bulk water and biofilm) and in bulk water of full-scale samples and Mycolicibacterium fortuitum dominated when chloramine residuals were high. Other different pathogenic bacterial species were observed dominant with decaying chloramine residuals. This study for the first time reports the diverse abundance of putative pathogenic bacteria resilient towards chloramine and highlights that metagenomics surveillance of drinking water can serve as a rapid assessment and an early warning of outbreaks of a large number of putative pathogenic bacteria.

Plasmonic nano-antimicrobials: properties, mechanisms and applications in microbe inactivation and sensing

Bacterial, viral and fungal infections pose serious threats to human health and well-being. The continuous emergence of acute infectious diseases caused by pathogenic microbes and the rapid development of resistances against conventional antimicrobial drugs necessitates the development of new and effective strategies for the safe elimination of microbes in water, food or on surfaces, as well as for the inactivation of pathogenic microbes in human hosts. The need for new antimicrobials has triggered the development of plasmonic nano-antimicrobials that facilitate both light-dependent and -independent microbe inactivation mechanisms. This review introduces the relevant photophysical mechanisms underlying these plasmonic nano-antimicrobials, and provides an overview of how the photoresponses and materials properties of plasmonic nanostructures can be applied in microbial pathogen inactivation and sensing applications. Through a systematic analysis of the inactivation efficacies of different plasmonic nanostructures, this review outlines the current state-of-the-art in plasmonic nano-antimicrobials and defines the application space for different microbial inactivation strategies. The advantageous optical properties of plasmonic nano-antimicrobials also enhance microbial detection and sensing modalities and thus help to avoid exposure to microbial pathogens. Sensitive and fast plasmonic microbial sensing modalities and their theranostic and targeted therapeutic applications are discussed.

Applications of electrowetting-on-dielectric (EWOD) technology for droplet digital PCR

Digital microfluidics is an elegant technique based on single droplets for the design, composition, and manipulation of microfluidic systems. In digital microfluidics, especially in the electrowetting on dielectric (EWOD) system, each droplet acts as an independent reactor, which enables a wide range of multiple parallel biological and chemical reactions at the microscale. EWOD digital microfluidics reduces reagent and energy consumption, accelerates analysis, enables point-of-care diagnostic, simplifies integration with sensors, etc. Such a digital microfluidic system is especially relevant for droplet digital PCR (ddPCR), thanks to its nanoliter droplets and well-controlled volume distribution. At low DNA concentration, these small volumes allow less than one DNA strand per droplet on average (limited dilution) so that after a fixed number of PCR cycles (endpoint PCR), only the DNA in droplets containing the sequence of interest has been amplified and can be detected by fluorescence to yield an accurate count of the sequences of interest using statistical models. Focusing on ddPCR, this article summarizes the latest development and research on EWOD technology for droplet PCR over the last decade.

High-throughput diagnosis of human pathogens and fecal contamination in marine recreational water

Waterborne pathogens and their associated diseases are major threats to public health, and surveillance of pathogens and identification of the sources of pollution are imperative for preventing infections. However, simultaneously quantitative detection of multiple pathogens and pollution sources in water environments is the major challenge. In this study, we developed and validated a highly sensitive (mostly >80%) and highly specific (>99%) high-throughput quantitative PCR (HT-qPCR) approach, which could simultaneously quantify 68 marker genes of 33 human pathogens and 23 fecal markers of 10 hosts. The HT-qPCR approach was then successfully used to investigate pathogens and fecal pollution in marine recreational water samples of Xiamen, China. Totally, seven pathogenic marker genes were found in 13 beach bathing waters, which targeted Acanthamoeba spp., Clostridium perfringens, enteropathogenic Escherichia coli, Klebsiella pneumoniae, Vibrio cholera/V. parahaemolyticus and Legionella spp.. Fecal markers from human and dog were the most frequently detected, indicating human and dog feces were the main contamination in the recreational waters. Nanopore sequencing of full-length 16S rRNA gene revealed that 28 potential human pathogens were detected and electrical conductivity, salinity, oxidation-reduction potential and dissolved oxygen were significantly correlated with the variation in bacterial community. Our results demonstrated that HT-qPCR approach had the potential rapid quantification of microbial contamination, providing useful data for assessment of microbial pathogen associated health risk and development of management practices to protect human health.

