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The engineering of a home-made portable double-layer filtration and concentration device with the common syringe for rapid analysis of water samples is reported. The core elements of the device were two installed filtration membranes with different pore sizes for respective functions. The upper filtration membrane was used for preliminary intercepting large interfering impurities (interception membrane), while the lower filtration membrane was used for collecting multiple target pathogens (enrichment membrane) for determination. This combination can make the contaminated environmental water, exemplified by surface water, filtrated quickly through the device and just retained the target bacteria of Escherichia coli O157:H7, Staphylococcus aureus, and Listeria monocytogenes on the lower enrichment membrane. Integrating with surface-enhanced Raman spectra (SERS) platform to decode the SERS-Tags (SERS-TagCVa, SERS-TagR6G, and SERS-TagMB) already labeled on each of the enriched bacteria based the antibody-mediated immuno-recognition effect, fast separation, concentration, and detection of multiple pathogenic bacteria from the bulk of contaminated environmental water were realized. Results show that within 30 min, all target bacteria in the lake water can be simultaneously and accurately measured in the range from 101 to 106 CFU mL−1 with detection limit of 10.0 CFU mL−1 without any pre-culture procedures. This work highlights the simplicity, rapidness, cheapness, selectivity, and the robustness of the constructed method for simultaneous detecting multiple pathogens in aqueous samples. This protocol opens a new avenue for facilitating the development of versatile analytical tools for drinking water and food safety monitoring in underdeveloped or developing countries. [ABSTRACT FROM AUTHOR]

To assess the residual risk of waterborne contamination by Pseudomonas aeruginosa from a water network colonized by a single genotype [sequence type (ST) 299] despite the presence of antimicrobial filters in a medical intensive care unit (ICU). During the first 19-month period since the ICU opened, contamination of the water network was assessed monthly by collecting water upstream of the filters. Downstream water was also sampled to assess the efficiency of the filters. P. aeruginosa isolates from patients were collected and compared with the waterborne ST299 P. aeruginosa by multiplex-rep polymerase chain reaction (PCR), pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing. Cross-transmission events by other genotypes of P. aeruginosa were also assessed. Overall, 1.3% of 449 samples of filtered water were positive for P. aeruginosa in inoculum, varying between 1 and 104 colony-forming units/100 mL according to the tap. All P. aeruginosa hydric isolates belonged to ST299 and displayed fewer than two single nucleotide polymorphisms (SNPs). Among 278 clinical isolates from 122 patients, 10 isolates in five patients showed identical profiles to the hydric ST299 clone on both multiplex-rep PCR and PFGE, and differed by an average of fewer than five SNPs, confirming the water network reservoir as the source of contamination by P. aeruginosa for 4.09% of patients. Cross-transmission events by other genotypes of P. aeruginosa were responsible for the contamination of 1.75% of patients. Antimicrobial filters are not sufficient to protect patients from waterborne pathogens when the water network is highly contaminated. A microbiological survey of filtered water may be needed in units hosting patients at risk of P. aeruginosa infections, even when all water points-of-use are fitted with filters. [ABSTRACT FROM AUTHOR]

Although brought to the forefront in the 1980s with the AIDS pandemic, microsporidia infecting humans are still little known. Enterocytozoon bieneusi, by far the most frequent microsporidia species causing diseases in humans, is responsible for intestinal illness in both non- and immunocompromised patients. This species presents an astonishing genetic diversity with more than 500 genotypes described, some of which having a strong zoonotic potential. Indeed, E. bieneusi infects a broad array of hosts, from wild to domestic animals. This emerging eukaryotic pathogen has thus been associated with foodborne/waterborne outbreaks. Several molecular assays have been developed to enhance its diagnosis or for epidemiological purposes, providing valuable new data. Here, we propose an overview of the current knowledge on this major species among the microsporidia, so far rather neglected in human medicine.

Waterborne disease threatens public health globally. Previous studies mainly consider that the birth of pathogens in water sources arises solely by the shedding of infected individuals. However, for free-living pathogens, intrinsic growth without the presence of hosts in environment could be possible. In this paper, a stochastic waterborne disease model with a logistic growth of pathogens is investigated. We obtain the sufficient conditions for the extinction of disease and also the existence and uniqueness of an ergodic stationary distribution if the threshold ℛ 0 s > 1. By solving the Fokker–Planck equation, an exact expression of probability density function near the quasi-endemic equilibrium is obtained. Results suggest that the intrinsic growth in bacteria population induces a large reproduction number to determine the disease dynamics. Finally, theoretical results are validated by numerical examples. [ABSTRACT FROM AUTHOR]

Accurate, rapid, and multiplexed nucleic acid detection is critical for environmental and biomedical monitoring. In recent years, CRISPR-Cas12a has shown great potential in improving the performance of DNA biosensing. However, the nonspecific trans-cleavage activity of Cas12a complicates the multiplexing capability of Cas12a biosensing. We report a 3D-printed composable microfluidic plate (cPlate) device that utilizes miniaturized wells and microfluidic loading for a multiplexed CRISPR-Cas12a assay. The device easily combines loop-mediated isothermal amplification (LAMP) and CRISPR-Cas12a readout in a simple and high-throughput workflow with low reagent consumption. To ensure the maximum performance of the device, the concentration of Cas12a and detection probe was optimized, which yielded a four-fold sensitivity improvement. Our device demonstrates sensitive detection to the fg mL− 1 level for four waterborne pathogens including shigella, campylobacter, cholera, and legionella within 1 h, making it suitable for low-resource settings. [ABSTRACT FROM AUTHOR]

