Environmental monitoring of waterborne Campylobacter: evaluation of the Australian standard and a hybrid extraction-free MPN-PCR method

FlashPCR: Revolutionising qPCR by Accelerating Amplification through Low ∆T Protocols

Versatility, sensitivity, and accuracy have made the real-time polymerase chain reaction (qPCR) a crucial tool for research, as well as diagnostic applications. However, for point-of-care (PoC) use, traditional qPCR faces two main challenges: long run times mean results are not available for half an hour or more, and the requisite high-temperature denaturation requires more robust and power-demanding instrumentation. This study addresses both issues and revises primer and probe designs, modified buffers, and low ∆T protocols which, together, speed up qPCR on conventional qPCR instruments and will allow for the development of robust, point-of-care devices. Our approach, called "FlashPCR", uses a protocol involving a 15-second denaturation at 79 °C, followed by repeated cycling for 1 s at 79 °C and 71 °C, together with high Tm primers and specific but simple buffers. It also allows for efficient reverse transcription as part of a one-step RT-qPCR protocol, making it universally applicable for both rapid research and diagnostic applications.

Plants release, pathogens decease: Plants with documented antimicrobial activity are associated with Campylobacter and faecal indicator attenuation in stormwater biofilters

Stormwater biofilters demonstrate promising treatment of faecal microorganisms, however performance can vary with design and operational conditions. This study investigated whether plants with significant documented antimicrobial activity could improve faecal bacterial treatment within biofilters. Laboratory-scale biofilters (n = 30) were dosed with synthetic stormwater containing faecal bacteria Escherichia coli, Enterococcus faecalis and Campylobacter jejuni under south-eastern Australian climatic conditions. Systems vegetated with Melaleuca species, renowned for their in vitro antimicrobial activity, consistently enhanced removal of all tested culturable bacteria in total outflow and submerged zone water relative to other plant configurations. Within just 1-2 days of stormwater dosing, M. linariifolia submerged zones demonstrated significantly reduced bacterial concentrations compared to C. appressa (p = 0.023 and <0.001 for C. jejuni and E. coli, respectively), removing ∼1.47 log10 MPN/100 mL E. coli, ∼1.14 log10 MPN/100 mL E. faecalis and ∼0.81 log10 MPN/L C. jejuni from inflow. These trends continued even after all but one M. linariifolia replicate perished during an extended drying period (p = 0.002 and 0.003 for C. jejuni and E. coli, respectively). Through a systematic process of elimination, these observations were attributed to enhanced bacterial attenuation with elevated plant inhibitory activity. Cumulative biofilter age reinforced plant-mediated bacterial treatment (p = 0.023 for E. faecalis), ostensibly due to increased plant size/growth and net biological activity. Notably, E. coli and E. faecalis attenuation improved with prolonged antecedent drying length (14 vs. 4 days; p < 0.0001 for both), while the converse was observed for C. jejuni (not significant). This study addresses significant knowledge gaps around plant-mediated faecal microbe treatment within biofilters, providing key direction for real-world system design to optimise stormwater pathogen treatment.

Molecular Methods for Pathogenic Bacteria Detection and Recent Advances in Wastewater Analysis

With increasing concerns about public health and the development of molecular techniques, new detection tools and the combination of existing approaches have increased the abilities of pathogenic bacteria monitoring by exploring new biomarkers, increasing the sensitivity and accuracy of detection, quantification, and analyzing various genes such as functional genes and antimicrobial resistance genes (ARG). Molecular methods are gradually emerging as the most popular detection approach for pathogens, in addition to the conventional culture-based plate enumeration methods. The analysis of pathogens in wastewater and the back-estimation of infections in the community, also known as wastewater-based epidemiology (WBE), is an emerging methodology and has a great potential to supplement current surveillance systems for the monitoring of infectious diseases and the early warning of outbreaks. However, as a complex matrix, wastewater largely challenges the analytical performance of molecular methods. This review synthesized the literature of typical pathogenic bacteria in wastewater, types of biomarkers, molecular methods for bacterial analysis, and their recent advances in wastewater analysis. The advantages and limitation of these molecular methods were evaluated, and their prospects in WBE were discussed to provide insight for future development.