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.

Hormetic Promotion of Biofilm Growth by Polyvalent Bacteriophages at Low Concentrations

Interactions between bacteriophages (phages) and biofilms are poorly understood despite their broad ecological and water quality implications. Here, we report that biofilm exposure to lytic polyvalent phages at low concentrations (i.e., 10²-10⁴ phages/mL) can counterintuitively promote biofilm growth and densification (corroborated by confocal laser scanning microscopy (CLSM)). Such exposure hormetically upregulated quorum sensing genes (by 4.1- to 24.9-fold), polysaccharide production genes (by 3.7- to 9.3-fold), and curli synthesis genes (by 4.5- to 6.5-fold) in the biofilm-dwelling bacterial hosts (i.e., Escherichia coli and Pseudomonas aeruginosa) relative to unexposed controls. Accordingly, the biofilm matrix increased its polysaccharide and extracellular DNA content relative to unexposed controls (by 41.8 ± 2.3 and 81.4 ± 2.2%, respectively), which decreased biofilm permeability and increased structural integrity. This contributed to enhanced resistance to disinfection with chlorine (bacteria half-lives were 6.08 ± 0.05 vs 3.91 ± 0.03 min for unexposed controls) and to subsequent phage infection (biomass removal was 18.2 ± 1.2 vs 32.3 ± 1.2% for unexposed controls), apparently by mitigating diffusion of these antibacterial agents through the biofilm. Overall, low concentrations of phages reaching a biofilm may result in unintended biofilm stimulation, which might accelerate biofouling, biocorrosion, or other biofilm-related water quality problems.

Improvement of Surface-Enhanced Raman Scattering Method for Single Bacterial Cell Analysis

Surface-enhanced Raman scattering (SERS) is a useful tool for label-free analysis of bacteria at the single cell level. However, low reproducibility limits the use of SERS. In this study, for the sake of sensitive and reproducible Raman spectra, we optimized the methods for preparing silver nanoparticles (AgNPs) and depositing AgNPs onto a cell surface. We found that fast dropwise addition of AgNO₃ into the reductant produced smaller and more stable AgNPs, with an average diameter of 45 ± 4 nm. Compared with that observed after simply mixing the bacterial cells with AgNPs, the SERS signal was significantly improved after centrifugation. To optimize the SERS enhancement method, the centrifugal force, method for preparing AgNPs, concentration of AgNPs, ionic strength of the solution used to suspend the cells, and density of the cells were chosen as impact factors and optimized through orthogonal experiments. Finally, the improved method could generate sensitive and reproducible SERS spectra from single Escherichia coli cells, and the SERS signals primarily arose from the cell envelope. We further verified that this optimal method was feasible for the detection of low to 25% incorporation of ¹³C isotopes by the cells and the discrimination of different bacterial species. Our work provides an improved method for generating sensitive and reproducible SERS spectra.

Quantitative detection of economically important Fusarium oxysporum f. sp. cubense strains in Africa in plants, soil and water