Building on a previously developed workflow for rapid and sensitive pathogen detection by qPCR, this work has established a sample treatment strategy that produces consistent quantification efficiencies (QEs) for Campylobacter jejuni against a complex and highly variable sample matrix from a suburban river. The individual treatments most effective at minimizing the inhibitory effects of the sample matrix were pH buffering with HEPES (50 mM, pH 5.7) and addition of the surfactant Tween 20 (2% v/v). Unexpectedly, sample acidification (pH 4–5) resulting from the use of aged Tween 20 that had undergone partial hydrolysis, appeared to play a key role in enhancing QE. This effect could be replicated by direct pH adjustment with dilute hydrochloric acid and may be linked to the solubilization and removal of inhibitory particles at an acidic pH. While the effectiveness of each individual treatment method varied, a combined treatment of either HEPES buffer + Tween 20, or direct pH adjustment + Tween 20, consistently produced QEs of 60%–70% and up to 100%, respectively, over a sampling period of one year. The consistency and scalability of this workflow make it a suitable alternative to culture-based ISO methods for detecting Campylobacter spp. [ABSTRACT FROM AUTHOR]

This document is an editorial titled "Advancing molecular diagnostic tools for robust surveillance of microbial water quality." It emphasizes the importance of monitoring microbial water quality for human, animal, and environmental health. The presence of microbial pollutants in water can have negative impacts, including waterborne outbreaks. The editorial discusses the use of molecular diagnostic tools, such as next-generation sequencing and CRISPR technology, for detecting and assessing microbial contamination in water. It also highlights the importance of integrated assessment tools and modeling for evaluating and predicting microbial water quality and health risks. The document concludes by emphasizing the need for coordinated and validated methods to ensure effective and reliable water quality assessment. [Extracted from the article]

The present study investigated the water quality index, microbial composition and antimicrobial resistance genes in urban water habitats. Combined chemicals testing, metagenomic analyses and qualitative PCR (qPCR) were conducted on 20 locations, including rivers from hospital surrounds (n = 7), community surrounds (n = 7), and natural wetlands (n = 6). Results showed that the indexes of total nitrogen, phosphorus, and ammonia nitrogen of hospital waters were 2-3 folds high than that of water from wetlands. Bioinformatics analysis revealed a total of 1,594 bacterial species from 479 genera from the three groups of water samples. The hospital-related samples had the greatest number of unique genera, followed by those from wetlands and communities. The hospitalrelated samples contained a large number of bacteria associated with the gut microbiome, including Alistipes, Prevotella, Klebsiella, Escherichia, Bacteroides, and Faecalibacterium, which were all significantly enriched compared to samples from the wetlands. Nevertheless, the wetland waters enriched bacteria from Nanopelagicus, Mycolicibacterium and Gemmatimonas, which are typically associated with aquatic environments. The presence of antimicrobial resistance genes (ARGs) that were associated with different species origins in each water sample was observed. The majority of ARGs from hospital-related samples were carried by bacteria from Acinetobacter, Aeromonas and various genera from Enterobacteriaceae, which each was associated with multiple ARGs. In contrast, the ARGs that were exclusively in samples from communities and wetlands were carried by species that encoded only 1 to 2 ARGs each and were not normally associated with human infections. The qPCR showed that water samples of hospital surrounds had higher concentrations of intI1 and antimicrobial resistance genes such as tetA, ermA, ermB, qnrB, sul1, sul2 and other beta-lactam genes. Further genes of functional metabolism reported that the enrichment of genes associated with the degradation/utilization of nitrate and organic phosphodiester were detected in water samples around hospitals and communities compared to those from wetlands. Finally, correlations between the water quality indicators and the number of ARGs were evaluated. The presence of total nitrogen, phosphorus, and ammonia nitrogen were significantly correlated with the presence of ermA and sul1. Furthermore, intI1 exhibited a significant correlation with ermB, sul1, and blaSHV, indicating a prevalence of ARGs in urban water environments might be due to the integron intI1's diffusion-promoting effect. However, the high abundance of ARGs was limited to the waters around the hospital, and we did not observe the geographical transfer of ARGs along with the river flow. This may be related to water purifying capacity of natural riverine wetlands. Taken together, continued surveillance is required to assess the risk of bacterial horizontal transmission and its potential impact on public health in the current region. [ABSTRACT FROM AUTHOR]

Construction activities in healthcare settings potentially expose building occupants to waterborne pathogens including Legionella and have been associated with morbidity and mortality. A Water Management for Construction—Infection Control Risk Assessment (WMC-ICRA) tool was developed addressing gaps in building water management programs. This enables healthcare organizations to meet the requirements of ANSI/ASHRAE Standard 188 referenced in numerous guidelines and regulations. A WMC-ICRA was modeled after the ICRA required for prevention and control of airborne pathogens to reduce the risk of healthcare associated infections. The tool allows users to evaluate risk from waterborne pathogen exposure by analyzing construction activities by project category and building occupant risk group. The users then select an appropriate level of risk mitigation measures. Technical aspects (e.g., water age/stagnation, flushing, filtration, disinfection, validation testing), are presented to assist with implementation. An exemplar WMC-ICRA tool is presented as ready for implementation by infection prevention and allied professionals, addressing current gaps in water management, morbidity/mortality risk, and regulatory compliance. To reduce exposure to waterborne pathogens in healthcare settings and improve regulatory compliance, organizations should examine the WMC-ICRA tool, customize it for organization-specific needs, while formulating an organizational policy to implement during all construction activities.

