Escherichia coli and Enterococcus spp. in rainwater tank samples: comparison of culture-based methods and 23S rRNA gene quantitative PCR assays

Utilizing novel Escherichia coli-specific conserved signature proteins for enhanced monitoring of recreational water quality

Escherichia coli serves as a proxy indicator of fecal contamination in aquatic ecosystems. However, its identification using traditional culturing methods can take up to 24 h. The application of DNA markers, such as conserved signature proteins (CSPs) genes (unique to all species/strains of a specific taxon), can form the foundation for novel polymerase chain reaction (PCR) tests that unambiguously identify and detect targeted bacterial taxa of interest. This paper reports the identification of three new highly-conserved CSPs (genes), namely YahL, YdjO, and YjfZ, which are exclusive to E. coli/Shigella. Using PCR primers based on highly conserved regions within these CSPs, we have developed quantitative PCR (qPCR) assays for the evaluation of E. coli/Shigella species in water ecosystems. Both in-silico and experimental PCR testing confirmed the absence of sequence match when tested against other bacteria, thereby confirming 100% specificity of the tested CSPs for E. coli/Shigella. The qPCR assays for each of the three CSPs provided reliable quantification for all tested enterohaemorrhagic and environmental E. coli strains, a requirement for water testing. For recreational water samples, CSP-based quantification showed a high correlation (r > 7, p < 0.01) with conventional viable E. coli enumeration. This indicates that novel CSP-based qPCR assays for E. coli can serve as robust tools for monitoring water ecosystems and other critical areas, including food monitoring.

Progress in methods for the detection of viable Escherichia coli

Escherichia coli (E. coli) is a prevalent enteric bacterium and a necessary organism to monitor for food safety and environmental purposes. Developing efficient and specific methods is critical for detecting and monitoring viable E. coli due to its high prevalence. Conventional culture methods are often laborious and time-consuming, and they offer limited capability in detecting potentially harmful viable but non-culturable E. coli in the tested sample, which highlights the need for improved approaches. Hence, there is a growing demand for accurate and sensitive methods to determine the presence of viable E. coli. This paper scrutinizes various methods for detecting viable E. coli, including culture-based methods, molecular methods that target DNAs and RNAs, bacteriophage-based methods, biosensors, and other emerging technologies. The review serves as a guide for researchers seeking additional methodological options and aiding in the development of rapid and precise assays. Moving forward, it is anticipated that methods for detecting E. coli will become more stable and robust, ultimately contributing significantly to the improvement of food safety and public health.

Scale and detection method impacted Salmonella prevalence and diversity in ponds

Site-specific approaches for managing food safety hazards in agricultural water require an understanding of foodborne pathogen ecology. This study identified factors associated with Salmonella contamination in Virginia ponds. Grab samples (250 mL, N = 600) were collected from 30 sites across nine ponds. Culture- and culture-independent (CIDT)-based methods were used to detect Salmonella in each sample. Salmonella isolated by culture-based methods were serotyped by Kauffman-White classification. Environmental data were collected for each sample. McNemar's χ2 was used to determine if Salmonella detection differed by testing method. Separate mixed effect models were used to identify environmental factors associated with culture and CIDT-based Salmonella detection. Separate models were built for each pond, and for all ponds combined. Salmonella detection differed significantly (p < 0.001) between CIDT (31 %; 183/600)- and culture (13 %; 77/600)-based methods. Culture-based methods yielded 11 different serovars. All cultured Salmonella samples were confirmed by CIDT; 42.1 % of CIDT Salmonella-positive samples could be cultured. Associations between environmental factors and Salmonella detection also varied substantially by pond and detection method. In the all-pond model, associations were observed for five factors (total coliforms, Escherichia coli, air temperature, UV, rain) for both culture- and CIDT-based Salmonella detection. Rain prior to sampling (24 h) increased odds of Salmonella detection for culture (OR = 5.09) and CIDT (OR = 3.62) in the all-pond model. When all the pond data were used, models masked associations at the individual pond level, as there were noticeable differences between ponds and the odds of isolating Salmonella by environmental factors. Ponds were within a 187-ha area in this study, emphasizing water management needs to be individualized (i.e., assess hazards/risks by pond). Results also highlight detection methods and scale strongly affect observed water quality and should be considered when developing monitoring programs to develop guidance for growers.