Banana is an important food crop and source of income in Africa. Sustainable production of banana, however, is at risk because of pests and diseases such as Fusarium wilt, caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc). Foc can be disseminated from infested to disease-free fields in plant material, water and soil. Early detection of Foc using DNA technologies is thus required to accurately identify the fungus and prevent its further dissemination with plants, soil and water. In this study, quantitative (q)PCR assays were developed for the detection of Foc Lineage VI strains found in central and eastern Africa (Foc races 1 and 2), Foc TR4 (vegetative compatibility groups (VCG) 01213/16) that is present in Mozambique, and Foc STR4 (VCG 0120/15) that occurs in South Africa. A collection of 127 fungal isolates were selected for specificity testing, including endophytic Fusarium isolates from banana pseudostems, non-pathogenic F. oxysporum strains and Foc isolates representing the 24 VCGs in Foc. Primer sets that proved to be specific to Foc Lineage VI, Foc TR4 and Foc STR4 were used to produce standard curves for absolute quantification, and the qPCR assays were evaluated based on the quality of standard curves, repeatability and reproducibility, and limits of quantification (LOQ) and detection (LOD). The qPCR assays for Foc Lineage VI, TR4 and STR4 were repeatable and reproducible, with LOQ values of 10⁻³–10⁻⁴ ng/μL and a LOD of 10⁻⁴–10⁻⁵ ng/μL. The quantitative detection of Foc strains in Africa could reduce the time and improve the accuracy for identifying the Fusarium wilt pathogen from plants, water and soil on the continent.

Preliminary Evidence of a Molecular Detection Method to Analyze Bacterial DNA as a Quality Indicator in Cosmetics

Cosmetics are a category of widely consumed and distributed products, and their manufacture is always subject to specific guidelines. Quality Control (QC) tests provide information supporting the absence of injurious organisms and regarding the microbiological stability of cosmetics. The microbiological risk analysis is typically performed using the plate count method, which is a time-consuming and operator-dependent approach. Molecular technologies allow a deeper and more sensitive testing than traditional cultures. The demand for rapid and sensitive methods is recently increasing. The aim of our study was to compare different DNA extraction methods in order to detect and quantify bacterial load in cosmetics using a qPCR system. Known numbers of microorganisms were spiked into six different cosmetics to simulate contaminated samples. DNA was extracted with seven extraction kits and then quantified by real-time qPCR. Results revealed differences in terms of cell recovery, DNA yield, and quality. The bead-beating approaches were the most suitable in our molecular workflow and lead to good quality DNA for analysis by qPCR within four hours. Combined with mechanical extraction, qPCR may represent an efficient and easy method for microorganism identification in cosmetics, and can be automated. This approach also is also applicable for the detection of probiotics used as beneficial biological components in cosmetic products. The results of our molecular method provided preliminary evidences for the rapid identification of cells (10–100) and nucleic acids in complex preparations employed for human health, in compliance with regulatory limits. The suggested methodology is easy, fast, and sensitive. Its scalability allows serial microbiological evaluation at every manufacturing step.

Simultaneous detection of Salmonella spp., Pseudomonas aeruginosa, Bacillus cereus, and Escherichia coli O157:H7 in environmental water using PMA combined with mPCR

A multiplex polymerase chain reaction (mPCR) with propidium monoazide (PMA) and internal amplification control (IAC) for the simultaneous detection of waterborne pathogens Salmonella spp., Pseudomonas aeruginosa, Bacillus cereus, and Escherichia coli O157:H7, was developed. This PMA-IAC-mPCR assay used four new specific primers based on the genes for invA, ecfX, cesB, and fliC, respectively. A 16S rRNA primer was chosen for IAC to eliminate false negative results. The photosensitive dye, propidium monoazide (PMA) was used to exclude signals from dead bacteria that could lead to false positive results. In pure culture, the limits of detection (LOD) were 10¹ CFU/ml for P. aeruginosa, 10² CFU/ml for both Salmonella spp. and E. coli O157:H7, and 10³ CFU/ml for B. cereus, respectively. In addition, with a 6-8 h enrichment of all four bacteria that were combined in a mixture that was spiked in water sample matrix, the LOD was 3 CFU/ml for Salmonella spp., 7 CFU/ml for E. coli O157:H7, 10 CFU/ml for B. cereus and 2 CFU/ml for P. aeruginosa. This PMA-IAC-mPCR assay holds potential for application in the multiplex assay of waterborne pathogens.