Cryptosporidiosis is a water- and food-borne zoonotic disease caused by the protozoon parasite of the genus Cryptosporidium. C. hominis and C. parvum are the main two species causing infections in humans and animals. The disease can be transmitted by the fecal–oral route as well as the respiratory route. The infective stage (sporulated oocysts) is resistant to different disinfectants including chlorine. Currently, no effective therapeutic drugs or vaccines are available to treat and control Cryptosporidium infection. To prevent cryptosporidiosis in humans and animals, we need to understand better how the disease is spread and transmitted, and how to interrupt its transmission cycle. This review focuses on understanding cryptosporidiosis, including its infective stage, pathogenesis, life cycle, genomics, epidemiology, previous outbreaks, source of the infection, transmission dynamics, host spectrum, risk factors and high-risk groups, the disease in animals and humans, diagnosis, treatment and control, and the prospect of an effective anti-Cryptosporidium vaccine. It also focuses on the role of the One Health approach in managing cryptosporidiosis at the animal–human–environmental interface. The summarized data in this review will help to tackle future Cryptosporidium infections in humans and animals and reduce the disease occurrence. [ABSTRACT FROM AUTHOR]

Metagenomics offers the highest level of strain discrimination of bacterial pathogens from complex food and water microbiota. With the rapid evolvement of assembly algorithms, defining an optimal assembler based on the performance in the metagenomic identification of foodborne and waterborne pathogens is warranted. We aimed to benchmark short-read assemblers for the metagenomic identification of foodborne and waterborne pathogens using simulated bacterial communities. Bacterial communities on fresh spinach and in surface water were simulated by generating paired-end short reads of Illumina HiSeq, MiSeq, and NovaSeq at different sequencing depths. Multidrug-resistant Salmonella Indiana SI43 and Pseudomonas aeruginosa PAO1 were included in the simulated communities on fresh spinach and in surface water, respectively. ABySS, IDBA-UD, MaSuRCA, MEGAHIT, metaSPAdes, and Ray Meta were benchmarked in terms of assembly quality, identifications of plasmids, virulence genes, Salmonella pathogenicity island, antimicrobial resistance genes, chromosomal point mutations, serotyping, multilocus sequence typing, and whole-genome phylogeny. Overall, MEGHIT, metaSPAdes, and Ray Meta were more effective for metagenomic identification. We did not obtain an optimal assembler when using the extracted reads classified as Salmonella or P. aeruginosa for downstream genomic analyses, but the extracted reads showed consistent phylogenetic topology with the reference genome when they were aligned with Salmonella or P. aeruginosa strains. In most cases, HiSeq, MiSeq, and NovaSeq were comparable at the same sequencing depth, while higher sequencing depths generally led to more accurate results. As assembly algorithms advance and mature, the evaluation of assemblers should be a continuous process. [ABSTRACT FROM AUTHOR]

• The finite difference time domain (FDTD) method is utilized to design and analyze the optical properties of silver@gold nanorods (Ag@Au-NR) that interact with waterborne pathogens. • Optimization of the Ag@Au-NR structure was conducted using response surface methodology to obtain nanoparticles that have superior detection performance. • The aspect ratio, width, and Au-thickness significantly influence the absorption spectrum and detection performance of the biosensor. • We propose a novel method to recognize waterborne pathogens such as Vibrio cholerae , Escherichia coli , and Salmonella typhimurium based on the absorption spectrum of Ag@Au-NR. The global issue of waterborne pathogen transmission in developing nations necessitates innovative solutions for pathogenic bacterial detection in drinking water sources. In this investigation, we present an innovative method for pathogen detection utilizing silver@gold nanorods (Ag@Au-NR) as optical-based biosensors, designed using the finite difference time domain approach. Additionally, we utilize response surface methodology to investigate and enhance the structure of Ag@Au-NR, thereby improving its performance in detecting specific pathogenic bacteria. Our research focuses on addressing the presence of three critical waterborne pathogens: Vibrio cholerae, Escherichia coli, and Salmonella typhimurium. We systematically optimize the Ag@Au-NR structure by varying parameters such as aspect ratio, nanorod width, and Au-thickness. Key response variables evaluated encompass localized surface plasmon resonance (LSPR) peak shift and detection accuracy. By employing rigorous calculations and optimization procedures, we obtained an Ag@Au-NR structure capable of undergoing a substantial shift in LSPR peak, reaching up to 13.099 nm. This achieved outcome is accompanied by a high detection accuracy of 0.016 during interactions with pathogens. This study also explores an optimal Ag@Au-NR structure to generate distinct LSPR peaks for individual pathogens, aiming to enhance the biosensor's selectivity properties. We present a two-step pathogen recognition approach reliant on the absorption peaks generated throughout the detection process. This method involves (i) discerning pathogens based on the LSPR peak shifting and (ii) evaluating the area under the absorption curve. The remarkable detection performance achieved in this study with Ag@Au-NR signifies a pivotal advancement in LSPR-based biosensors. This breakthrough offers promising avenues for developing highly efficient biosensors for safeguarding public health and addressing waterborne pathogen contamination in resource-constrained regions. [ABSTRACT FROM AUTHOR]

Waterborne pathogens in urban rivers of estuarine areas pose a great threat to human health. In this study, both bacterial and fungal community structures of four urban rivers in the Pearl River estuarine area were investigated using high-throughput sequencing. Results showed that the diversity and richness indices of the bacterial community were higher than that of fungi. Taxonomic analysis indicated that the most abundant bacterial phylum was Actinobacteria, while the most abundant fungal phylum was Ascomycota. In addition, 35 major pathogens were found at the level of genus with Mycobacterium being the most abundant. Specifically, pathogens of Burkholderiales, Bartonella, Rhizobiales, Bordetella and Brucella were first detected in this area, although with relative low abundances. Spearman correlation analysis revealed that temperature, TOC and TDP were significant factors shaping both total microbial community and pathogenic microbial community structure. TDP was positively correlated with almost all the potential pathogenic genera. PICRUSt analysis further predicted that bacterial infectious disease was the most abundant pathway associated with microbial functions of human disease in all the studied rivers. This work provides useful information not only for in-depth understanding of bacterial and fungal communities in urban rivers of estuarine areas under anthropogenic disturbances but also for environmental risk management of potential waterborne pathogens.