QT-AMP: Sequencing PCR amplicons from Quanti-Tray wells to analyze enterococci communities

Enterococcus is ubiquitous in human feces and has been adopted as a useful indicator of human fecal pollution in water. Although regular enterococci monitoring only examines their numbers, identifying human-specific Enterococcus species or genotypes could help discriminate human fecal contamination from other environmental sources. We documented a new approach to characterize enterococci using a high-throughput 16S rRNA gene amplicon sequencing platform from Quanti Trays after following the counting of the most probable numbers of enterococci. We named this method QT-AMP (Quanti-Tray-based amplicon sequencing). We tested surface water samples collected from three rivers in southwest Florida. We detected 11 Enterococcus species from 45 samples in 1.1 million sequence reads. The method detected three rare species and eight cosmopolitan species (Enterococcus faecalis, E. faecium, E. casseliflavus, E. hirae, E. mundtii, E. gallinarum, E. avium, and E. durans) which have been commonly documented in previous studies. The approximate detection level of QT-AMP was four orders of magnitude higher than regular 16S rRNA gene amplicon sequencing. The current Enterolert MPN method only provides quantitative information but now we can look into the relative abundance of Enterococci species composition by accompanying Illumina sequencing. This QT-AMP could be a useful tool to streamline the quantification and identification of enterococci and could be used in various water management projects and human health risk assessment.

PCR-based detection of pathogens in improved water sources: a scoping review protocol of the evidence in low-income and middle-income countries

INTRODUCTION

Occurrence of diverse human enteric bacterial, viral and protozoal pathogens in improved drinking water because of pathogenic microbial contamination is of increasing public health concern, particularly in low-income and middle-income countries (LMICs). Detecting microbial pathogens in water supplies comprehensively and accurately is beneficial to ensure the safety of water in LMICs where water contamination is a major concern. Application of PCR-based methods in detecting the microbial quality of water provides more accurate, sensitive and rapid outcomes over conventional methods of microbial identification and quantification. Therefore, exploring water quality outcomes generated through PCR-based methods is important to better understand the status and monitor progress towards internationally set goals for LMICs. This scoping review aims to map the existing evidence on the magnitude and characteristics of diarrhoeagenic pathogens as detected by PCR-based methods in improved water sources within the context of LMICs.

METHODS AND ANALYSIS

This study will be undertaken in line with the Joanna Briggs Institute (JBI) methodology for scoping reviews. We will consider the available publications covering PCR-based microbial water quality assessment of improved drinking water sources in LMICs. Searches will be undertaken in PubMed/Medline, Scopus, Web of Science, JBI, Cochrane Library and Google Scholar. A grey literature search will be conducted in Google and ProQuest.

ETHICS AND DISSEMINATION

The College of Natural and Computational Science Institution Review Board of Addis Ababa University gave formal ethical approval to this study protocol. The findings of this study will be disseminated to the concerned body through peer-reviewed publications, presentations and summaries.

Opportunistic pathogens exhibit distinct growth dynamics in rainwater and tap water storage systems

Opportunistic pathogens (OPs) are emerging microbial contaminants in engineered water systems, yet their growth potential in rainwater systems has not been evaluated. The purpose of this study was to compare the growth dynamics of bacterial OPs and related genera (Pseudomonas aeruginosa, Legionella spp., L. pneumophila, Mycobacterium spp., and M. avium), two amoebal hosts (Acanthamoeba spp. and Vermamoeba vermiformis), and the fecal indicator Escherichia coli in simulated rainwater and tap water storage systems (SWSSs). Quantitative polymerase chain reaction (q-PCR) analysis of target microorganisms in SWSS influents and effluents demonstrated that P. aeruginosa and Legionella thrived in rainwater, but not in tap water. V. vermiformis proliferated in both rainwater and tap water polyvinyl chloride (PVC) SWSSs, while mycobacteria were largely absent in rainwater SWSSs. Tank materials exerted stronger influence on target microorganisms in rainwater SWSSs relative to tap water SWSSs, with species-specific responses noted in bulk water and biofilm. For instance, P. aeruginosa and V. vermiformis had the highest gene copy numbers in PVC rainwater SWSS effluents and biofilm, while Legionella peaked in stainless steel rainwater SWSS effluents and PVC rainwater SWSS biofilm. These results highlighted the OP contamination risks in rainwater storage systems and provided insights into rainwater system design and operation in terms of OP control.