Rapid and highly sensitive detection of Escherichia coli O157:H7 in food with loop-mediated isothermal amplification coupled to a new bioluminescent assay

Testing for bioluminescent pyrophosphate is a convenient method of DNA detection without complex equipments, but it is insufficiently sensitive and offers no particular time advantage over other rapid detection methods. The shortcomings of the traditional bioluminescent pyrophosphate method have been addressed by using 2-deoxyadenosine-5-(α-thio)-triphosphate (dATPαS) instead of dATP for LAMP, thus reducing the high background signal and generating a constant background value. In this study, LAMP coupled to a novel bioluminescent pyrophosphate assay was developed to detect E. coli O157:H7. The new method has a limit of detection of <10 copies/μL or 5 CFU/mL; its sensitivity is higher than that of the conventional LAMP assay. Moreover, a food-borne pathogen can be detected when a single DNA template is included in the LAMP assay, making it 100 times more sensitive than the traditional LAMP method. Three hundred food samples were tested with this assay and the accuracy of detection was verified with a culture method and MALDI Biotyper. The assay only took 90-120 min and detected <10 copies of the pathogen. This method had the advantages of rapidity, sensitivity, and simplicity, so it is very competitive for the rapid and highly sensitive detection of food-borne pathogens.

Synthesis and application of superabsorbent polymer microspheres for rapid concentration and quantification of microbial pathogens in ambient water

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A portable, hand-pressed 3D-printed system with SAP microspheres was developed.

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This system could achieve efficient concentration of environmental microorganisms.

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Superior performance was achieved with varying ionic strengths in a short time.

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Optimized SAP microspheres could be reused 20 times with simple procedures.

Even though numerous methods have been developed for the detection and quantification of waterborne pathogens, the application of these methods is often hindered by the very low pathogen concentrations in natural waters. Therefore, rapid and efficient sample concentration methods are urgently needed. Here we present a novel method to pre-concentrate microbial pathogens in water using a portable 3D-printed system with super-absorbent polymer (SAP) microspheres, which can effectively reduce the actual volume of water in a collected sample. The SAP microspheres absorb water while excluding bacteria and viruses by size exclusion and charge repulsion. To improve the water absorption capacity of SAP in varying ionic strength waters (0–100 mM), we optimized the formulation of SAP to 180 g⋅L⁻¹ Acrylamide, 75 g⋅L⁻¹ Itaconic Acid and 4.0 g⋅L⁻¹ Bis-Acrylamide for the highest ionic strength water as a function of the extent of cross-linking and the concentration of counter ions. Fluorescence microscopy and double-layer agar plating respectively showed that the 3D-printed system with optimally-designed SAP microspheres could rapidly achieve a 10-fold increase in the concentration of Escherichia coli (E. coli) and bacteriophage MS2 within 20 min with concentration efficiencies of 87% and 96%, respectively. Fold changes between concentrated and original samples from qPCR and RT-qPCR results were found to be respectively 11.34–22.27 for E. coli with original concentrations from 10⁴ to 10⁶ cell·mL⁻¹, and 8.20–13.81 for MS2 with original concentrations from 10⁴ to 10⁶ PFU·mL⁻¹. Furthermore, SAP microspheres can be reused for 20 times without performance loss, significantly decreasing the cost of our concentration system.

Integrated Electrochemical Biosensors for Detection of Waterborne Pathogens in Low-Resource Settings

More than 783 million people worldwide are currently without access to clean and safe water. Approximately 1 in 5 cases of mortality due to waterborne diseases involve children, and over 1.5 million cases of waterborne disease occur every year. In the developing world, this makes waterborne diseases the second highest cause of mortality. Such cases of waterborne disease are thought to be caused by poor sanitation, water infrastructure, public knowledge, and lack of suitable water monitoring systems. Conventional laboratory-based techniques are inadequate for effective on-site water quality monitoring purposes. This is due to their need for excessive equipment, operational complexity, lack of affordability, and long sample collection to data analysis times. In this review, we discuss the conventional techniques used in modern-day water quality testing. We discuss the future challenges of water quality testing in the developing world and how conventional techniques fall short of these challenges. Finally, we discuss the development of electrochemical biosensors and current research on the integration of these devices with microfluidic components to develop truly integrated, portable, simple to use and cost-effective devices for use by local environmental agencies, NGOs, and local communities in low-resource settings.