Nontuberculous mycobacteria (NTM) are common in the environment and certain species can cause serious infections. Improved environmental surveillance methods are needed to combat the increased incidence of NTM disease. Recently, two methods were developed to improve NTM detection. The MYChrOme™ Culture Plate (patent-pending, Phigenics, LLC, Reno, NV, USA) is the first chromogenic medium for rapid-growing NTM detection in water samples. NTM Elite agar (Biomerieux, Marcy-l'Étoile, France), was developed for rapid-growing NTM detection in clinical samples. Fifty water samples (25 potable and 25 non-potable) with three technical replicates were analyzed by each method and Middlebrook 7H11 selective medium (7H11S) (ASTM E2563-07 method modified for water). The MYChrOme method was overall equivalent to or better than 7H11S medium and NTM Elite agar for the detection of rapid-growing NTM in potable water. All three methods detected similar amounts of NTM in non-potable water samples. The chromogenic property of MYChrOme allowed NTM colonies to be quickly identified and differentiated from other bacteria. Additional analysis is required for colony confirmation on 7H11S medium and NTM Elite agar. The use of innovative environmental NTM diagnostics, in addition to proper water management, can greatly reduce the risk of NTM disease. [ABSTRACT FROM AUTHOR]

Construction activities in healthcare settings potentially expose building occupants to waterborne pathogens including Legionella and have been associated with morbidity and mortality. A Water Management for Construction—Infection Control Risk Assessment (WMC-ICRA) tool was developed addressing gaps in building water management programs. This enables healthcare organizations to meet the requirements of ANSI/ASHRAE Standard 188 referenced in numerous guidelines and regulations. A WMC-ICRA was modeled after the ICRA required for prevention and control of airborne pathogens to reduce the risk of healthcare associated infections. The tool allows users to evaluate risk from waterborne pathogen exposure by analyzing construction activities by project category and building occupant risk group. The users then select an appropriate level of risk mitigation measures. Technical aspects (e.g., water age/stagnation, flushing, filtration, disinfection, validation testing), are presented to assist with implementation. An exemplar WMC-ICRA tool is presented as ready for implementation by infection prevention and allied professionals, addressing current gaps in water management, morbidity/mortality risk, and regulatory compliance. To reduce exposure to waterborne pathogens in healthcare settings and improve regulatory compliance, organizations should examine the WMC-ICRA tool, customize it for organization-specific needs, while formulating an organizational policy to implement during all construction activities. [ABSTRACT FROM AUTHOR]

Sea urchins are primary herbivores on coral reefs, regulating algal biomass and facilitating coral settlement and growth. 1,2,3,4,5,6,7,8,9,10,11,12 Recurring mass mortality events (MMEs) of Diadema species Gray, 1825 have been recorded globally, 13,14,15,16,17,18,19,20,21,22,23 the most notorious and ecologically significant of which occurred in the Caribbean in 1983, 14,17,19,20 contributing to the shift from coral to algal-dominated ecosystems. 17,24,25 Recently, first evidence of Diadema setosum mass mortality was reported from the eastern Mediterranean Sea. 23 Here, we report extensive mass mortalities of several diadematoid species inhabiting the Red Sea and Western Indian Ocean (WIO) 26,27,28 including first evidence of mortalities in the genus Echinothrix Peters, 1853. Mortalities initiated in the Gulf of Aqaba on December 2022 and span the Red Sea, the Gulf of Oman, and the Western Indian Ocean (Réunion Island), with population declines reaching 100% at some sites. Infected individuals are characterized by spine loss and tissue necrosis, resulting in exposed skeletons (i.e., tests) and mortality. Molecular diagnostics of the 18S rRNA gene confirm the presence of a waterborne scuticociliate protozoan most closely related to Philaster apodigitiformis in infected specimens—identical to the pathogen found in the 2022 Caribbean mass mortality of Diadema antillarum. 13,15,18 Collapse of these key benthic grazers in the Red Sea and Western Indian Ocean may lead to algal dominance over corals, threatening the stability of coral reefs on a regional scale. 29,30,31,32 We issue a warning regarding the further expansion of mortalities and call for immediate monitoring and conservation efforts for these key ecological species. • Mass mortalities of diadematoid sea urchins spread through the Red Sea and WIO • Species of both Diadema and Echinothrix are susceptible to mortalities • Population declines in D. setosum and E. calamaris in the Gulf of Aqaba reach 100% • Molecular analyses confirm the presence of a Philaster -like scutocilliate protozoan Roth et al. report regional-scale mass mortalities of diadematoid sea urchins in the Red Sea and Western Indian Ocean, driving population declines of up to 100% in Diadema and Echinothrix species since December 2022. Genetic analyses confirm the presence of the Caribbean D. antillarum pathogen, a Philaster- like scuticociliate, in infected specimens. [ABSTRACT FROM AUTHOR]

Waterborne pathogens in urban rivers of estuarine areas pose a great threat to human health. In this study, both bacterial and fungal community structures of four urban rivers in the Pearl River estuarine area were investigated using high-throughput sequencing. Results showed that the diversity and richness indices of the bacterial community were higher than that of fungi. Taxonomic analysis indicated that the most abundant bacterial phylum was Actinobacteria, while the most abundant fungal phylum was Ascomycota. In addition, 35 major pathogens were found at the level of genus with Mycobacterium being the most abundant. Specifically, pathogens of Burkholderiales, Bartonella, Rhizobiales, Bordetella and Brucella were first detected in this area, although with relative low abundances. Spearman correlation analysis revealed that temperature, TOC and TDP were significant factors shaping both total microbial community and pathogenic microbial community structure. TDP was positively correlated with almost all the potential pathogenic genera. PICRUSt analysis further predicted that bacterial infectious disease was the most abundant pathway associated with microbial functions of human disease in all the studied rivers. This work provides useful information not only for in-depth understanding of bacterial and fungal communities in urban rivers of estuarine areas under anthropogenic disturbances but also for environmental risk management of potential waterborne pathogens. [ABSTRACT FROM AUTHOR]