Effect of temperature on opportunistic pathogen gene markers and microbial communities in long-term stored roof-harvested rainwater

Roof-harvested rainwater (RHRW) has received increasing attention in recent years as an alternative water source for domestic use, yet its biological stability during storage is not fully understood. This study investigated the effects of temperature (4 °C, 20 °C and 30 °C) on the microbiological characteristics of RHRW over a storage period of 60 days by targeting different microbial groups including total bacteria and fecal indictor Escherichia coli, bacterial opportunistic pathogen genera and species (Legionella spp, Legionella pneumophila, Mycobacterium spp, Mycobacterium avium, Pseudomonas aeruginosa), and two amoebas (Acanthamoeba and Vermamoeba vermiformis). The rainwater chemistry demonstrated no obvious change during storage. The highest biomass was observed in RHRW stored at 30 °C, as measured by heterotrophic bacterial counts, adenosine triphosphate, and 16S rRNA gene numbers. Gene markers of E. coli, Legionella spp., P. aeruginosa, and V. vermiformis were detected in fresh RHRW and can persist during RHRW storage; whereas P. aeruginosa was the only species demonstrated significant regrowth at higher storage temperatures (P < 0.05). Acanthamoeba spp. was only detected in RHRW after 50 days of storage at three investigated temperatures, highlighting increased health risks in long-term stored RHRW. Bacterial community compositions were significantly different in RHRW stored at different temperatures, with increased variations among triplicate storage bottles noted at higher temperatures along with storage time. The results provide insights into RHRW storage practices in terms of mitigating microbial contamination risks.

Status of faecal pollution in ports: A basin-wide investigation in the Adriatic Sea

Ports are subject to a variety of anthropogenic impacts, and there is mounting evidence of faecal contamination through several routes. Yet, little is known about pollution in ports by faecal indicator bacteria (FIB). FIB spatio-temporal dynamics were assessed in 12 ports of the Adriatic Sea, a semi-enclosed basin under strong anthropogenic pressure, and their relationships with environmental variables were explored to gain insight into pollution sources. FIB were abundant in ports, often more so than in adjacent areas; their abundance patterns were related to salinity, oxygen, and nutrient levels. In addition, a molecular method, quantitative (q)PCR, was used to quantify FIB. qPCR enabled faster FIB determination and water quality monitoring that culture-based methods. These data provide robust baseline evidence of faecal contamination in ports and can be used to improve the management of routine port activities (dredging and ballast water exchange), having potential to spread pathogens in the sea.

Autonomous online measurement of β-D-glucuronidase activity in surface water: is it suitable for rapid E. coli monitoring?

Microbiological water quality is traditionally assessed using culture-based enumeration of faecal indicator bacteria such as Escherichia coli. Despite their relative ease of use, these methods require a minimal 18-24 h-incubation step before the results are obtained. This study aimed to assess the suitability of an autonomous online fluorescence-based technology measuring β-glucuronidase (GLUC) activity for rapid near-real time monitoring of E. coli in water. The analytical precision was determined and compared to an automated microbial detection system, two culture-based assays and quantitative real-time PCR (qPCR). Using replicate measurements of grab samples containing E. coli concentrations between 50 and 2330 CFU.100 mL^-1, the autonomous GLUC activity measurement technology displayed an average coefficient of variation (CV) of less than 5% that was 4-8-fold lower than other methods tested. Comparable precision was observed during online in situ monitoring of GLUC activity at a drinking water intake using three independent instruments. GLUC activity measurements were not affected by sewage or sediments at concentrations likely to be encountered during long-term monitoring. Furthermore, significant (p < 0.05) correlations were obtained between GLUC activity and the other assays including defined substrate technology (r = 0.77), membrane filtration (r = 0.73), qPCR (r = 0.55) and the automated microbial detection system (r = 0.50). This study is the first to thoroughly compare the analytical performance of rapid automated detection technologies to established culture and molecular-based methods. Results show that further research is required to correlate GLUC activity to the presence of viable E. coli as measured in terms of CFU.100 mL^-1. This would allow the use of autonomous online GLUC activity measurements for rapid E. coli monitoring in water supplies used for drinking water production and recreation.