Fast, sensitive, and reliable detection of waterborne pathogens by digital PCR after coagulation and foam concentration

The quantification of pathogens is important for assessing water safety and preventing disease outbreaks. Culture-independent approaches, such as quantitative PCR (qPCR) and digital PCR (dPCR), are useful techniques for quantifying pathogens in water samples. However, since pathogens are usually present at low concentrations in water, it is necessary to concentrate microbial cells before extracting their DNA. Many existing microbial concentration methods are inefficient or take a long time to perform. In this study, we applied a coagulation and foam separation method to concentrate environmental water samples of between 1000 and 5000 mL to 100 μL of DNA (i.e., a 1-5 × 10⁴-fold concentration). The concentration process took <1 h. The DNA samples were then used to quantify various target pathogens using dPCR. One gene, the Shiga toxin gene (stx₂) of Shiga toxin-producing Escherichia coli, was detected at 32 copies/100 mL in a river water sample. The coagulation and foam concentration method followed by dPCR reported herein is a fast, sensitive, and reliable method to quantify pathogen genes in environmental water samples.

Quantification of bacteria in water using PLS analysis of emission spectra of fluorescence and excitation-emission matrices

Bacterial contamination of drinking water is a considerable concern for public health. Tryptophan-like fluorescence (TLF) has been widely suggested to enable fast and inexpensive monitoring and quantification of bacterial contamination of water. Typically, TLF is determined at a certain excitation (ex)/emission (em) wavelengths pair. The aim of this study was to assess fluorescence spectroscopy supported with partial least squares (PLS) algorithms as a tool for a rapid evaluation of the microbial quality of water, by comparing the use of a single ex/em wavelengths pair, of the spectrum of emission obtained at a single excitation wavelength to that of whole excitation-emission matrices (EEMs). For that, laboratory-grown Escherichia coli, Bacillus subtilis and Pseudomonas aeruginosa were studied as the model systems, as well as 90 groundwater samples from 6 different wells in Israel. The groundwater samples were characterized for fluorescence emission, coliforms, fecal coliforms, fecal streptococci and heterotrophic plate counts. The PLS analysis of emission spectra and, especially, of EEMs was capable of meaningfully reducing the detection limit of microorganisms in model systems, as compared with the single ex/em wavelengths pair-based determination commonly used, reaching a detection threshold as low as 10 CFU/ml. Use of PLS-analyzed EEMs becomes beneficial also in terms of correlation and similarity between the actual and predicted bacterial concentrations. Similarly, improved detection of bacteria was also achieved in groundwater samples. Furthermore, at a level of >10⁴ CFU/ml, use of EEMs coupled with PLS enabled discrimination between E. coli, B. subtilis and P. aeruginosa.

New bioluminescence pyrophosphate assay for high-sensitivity detection of food-borne pathogens

Traditional methods of identifying food-borne pathogens are time consuming and laborious, so innovative methods for their rapid identification must be developed. Testing for bioluminescence pyrophosphate is a convenient and fast method of detecting pathogens without complex equipment. However, the sensitivity of the method is not as high as that of other methods, and it has a very high detection limit. In this study, the method was optimized to improve its sensitivity. The shortcomings of the method were first identified and corrected using dATPαS instead of dATP for the polymerase chain reaction (PCR), therefore reducing the background signal. Also, when the DNA template extracted from the food-borne pathogens was purified, the new bioluminescence pyrophosphate assay had a limit of detection of <10 copy/μl or 10 colony-forming units/ml, and its sensitivity was higher than that of fluorescent real-time quantitative PCR. Moreover, a single copy of a food-borne pathogen could be detected when a single DNA template was included in the PCR. Salmonella was detected in and isolated from 60 samples of broiler chicken, and the accuracy of the results was verified using a culture method (GB 4789.4-2010). These results showed that the new bioluminescence pyrophosphate assay has the advantages of an intuitive detection process, convenient operation, and rapid measurements. Therefore, it can be used for the rapid detection of pathogenic bacteria and probiotics in various fields.