Background: An important part of water quality control is waterborne pathogen detection. Conventional microorganism detections are done by costly and complicated biochemical approaches, which leave chemical pollutions and require professional laboratories, technicians, and much time. Recently, machine-learning-based image classification algorithms are developed for faster, cheaper, simpler, and more environmentally friendly microorganism detection. Most of them are designed for conventional microscopic images. On the other hand, the optofluidic system is a smaller and cheaper alternative to conventional microscopes, so we aim to propose a microorganism classification algorithm for optofluidic images. Method: In our previous study, the Binarized-Greyscale-Hybrid Algorithm with Multi-Region Binarization (BiGHAM) algorithm was developed for our optofluidic image dataset. In this paper, a new circle-based region partition method for the Multi-Region Binarization and a new mutual-information-based feature selection method were proposed to improve the BiGHAM method. Additionally, an implementation example of how to adapt and apply our method on an open dataset was presented. Results and conclusion: With the circle-based region partition method and the new feature combination selected based on mutual information, the improved-BiGHAM algorithm achieved higher classification accuracies, and the algorithm is simpler than the previous BiGHAM method during training. For our optofluidic image dataset, the accuracy improvement for the 1000-image-per-class case was from 94.8 to 96.3%, and for the 30-image-per-class case was from 77.8 to 85.6% with the support vector machine as the classifier. The adapted algorithm also works well on the open dataset, showing the potential to be extended to applications on different microorganism images.

Metagenomics offers the highest level of strain discrimination of bacterial pathogens from complex food and water microbiota. With the rapid evolvement of assembly algorithms, defining an optimal assembler based on the performance in the metagenomic identification of foodborne and waterborne pathogens is warranted. We aimed to benchmark short-read assemblers for the metagenomic identification of foodborne and waterborne pathogens using simulated bacterial communities. Bacterial communities on fresh spinach and in surface water were simulated by generating paired-end short reads of Illumina HiSeq, MiSeq, and NovaSeq at different sequencing depths. Multidrug-resistant Salmonella Indiana SI43 and Pseudomonas aeruginosa PAO1 were included in the simulated communities on fresh spinach and in surface water, respectively. ABySS, IDBA-UD, MaSuRCA, MEGAHIT, metaSPAdes, and Ray Meta were benchmarked in terms of assembly quality, identifications of plasmids, virulence genes, Salmonella pathogenicity island, antimicrobial resistance genes, chromosomal point mutations, serotyping, multilocus sequence typing, and whole-genome phylogeny. Overall, MEGHIT, metaSPAdes, and Ray Meta were more effective for metagenomic identification. We did not obtain an optimal assembler when using the extracted reads classified as Salmonella or P. aeruginosa for downstream genomic analyses, but the extracted reads showed consistent phylogenetic topology with the reference genome when they were aligned with Salmonella or P. aeruginosa strains. In most cases, HiSeq, MiSeq, and NovaSeq were comparable at the same sequencing depth, while higher sequencing depths generally led to more accurate results. As assembly algorithms advance and mature, the evaluation of assemblers should be a continuous process.

Cryptosporidiosis is a water- and food-borne zoonotic disease caused by the protozoon parasite of the genus Cryptosporidium. C. hominis and C. parvum are the main two species causing infections in humans and animals. The disease can be transmitted by the fecal–oral route as well as the respiratory route. The infective stage (sporulated oocysts) is resistant to different disinfectants including chlorine. Currently, no effective therapeutic drugs or vaccines are available to treat and control Cryptosporidium infection. To prevent cryptosporidiosis in humans and animals, we need to understand better how the disease is spread and transmitted, and how to interrupt its transmission cycle. This review focuses on understanding cryptosporidiosis, including its infective stage, pathogenesis, life cycle, genomics, epidemiology, previous outbreaks, source of the infection, transmission dynamics, host spectrum, risk factors and high-risk groups, the disease in animals and humans, diagnosis, treatment and control, and the prospect of an effective anti-Cryptosporidium vaccine. It also focuses on the role of the One Health approach in managing cryptosporidiosis at the animal–human–environmental interface. The summarized data in this review will help to tackle future Cryptosporidium infections in humans and animals and reduce the disease occurrence.

Methods for recovery and identification of Legionella spp. in water have not been improved significantly since the traditional culture method using buffered charcoal yeast extract (BCYE) agar was developed in 1979. Variations to the BCYE method include sample concentration techniques, acid and heat treatment of samples, and inclusions of antibiotics and dyes in the medium to improve Legionella recovery. A new culture method—Legiolert—was developed and is targeted specifically for recovery and enumeration of Legionella pneumophila, the pathogen responsible for >97% of Legionella pneumonia cases. This study assessed the performance of the Legiolert and BCYE methods in water samples. A total of 247 potable water samples were collected and analyzed using both methods. Mean recoveries in reagent water were similar for both methods (~70%), while Legiolert was more likely than BCYE to detect L. pneumophila when it is present in low numbers. Article Impact Statement: The Legiolert method for enumeration of Legionella pneumophila in water is a significant improvement over the buffered charcoal yeast extract method and should be adopted. [ABSTRACT FROM AUTHOR]