Marker genes of fecal indicator bacteria and potential pathogens in animal feces in subtropical catchments

We investigated the abundance of marker genes of two fecal indicator bacteria (FIB) and eight potential pathogens in fecal samples of humans (n = 14) and 10 domestic and native wild animals (n = 134). For each target animal, between 10 and 14 individual fecal samples were collected (n = 148 individual fecal samples in total). The abundance of FIB and potential pathogens within each sample was determined using quantitative PCR (qPCR) assays. All animals tested were positive for Escherichia coli (EC) and the concentrations ranged from 6.13 (flying fox) to 8.87 (chicken) log₁₀ GC/g of feces. These values for Enterococcus spp. (ENT) were 5.25 log₁₀ GC/g for flying fox and 8.12 log₁₀ GC/g of feces for chicken. Moderate correlations were observed between EC with P. aeruginosa, EC O157 and Cryptosporidium parvum, whereas weak correlations were observed between EC and Salmonella spp. and Giardia lamblia, Mycobacterium avium complex (MAC) and Campylobacter spp. The prevalence of MAC and P. aeruginosa were low in dog (14.3% each) and moderate (57.2%, MAC; 42.9% P. aeruginosa) in Eastern grey kangaroo fecal samples. Cryptosporidium parvum was detected in one cattle and one human fecal sample, while G. lamblia was detected in one dog, one flying fox, and one pig fecal samples. Among the eight potential pathogens tested, five pathogens were detected in chicken and dog fecal samples. The remaining animal species contained up to three potential pathogens in their feces. The data generated in this study may aid in the calculation of pathogen loads in the environment, and hence to assess the risks from human and animal fecal contamination of source waters.

Comparative decay of sewage-associated marker genes in beach water and sediment in a subtropical region

There is a growing move towards using the quantitative polymerase chain (qPCR)-based sewage-associated marker genes to assess surface water quality. However, a lack of understanding about the persistence of many sewage-associated markers creates uncertainty for those tasked with investigating microbial water quality. In this study, we investigated the decay of two qPCR FIB [E. coli (EC), and Enterococcus spp. (ENT) 23S rRNA genes] and four sewage-associated microbial source tracking (MST) marker genes [human Bacteroides HF183 16S rRNA, adenovirus (HAdV), and polyomavirus (HPyV), and crAssphage, a recently described bacteriophage in feces], in outdoor mesocosms containing fresh and marine waters and their corresponding sediments. Decay rates of EC 23S rRNA, ENT 23S rRNA, and HF183 16S rRNA were significantly (p < 0.05) faster than the HAdV, HPyV and crAssphage markers in water samples from all mesocosms. In general, decay rates of bacterial targets were similar in the water columns of the studied mesocosms. Similarly, decay rates of viral targets were also alike in mesocosm water columns in relation to each other. The decay rates of FIB and sewage-associated markers were significantly faster in water samples compared to sediments in all three mesocosms. In the event of resuspension, FIB and marker genes from sediments can potentially recontaminate overlying waters. Thus, care should be taken when interpreting the occurrence of FIB and sewage-associated MST markers in water, which may have originated from sediments. The differential decay of these targets may also influence health outcomes and need to be considered in risk assessment models.