Interlaboratory Comparative Study to Detect Potentially Infectious Human Enteric Viruses in Influent and Effluent Waters

Wastewater represents the main reusable water source after being adequately sanitized by wastewater treatment plants (WWTPs). In this sense, only bacterial quality indicators are usually checked to this end, and human pathogenic viruses usually escape from both sanitization procedures and controls, posing a health risk on the use of effluent waters. In this study, we evaluated a protocol based on aluminum adsorption-precipitation to concentrate several human enteric viruses, including norovirus genogroup I (NoV GI), NoV GII, hepatitis A virus (HAV), astrovirus (HAstV), and rotavirus (RV), with limits of detection of 4.08, 4.64, 5.46 log genomic copies (gc)/L, 3.31, and 5.41 log PCR units (PCRU)/L, respectively. Furthermore, the method was applied in two independent laboratories to monitor the presence of NoV GI, NoV GII, and HAV in effluent and influent waters collected from five WWTPs at two different sampling dates. Concomitantly, a viability PMAxx-RT-qPCR was applied to all the samples to get information on the potential infectivity of both influent and effluent waters. The ranges of the titers in influent waters for NoV GI, NoV GII, RV, and HAstV were 4.80-7.56, 5.19-7.31 log gc/L, 5.41-6.52, and 4.59-7.33 log PCRU/L, respectively. In effluent waters, the titers ranged between 4.08 and 6.27, 4.64 and 6.08 log gc/L, < 5.51, and between 3.31 and 5.58 log PCRU/L. Moreover, the viral titers detected by viability RT-qPCR showed statistical differences with RT-qPCR alone, suggesting the potential viral infectivity of the samples despite some observed reductions. The proposed method could be applied in ill-equipped laboratories, due to the lack of a requirement for a specific apparatus (i.e., ultracentrifuge).

Point-of-Care Strategies for Detection of Waterborne Pathogens

Waterborne diseases that originated due to pathogen microorganisms are emerging as a serious global health concern. Therefore, rapid, accurate, and specific detection of these microorganisms (i.e., bacteria, viruses, protozoa, and parasitic pathogens) in water resources has become a requirement of water quality assessment. Significant research has been conducted to develop rapid, efficient, scalable, and affordable sensing techniques to detect biological contaminants. State-of-the-art technology-assisted smart sensors have improved features (high sensitivity and very low detection limit) and can perform in a real-time manner. However, there is still a need to promote this area of research, keeping global aspects and demand in mind. Keeping this view, this article was designed carefully and critically to explore sensing technologies developed for the detection of biological contaminants. Advancements using paper-based assays, microfluidic platforms, and lateral flow devices are discussed in this report. The emerging recent trends, mainly point-of-care (POC) technologies, of water safety analysis are also discussed here, along with challenges and future prospective applications of these smart sensing technologies for water health diagnostics.