A universal filtration and enzyme-based workflow has been established to allow for the rapid and sensitive quantification of leading pathogens Cryptosporidium parvum, Giardia gamblia, Campylobacter jejuni, and Escherichia coli from tap water samples with volumes up to 100 mL, and the potential to scale up to larger volumes. qPCR limits of quantification as low as four oocysts for Cryptosporidium, twelve cysts for Giardia, two cells for C. jejuni, and nineteen cells for E. coli per reaction were achieved. A polycarbonate filter-based sampling method coupled with the prepGEM enzyme-based DNA extraction system created a single-step transfer workflow that required as little as 20 min of incubation time and a 100 µL reaction mix. The quantification via qPCR was performed directly on the prepGEM extract, bypassing time-consuming, labour-intensive conventional culture-based methods. The tap water samples were shown to contain insoluble particles that inhibited detection by reducing the quantification efficiency of a representative pathogen (C. jejuni) to 30–60%. This sample inhibition was effectively removed by an on-filter treatment of 20% (v/v) phosphoric acid wash. Overall, the established workflow was able to achieve quantification efficiencies of 92% and higher for all four leading water pathogens, forming the basis of a rapid, portable, and low-cost solution to water monitoring.

Human viruses are ubiquitous contaminants in surface waters, where they can persist over extended periods of time. Among the factors governing their environmental persistence, the control (removal or inactivation) by microorganisms remains poorly understood. Here, we determined the contribution of indigenous bacteria and protists to the decay of human viruses in surface waters. Incubation of echovirus 11 (E11) in freshwater from Lake Geneva and seawater from the Mediterranean Sea led to a 2.5-log10 reduction in the infectious virus concentration within 48 h at 22°C, whereas E11 was stable in sterile controls. The observed virus reduction was attributed to the action of both bacteria and protists in the biologically active matrices. The effect of microorganisms on viruses was temperature dependent, with a complete inhibition of microbial virus control in lake water at temperatures of ≤16°C. Among three protist isolates tested (Paraphysomonas sp., Uronema marinum, and Caecitellus paraparvulus), Caecitellus paraparvulus was particularly efficient at controlling E11 (2.1-log10 reduction over 4 days with an initial protist concentration of 103 cells ml-1). In addition, other viruses (human adenovirus type 2 and bacteriophage H6) exhibited different grazing kinetics than E11, indicating that the efficacy of antiviral action also depended on the type of virus. In conclusion, indigenous bacteria and protists in lake water and seawater can modulate the persistence of E11. These results pave the way for further research to understand how microorganisms control human viral pathogens in aquatic ecosystems and to exploit this process as a treatment solution to enhance microbial water safety. [ABSTRACT FROM AUTHOR]

While harvested rainwater can serve as an alternative water supply, microbial contaminants within the collection system can negatively affect water quality. Here, we investigated the impact of roofing material on the microbial quality of rainwater freshly harvested from pilot-scale roofs (concrete tile, cool, green, Galvalume® metal, and asphalt fiberglass shingle). The microbial quality of freshly harvested rainwater from six rain events over two years was analyzed by high-throughput sequencing and culture-dependent and -independent techniques. The concentrations of total coliform were significantly different among rainwaters harvested from the various roofing materials (p-value >0.05). However, the fecal coliform concentrations and the copy numbers of Enterococcus 23S rRNA genes and total Bacteria 16S rRNA genes did not vary by type of roofing material in a statistically significant way. Potential human pathogens such as Legionella, Escherichia coli O157:H7, Shiga-toxin-producing Escherichia coli , and adenovirus were detected at least once in rainwater harvested from the different roofing materials, even though the lowest occurrence of those potential human pathogens was noted from the metal roof. Also, substantial variation in the microbial communities from the different roofing materials was observed at the family and genus levels. These results demonstrate that the type of roofing material affects the microbial quality of freshly harvested rainwater, indicating that the choice of roofing material could shape the microbial community structure entering a rainwater storage tank. Given that detection of potential pathogens in the freshly harvested rainwater also differed between roofing materials, the type of roofing used to capture rainwater needs to be considered in rainwater harvesting system design, particularly if the water is intended for potable use. Image 1 • Using culture-dependent and -independent techniques, microbial water qualities from roof-harvested rainwater was examined. • The potential human pathogens were detected in harvested rainwater from different roofing material. • Types of roofing materials shape microbial community structure from harvested rainwater. • The metal roof tends to have least human pathogen and microbial community was similar to ambient rainwater. [ABSTRACT FROM AUTHOR]

Leptospirosis is a disease endemic to both rural and urban areas of tropical countries and resource-poor communities. Little information is available on the presence of Leptospira spp. in urban water sources. A study was conducted to detect pathogenic Leptospira in ornamental water fountains in Cali, Colombia. Twenty-seven water fountains were tested for pathogenic Leptospira using a multiplex PCR assay targeting the secY and the flaB genes. Pathogenic Leptospira was confirmed in 11 (41%) ornamental water fountains. Plazas, building exteriors, and sidewalks presented the highest proportion (67%) of pathogenic Leptospira-positive water fountains. Urban ornamental water fountains might be sources of pathogenic Leptospira and might pose a risk to humans who come into close contact, although relevance from a public health perspective is yet to be established. [ABSTRACT FROM AUTHOR]

In this paper, we first propose a reaction–diffusion waterborne pathogen model with general incidence rate, incorporating both direct and indirect transmission pathways. Then, using the basic reproduction number we investigate the global dynamical behaviors of the continuous model. By nonstandard finite difference scheme, we derive a discrete counterpart of the continuous model. Then, the global properties of the discretized model are investigated. Finally, we conclude the paper by an example and numerical simulations. [ABSTRACT FROM AUTHOR]