Detection of viable Escherichia coli in environmental water using combined propidium monoazide staining and quantitative PCR

The objectives of this study were to specifically detect viable Escherichia coli in environmental waters by targeting the ycjM gene in a propidium monoazide (PMA)-qPCR assay. PMA is a viability dye that can inhibit the amplification of DNA from dead cells, thus allowing for the detection and quantification of only viable cells. The ycjM primers were used to target E. coli that directly originated from the feces of warm blooded animals, and avoid false positive detection caused by "naturalized" E. coli that can exist in the environment. In this study, tap water and environmental waters were inoculated with E. coli isolated from animal feces. Following cell collection, samples were treated with PMA, followed by DNA isolation and qPCR detection. For pure cultures, 5 μM PMA with a 10-min light exposure was efficient at inhibiting the amplification of DNA from 10⁵ CFU/mL dead E. coli cells, with a detection limit of 10² CFU/100 mL viable cells. For tap and environmental waters collected in the winter, a 10 μM PMA was required and as low as 10³ CFU/100 mL viable cells could be detected in the presence of 10⁵ CFU/100 mL dead cells. For water samples collected during the summer, 10² CFU/10 mL viable cells could be detected in the presence of 10⁴ CFU/10 mL dead cells, after a 20 μM PMA treatment. No significant differences were found among the PMA-qPCR assay and two other standard culture-based methods for detection of viable E. coli in environmental water. In conclusion, with proper pretreatment of environmental water samples, this PMA-qPCR assay that targets the ycjM gene could quantify viable E. coli cells that directly come from the feces of warm-blooded animals, and therefore effectively and accurately indicate the quality of environmental water.

Microbial quality of irrigation water used in leafy green production in Southern Brazil and its relationship with produce safety

Irrigation water has been recognized as an important microbial risk factor for fruits and vegetables in many production areas, but there is still a lack of information about how the microbiological quality of different irrigation water sources and climatic conditions influence the safety of vegetables produced in Brazil. This study evaluated the distribution of generic E. coli and the prevalence of E. coli O157:H7 in two different water sources (ponds and streams bordering farmlands and urban areas) used for irrigation and on commercially produced lettuces in Southern Brazil. We also evaluated the effect of agricultural factors and meteorological conditions in the potential contamination of water and produce samples. A longitudinal study was conducted on four farms during a year (July 2014 to August 2015). The results showed generic E. coli prevalence of 84.8% and 38.3% in irrigation water samples and on lettuces, respectively, indicating irrigation water as an important source of contamination of lettuces. No significant differences were detected in the counts of E. coli between the two different surface water sources. The climatic conditions, particularly rainfall and environmental temperature, have influenced the high concentration of E. coli. The highest loads of E. coli in irrigation water and on lettuces were found during the warmest time of the year. E. coli O157:H7 was detected by qualitative polymerase chain reaction (qPCR) in 13 water samples but only 4 were confirmed by isolation in culture media.

Distributions of Fecal Markers in Wastewater from Different Climatic Zones for Human Fecal Pollution Tracking in Australian Surface Waters

Recreational and potable water supplies polluted with human wastewater can pose a direct health risk to humans. Therefore, sensitive detection of human fecal pollution in environmental waters is very important to water quality authorities around the globe. Microbial source tracking (MST) utilizes human fecal markers (HFMs) to detect human wastewater pollution in environmental waters. The concentrations of these markers in raw wastewater are considered important because it is likely that a marker whose concentration is high in wastewater will be more frequently detected in polluted waters. In this study, quantitative PCR (qPCR) assays were used to determine the concentrations of fecal indicator bacteria (FIB) Escherichia coli and Enterococcus spp., HFMs Bacteroides HF183, human adenoviruses (HAdVs), and polyomaviruses (HPyVs) in raw municipal wastewater influent from various climatic zones in Australia. E. coli mean concentrations in pooled human wastewater data sets (from various climatic zones) were the highest (3.2 × 10(6) gene copies per ml), followed by those of HF183 (8.0 × 10(5) gene copies per ml) and Enterococcus spp. (3.6 × 10(5) gene copies per ml). HAdV and HPyV concentrations were 2 to 3 orders of magnitude lower than those of FIB and HF183. Strong positive and negative correlations were observed between the FIB and HFM concentrations within and across wastewater treatment plants (WWTPs). To identify the most sensitive marker of human fecal pollution, environmental water samples were seeded with raw human wastewater. The results from the seeding experiments indicated that Bacteroides HF183 was more sensitive for detecting human fecal pollution than HAdVs and HPyVs. Since the HF183 marker can occasionally be present in nontarget animal fecal samples, it is recommended that HF183 along with a viral marker (HAdVs or HPyVs) be used for tracking human fecal pollution in Australian environmental waters.