Bacillus-Dominant Airborne Bacterial Communities Identified During Asian Dust Events

Asian dust (AD) events have received significant attention due to their adverse effects on ecosystems and human health. However, detailed information about airborne pathogens associated with AD events is limited. This study monitored airborne bacterial communities and identified AD-specific bacteria and the potential hazards associated with these bacteria during AD events. Over a 33-month period, 40 air samples were collected under normal atmospheric conditions (non-AD events; n = 34) and during AD events (n = 6). The airborne bacterial communities in the air samples collected during non-AD events (non-AD sample) and AD events (AD sample) were evaluated using both culture-dependent and culture-independent methods. The bacterial diversity increased significantly, along with the 16S rRNA gene copy number, in AD samples (p < 0.05) and was positively correlated with PM₁₀ concentration. High throughput sequencing of the 16S rRNA gene revealed that the relative abundance of the phylum Firmicutes increased substantially in AD samples (44.3 ± 5.0%) compared with non-AD samples (27.8 ± 4.3%). Within the phylum Firmicutes, AD samples included a greater abundance of Bacillus species (almost 23.8%) than non-AD samples (almost 13.3%). Both culture-dependent and culture-independent methods detected common predominant species closely related to Bacillus cereus during AD events. Subsequent multilocus sequence typing (MLST) and enterotoxin gene assays confirmed the presence of virulence factors in B. cereus isolates from AD samples. Furthermore, the abundance of bceT, encoding enterotoxin in B. cereus, was significantly higher in AD samples (p < 0.05). The systematic characterization of airborne bacterial communities in AD samples in this study suggests that B. cereus pose risks to public health.

Integrated microfluidic systems with sample preparation and nucleic acid amplification

Rapid, efficient and accurate nucleic acid molecule detection is important in the screening of diseases and pathogens, yet remains a limiting factor at point of care (POC) treatment. Microfluidic systems are characterized by fast, integrated, miniaturized features which provide an effective platform for qualitative and quantitative detection of nucleic acid molecules. The nucleic acid detection process mainly includes sample preparation and target molecule amplification. Given the advancements in theoretical research and technological innovations to date, nucleic acid extraction and amplification integrated with microfluidic systems has advanced rapidly. The primary goal of this review is to outline current approaches used for nucleic acid detection in the context of microfluidic systems. The secondary goal is to identify new approaches that will help shape future trends at the intersection of nucleic acid detection and microfluidics, particularly with regard to increasing disease and pathogen detection for improved diagnosis and treatment.

Biological Particles in the Indoor Environment

Airborne microorganisms are very difficult to assess accurately under field conditions owing to differences in the sample collection efficiency of the selected sampler and variations in DNA extraction efficiencies. Consequently, bioaerosol abundance and biodiversity can be underestimated, making it more difficult to link specific bioaerosol components to diseases and human health risk. Owing to the low biomass in air samples, it remains a challenge to obtain a representative microbiological sample to recover sufficient DNA for downstream analyses. Improved sampling methods are particularly crucial, especially for investigating viral communities, owing to the extremely low biomass of viral particles in the air compared with other environments. Without detailed information about sampling, characterization and enumeration techniques, interpretation of exposure level is very difficult. Despite this, bioaerosol research has been enhanced by molecular tools, especially next-generation sequencing approaches that have allowed faster and more detailed characterization of air samples.

Diversity and abundance of bacterial pathogens in urban rivers impacted by domestic sewage

In developing countries, many urban rivers are suffering from heavy contamination by untreated sewage, which implies great microbial risks. However, information regarding the bacterial pathogen diversity and distribution in urban rivers is highly limited. In this study, 41 water samples of fifteen rivers and eight samples from two sewage treatment plants in Changzhou City of Yangtze River Delta were sampled. Next-generation sequencing and a self-built reference pathogen database were used to investigate the diversity of enteric and environmental pathogens. The results indicated that the studied urban rivers were harboring diverse potential pathogen species, which primarily included enteric pathogens in Arcobacter and Bacteroides, and environmental pathogens in Acinetobacter, Aeromonas and Pseudomonas. Quantification of twelve pathogens/indicators of interest by qPCR showed that Escherichia coli, Enterococcus faecalis, Campylobacter jejuni, Arcobacter cryaerophilus, Acinetobacter johnsonii, Acinetobacter lwoffii and Aeromonas spp. were abundant, with median values ranging from 3.30 to 5.85 log₁₀ copies/100 mL, while Salmonella, Legionella pheumophila, Mycobacterium avium, Pseudomonas aeruginosa and Staphylococcus aureus were infrequently quantified. The pollution of nutrients and human intestinal microorganisms indicated by specific markers were found to be prevalent but with different levels in the rivers. The correlation analyses revealed that the diversity (p < 0.01) and concentrations (p < 0.05) of the enteric pathogens highly correlated to the human fecal marker abundances, which indicated that the enteric pathogens in the urban rivers were likely to have originated from domestic sewage. The environmental pathogens, which are different from the enteric ones, showed various distribution patterns, and some of them were more abundant in the rivers of rich nutrient. Our findings provide a comprehensive understanding of the bacterial pathogen distribution and influencing factors in urban rivers that are impacted by domestic sewage, thereby establishing the foundation for urban water management.