Environmental waters (EW) substantially lend to the transmission of Helicobacter pylori (Hp). But the increase in Hp infections and antimicrobial resistance is often attributed to socioeconomic status. The connection between socioeconomic status and Hp prevalence in EW is however yet to be investigated. This study aimed to assess the impacts of socioeconomic indices (SI: continent, world bank region (WBR), world bank income (WBI), WHO region, Socio-demographic Index (SDI quintile), Sustainable Development Index (SuDI), and Human Development Index (HDI)) on the prevalence of Hp in EW. Hp-EW data were fitted to a generalized linear mixed-effects model and SI-guided meta-regression models with a 1000-resampling test. The worldwide prevalence of Hp in EW was 21.76% [95% confidence interval [CI]: 10.29–40.29], which declined significantly from 59.52% [43.28–74.37] in 1990–99 to 19.36% [3.99–58.09] in 2010–19 and with increasing trend in 2020–22 (33.33%, 22.66–45.43). Hp prevalence in EW was highest in North America (45.12%, 17.07–76.66), then Europe (22.38%, 5.96–56.74), South America (22.09%, 13.76–33.49), Asia (2.98%, 0.02–85.17), and Africa (2.56%, 0.00–99.99). It was negligibly different among sampling settings, WBI, and WHO regions demonstrating highest prevalence in rural location [42.62%, 3.07–94.56], HIEs [32.82%, 13.19–61.10], and AMR [39.43%, 19.92–63.01], respectively. However, HDI, sample size, and microbiological method robustly predict Hp prevalence in EW justifying 26.08%, 21.15%, and 16.44% of the true difference, respectively. In conclusion, Hp is highly prevalence in EW across regional/socioeconomic strata and thus challenged the uses of socioeconomic status as surrogate for hygienic/sanitary practices in estimating Hp infection prevalence. [Display omitted] • Environmental waters (EW) add to H. pylori (Hp) spread via (in)direct pathways. • Global Hp prevalence in EW was 21.76% [95%CI: 10.29 – 40.29]. • Human development index, sample size, & methods robustly predict Hp prevalence in EW. • Hp is highly prevalence in EW dismissing regional socioeconomic strength. [ABSTRACT FROM AUTHOR]

Fecal indicator bacteria (FIB) are the basis for water quality regulations and are considered proxies for waterborne pathogens when conducting human health risk assessments. The direct detection of pathogens in water and simultaneous identification of the source of fecal contamination are possible with microarrays, circumventing the drawbacks to FIB approaches. A multigene target microarray was used to assess the prevalence of waterborne pathogens in a fecally impaired mixed-use watershed. The results indicate that fecal coliforms have improved substantially in the watershed since its listing as a 303(d) impaired stream in 2002 and are now near United States recreational water criterion standards. However, waterborne pathogens are still prevalent in the watershed, as viruses (bocavirus, hepatitis E and A viruses, norovirus, and enterovirus G), bacteria (Campylobacter spp., Clostridium spp., enterohemorrhagic and enterotoxigenic Escherichia coli, uropathogenic E. coli, Enterococcus faecalis, Helicobacter spp., Salmonella spp., and Vibrio spp.), and eukaryotes (Acanthamoeba spp., Entamoeba histolytica, and Naegleria fowleri) were detected. A comparison of the stream microbial ecology with that of sewage, cattle, and swine fecal samples revealed that human sources of fecal contamination dominate in the watershed. The methodology presented is applicable to a wide range of impaired streams for the identification of human health risk due to waterborne pathogens and for the identification of areas for remediation efforts. [ABSTRACT FROM AUTHOR]

Sewage treatment plants (STPs) are one of the sources of pathogens discharged into surface water. An investigation was carried out over the duration of 12 months in Henan Province, China, to evaluate the health influence of municipal wastewater effluent discharge on water quality of the receiving water. A discharge-based quantitative microbial risk assessment (QMRA) was employed, taking into account the vegetables consumption habits of the Chinese, population subgroups with different immune statuses and ages, to evaluate the incremental disease burden from agricultural irrigation and swimming exposure scenarios associated with increased concentration of the protozoan Cryptosporidium and/or Giardia in the receiving river. The results shown that all the STP influent samples contained Cryptosporidium and Giardia with average density of 142.31 oocysts/L and 1187.06 cysts/L, respectively. The QMRA results demonstrated that the estimated additional health burdens due to discharged effluent for both parasites were slightly violated the threshold of 10 −6 DALYs per person per year set by WHO. Mitigation measures should be planned and executed by season since more disease burdens were borne during hot season than other seasons. The sensitivity analysis highlighted the great importance of stability of STP treatment process. This study provides useful information to improve the safety of surface water and deduce the disease burden of the protozoa in Henan Province and other region inside and outside China. [ABSTRACT FROM AUTHOR]

In order to evaluate if the reuse of food industry treated wastewater is compatible for irrigation of food crops, without increased health risk, in the present study a cropping system, in which ground water and treated wastewater were used for irrigation of tomato and broccoli, during consecutive crop seasons was monitored. Water, crop environment and final products were monitored for microbial indicators and pathogenic bacteria, by conventional and molecular methods. The microbial quality of the irrigation waters influenced sporadically the presence of microbial indicators in soil. No water sample was found positive for pathogenic bacteria, independently from the source. Salmonella spp. and Listeria monocytogenes were detected in soil samples, independently from the irrigation water source. No pathogen was found to contaminate tomato plants, while Listeria monocytogenes and E. coli O157:H7 were detected on broccoli plant, but when final produce were harvested, no pathogen was detected on edible part. The level of microbial indicators and detection of pathogenic bacteria in field and plant was not dependent upon wastewater used. Our results, suggest that reuse of food industry wastewater for irrigation of agricultural crop can be applied without significant increase of potential health risk related to microbial quality. [ABSTRACT FROM AUTHOR]