Persistence of Multi-Drug Resistance Plasmids in Sterile Water under Very Low Concentrations of Tetracycline

The persistence of the multi-drug resistance plasmids pAQU1 and IncFIB was examined in bacterial populations under very low selective pressure. We herein demonstrated that these plasmids stably remained not only in the original host, but also in a transconjugant, even after being in a non-culturable state. In seawater microcosms containing Photobacterium damselae 04Ya311 possessing pAQU1, no significant loss of pAQU1 was observed during a 30-d starvation period. The copy numbers of pAQU1 and IncFIB in E. coli were constant. The results of the present study suggest that these plasmids have the ability to remain among various bacteria under oligotrophic conditions with low antibiotic selection pressure.

Microbes in Beach Sands: Integrating Environment, Ecology and Public Health

Beach sand is a habitat that supports many microbes, including viruses, bacteria, fungi and protozoa (micropsammon). The apparently inhospitable conditions of beach sand environments belie the thriving communities found there. Physical factors, such as water availability and protection from insolation; biological factors, such as competition, predation, and biofilm formation; and nutrient availability all contribute to the characteristics of the micropsammon. Sand microbial communities include autochthonous species/phylotypes indigenous to the environment. Allochthonous microbes, including fecal indicator bacteria (FIB) and waterborne pathogens, are deposited via waves, runoff, air, or animals. The fate of these microbes ranges from death, to transient persistence and/or replication, to establishment of thriving populations (naturalization) and integration in the autochthonous community. Transport of the micropsammon within the habitat occurs both horizontally across the beach, and vertically from the sand surface and ground water table, as well as at various scales including interstitial flow within sand pores, sediment transport for particle-associated microbes, and the large-scale processes of wave action and terrestrial runoff. The concept of beach sand as a microbial habitat and reservoir of FIB and pathogens has begun to influence our thinking about human health effects associated with sand exposure and recreational water use. A variety of pathogens have been reported from beach sands, and recent epidemiology studies have found some evidence of health risks associated with sand exposure. Persistent or replicating populations of FIB and enteric pathogens have consequences for watershed/beach management strategies and regulatory standards for safe beaches. This review summarizes our understanding of the community structure, ecology, fate, transport, and public health implications of microbes in beach sand. It concludes with recommendations for future work in this vastly under-studied area.

Microbial quality and phylogenetic diversity of fresh rainwater and tropical freshwater reservoir

The impact of rainwater on the microbial quality of a tropical freshwater reservoir through atmospheric wet deposition of microorganisms was studied for the first time. Reservoir water samples were collected at four different sampling points and rainwater samples were collected in the immediate vicinity of the reservoir sites for a period of four months (January to April, 2012) during the Northeast monsoon period. Microbial quality of all fresh rainwater and reservoir water samples was assessed based on the counts for the microbial indicators: Escherichia coli (E. coli), total coliforms, and Enterococci along with total heterotrophic plate counts (HPC). The taxonomic richness and phylogenetic relationship of the freshwater reservoir with those of the fresh rainwater were also assessed using 16 S rRNA gene clone library construction. The levels of E. coli were found to be in the range of 0 CFU/100 mL – 75 CFU/100 mL for the rainwater, and were 10–94 CFU/100 mL for the reservoir water. The sampling sites that were influenced by highway traffic emissions showed the maximum counts for all the bacterial indicators assessed. There was no significant increase in the bacterial abundances observed in the reservoir water immediately following rainfall. However, the composite fresh rainwater and reservoir water samples exhibited broad phylogenetic diversity, including sequences representing Betaproteobacteria, Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Lentisphaerae and Bacteriodetes. Members of the Betaproteobacteria group were the most dominant in both fresh rainwater and reservoir water, followed by Alphaproteobacteria, Sphingobacteria, Actinobacteria and Gammaproteobacteria.