Occurrence of antibiotic resistance genes and bacterial pathogens in water and sediment in urban recreational water

The emergence and prevalence of antibiotic resistance genes (ARGs) and pathogens in the environment are serious global health concern. However, information about the occurrence of ARGs and pathogens in recreational water is still limited. Accordingly, we investigated the occurrence of six ARGs and human pathogens in three recreational lakes, and the correlations between ARGs and one mobile genetic element (intI1) were analyzed. The quantitative PCR results showed that the concentration of ARGs ranged from 4.58 × 10⁰ to 5.0 × 10⁵ copies/mL in water and from 5.78 × 10³ to 5.89 × 10⁸ copies/g dry weight (dw) in sediment. Sul1 exhibited the highest level among the five quantifiable ARGs. The concentrations of sul1, bla_-TEM, and tetX exhibited significant positive correlations with intI1 (p < 0.05), indicating that intI1 may be involved in their proliferation. The detection frequencies of ARGs ranged from 75%-100%, indicating the prevalence of these risks in this region. The concentration of Escherichia coli, Aeromonas spp., Mycobacterium avium, Pseudomonas aeruginosa, and Salmonella enterica ranged from 10³ to 10⁵ copies/100 mL in water and 10⁴-10⁶ copies/g dw in sediment. In total, 25% of the samples harbored all pathogen genes, indicating the prevalence of these pathogens in recreational lakes. Furthermore, the next-generation sequencing results showed that 68 genera of pathogens were present, among which Aeromonas, Mycobacterium, and Pseudomonas were the dominant ones in this region, posing a considerable potential health risk to public health. Overall, the widespread distribution of ARGs and pathogens underscores the need to better monitor and mitigate their propagation in recreational lakes and the associated risks to human health.

Detectability vs. time and costs in pooled DNA extraction of cutaneous swabs: a study on the amphibian chytrid fungi

Epidemiology relies on understanding the distribution of pathogens which often can be detected through DNA-based techniques, such as quantitative Polymerase Chain Reaction (qPCR). Typically, the DNA of each individual sample is separately extracted and undergoes qPCR analysis. However, when performing field surveys and long-term monitoring, a large fraction of the samples is generally expected to be negative, especially in geographical areas still considered free of the pathogen. If pathogen detection within a population – rather than determining its individual prevalence – is the focus, work load and monetary costs can be reduced by pooling samples for DNA extraction. We test and refine a user-friendly technique where skin swabs can be pooled during DNA extraction to detect the amphibian chytrid fungi, Batrachochytrium dendrobatidis and B. salamandrivorans (Bsal). We extracted pools with different numbers of samples (from one to four swabs), without increasing reaction volumes, and each pool had one sample inoculated with a predetermined zoospore amount. Pool size did not reduce the ability to detect the two fungi, except if inoculated with extremely low zoospore amounts (one zoospore). We confirm that pooled DNA extraction of cutaneous swabs can substantially reduce processing time and costs without minimizing detection sensitivity. This is of relevance especially for the new emerging pathogen Bsal, for which pooled DNA extraction had so far not been tested and massive monitoring efforts in putatively unaffected regions are underway.