Fish blood is one of the crucial tissues of innate immune system, but the full repertoire of fish serum components involved in antibacterial defense is not fully identified. In this study, we demonstrated that turbot serum, but not the heat-inactivated control, significantly reduced the number of Edwardsiella tarda ( E. tarda ). By conjugating serum proteins with fluorescent dyes, we showed that E. tarda were coated with multiple fish proteins. In order to identify these proteins, we used E. tarda to capture turbot serum proteins and subjected the samples to shotgun proteomic analysis. A total of 76 fish proteins were identified in high confidence, including known antimicrobial proteins such as immunoglobins and complement components. 34 proteins with no previously known immunological functions were also identified. The expression of one of these proteins, IQ motif containing H (IQCH), was exclusively in fish brain and gonads and was induced during bacterial infection. This approach also allowed the study of the corresponding proteomic changes in E. tarda exposed to turbot serum, which is a general decrease of bacterial protein expression except for an upregulation of membrane components after serum treatment. Interestingly, while most other known stresses stimulate bacterial antioxidant enzymes, fish serum induced a rapid suppression of antioxidant proteins and led to an accumulation of reactive oxygen species. Heat treatment of fish serum eliminated this effect, suggesting that heat labile factors in the fish serum overrode bacterial antioxidant defenses. Taken together, this work offers a comprehensive view of the interactions between fish serum proteins and bacteria, and reveals previously unknown factors and mechanisms in fish innate immunity. [ABSTRACT FROM AUTHOR]

The present study investigated the water quality index, microbial composition and antimicrobial resistance genes in urban water habitats. Combined chemicals testing, metagenomic analyses and qualitative PCR (qPCR) were conducted on 20 locations, including rivers from hospital surrounds ( n = 7), community surrounds ( n = 7), and natural wetlands ( n = 6). Results showed that the indexes of total nitrogen, phosphorus, and ammonia nitrogen of hospital waters were 2-3 folds high than that of water from wetlands. Bioinformatics analysis revealed a total of 1,594 bacterial species from 479 genera from the three groups of water samples. The hospital-related samples had the greatest number of unique genera, followed by those from wetlands and communities. The hospital-related samples contained a large number of bacteria associated with the gut microbiome, including Alistipes , Prevotella , Klebsiella , Escherichia , Bacteroides , and Faecalibacterium , which were all significantly enriched compared to samples from the wetlands. Nevertheless, the wetland waters enriched bacteria from Nanopelagicus , Mycolicibacterium and Gemmatimonas , which are typically associated with aquatic environments. The presence of antimicrobial resistance genes (ARGs) that were associated with different species origins in each water sample was observed. The majority of ARGs from hospital-related samples were carried by bacteria from Acinetobacter , Aeromonas and various genera from Enterobacteriaceae , which each was associated with multiple ARGs. In contrast, the ARGs that were exclusively in samples from communities and wetlands were carried by species that encoded only 1 to 2 ARGs each and were not normally associated with human infections. The qPCR showed that water samples of hospital surrounds had higher concentrations of intI1 and antimicrobial resistance genes such as tetA, ermA, ermB, qnrB, sul1, sul2 and other beta-lactam genes. Further genes of functional metabolism reported that the enrichment of genes associated with the degradation/utilization of nitrate and organic phosphodiester were detected in water samples around hospitals and communities compared to those from wetlands. Finally, correlations between the water quality indicators and the number of ARGs were evaluated. The presence of total nitrogen, phosphorus, and ammonia nitrogen were significantly correlated with the presence of ermA and sul1 . Furthermore, intI1 exhibited a significant correlation with ermB , sul1 , and bla SHV , indicating a prevalence of ARGs in urban water environments might be due to the integron intI1 's diffusion-promoting effect. However, the high abundance of ARGs was limited to the waters around the hospital, and we did not observe the geographical transfer of ARGs along with the river flow. This may be related to water purifying capacity of natural riverine wetlands. Taken together, continued surveillance is required to assess the risk of bacterial horizontal transmission and its potential impact on public health in the current region., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Ye, Li, Su, Shi, Li, Hong, Wang, Zhao, Zheng, Dong, Ye, Lou, Zhou and Du.)

Arcobacter butzleri is a suspected waterborne enteric pathogen that is ubiquitous in the environment, but the degree to which wastewater treatment prevents entry of A. butzleri into environmental waters and the risks posed are not well established. Untreated and treated wastewater samples (n = 260) were collected weekly from the Lethbridge and Fort Macleod wastewater treatment facilities (the two major municipal inputs in southwestern Alberta, Canada) from May 2008 to April 2009. Untreated wastewaters contained high densities of A. butzleri and fecal coliform indicators, and densities at Lethbridge were typically higher than at Fort Macleod. Data indicated that A. butzleri and fecal coliform densities in wastewater were greatest in autumn and lowest in winter. Mechanical and biological treatment of wastewaters reduced but did not eliminate fecal coliform indicators or A. butzleri . At Lethbridge, UVB irradiation of mechanically and biologically treated wastewater further reduced densities of fecal coliform indicators. There was high A. butzleri genotype diversity in all sample sources, and survival during treatment was not strain-dependent. No genotype was dominant in any sample source, but 8.9% of genotypes were recurrent over time, and 4.4% of genotypes were detected at both wastewater treatment facilities. The current study demonstrates that viable A. butzleri are able to survive wastewater treatment, including UVB irradiation, which may lead to increased density and genetic diversity of this suspected pathogen in environmental waters via wastewater effluent discharge. [ABSTRACT FROM AUTHOR]