Universal Enzyme-Based Field Workflow for Rapid and Sensitive Quantification of Water Pathogens

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.

Rapid quantification of fecal indicator bacteria in water using the most probable number - loop-mediated isothermal amplification (MPN-LAMP) approach on a polymethyl methacrylate (PMMA) microchip

Fecal contamination of water and its associated pathogens are a major public health concern in both developing and industrialized areas. Fecal indicator bacteria (FIB) are commonly used to assess microbial water quality, but they require a relatively long period of incubation time. Currently, molecular techniques have been applied to rapidly detect FIB. However, these molecular techniques require expensive and sophisticated equipment. In this study, we developed a rapid on-chip gene quantification method based on loop-mediated isothermal amplification (LAMP) PCR. The LAMP assays can measure the target genes of the fecal indicator bacteria (FIB), including E. coli and Enterococcus spp, using the most probable number (MPN) approach. The colorimetric LAMP assay allows for naked-eye observation of the PCR reaction as few as 4 gene copies / well. When the reaction ends, MPN measurement of positive outcomes on the white-based PMMA (polymethacrylic acid) microchips provides the concentrations of the target genes of FIB with a confidence interval. We validated the feasibility of the MPN-LAMP approach by obtaining a strong correlation between the results of the MPN estimations and the qPCR analysis. Moreover, the MPN-LAMP approach was used to quantify the FIB in different environmental water collected from the freshwater reservoirs, beach, agriculture farm, and sewage. Our research demonstrates that the MPN- LAMP method enables us to easily and quickly quantifying FIB genes isolated from the environment without expensive qPCR instruments.

Study design, rationale and methods of the Revitalising Informal Settlements and their Environments (RISE) study: a cluster randomised controlled trial to evaluate environmental and human health impacts of a water-sensitive intervention in informal settlements in Indonesia and Fiji

INTRODUCTION

Increasing urban populations have led to the growth of informal settlements, with contaminated environments linked to poor human health through a range of interlinked pathways. Here, we describe the design and methods for the Revitalising Informal Settlements and their Environments (RISE) study, a transdisciplinary randomised trial evaluating impacts of an intervention to upgrade urban informal settlements in two Asia-Pacific countries.

METHODS AND ANALYSIS

RISE is a cluster randomised controlled trial among 12 settlements in Makassar, Indonesia, and 12 in Suva, Fiji. Six settlements in each country have been randomised to receive the intervention at the outset; the remainder will serve as controls and be offered intervention delivery after trial completion. The intervention involves a water-sensitive approach, delivering site-specific, modular, decentralised infrastructure primarily aimed at improving health by decreasing exposure to environmental faecal contamination. Consenting households within each informal settlement site have been enrolled, with longitudinal assessment to involve health and well-being surveys, and human and environmental sampling. Primary outcomes will be evaluated in children under 5 years of age and include prevalence and diversity of gastrointestinal pathogens, abundance and diversity of antimicrobial resistance (AMR) genes in gastrointestinal microorganisms and markers of gastrointestinal inflammation. Diverse secondary outcomes include changes in microbial contamination; abundance and diversity of pathogens and AMR genes in environmental samples; impacts on ecological biodiversity and microclimates; mosquito vector abundance; anthropometric assessments, nutrition markers and systemic inflammation in children; caregiver-reported and self-reported health symptoms and healthcare utilisation; and measures of individual and community psychological, emotional and economic well-being. The study aims to provide proof-of-concept evidence to inform policies on upgrading of informal settlements to improve environments and human health and well-being.

ETHICS

Study protocols have been approved by ethics boards at Monash University, Fiji National University and Hasanuddin University.

TRIAL REGISTRATION NUMBER

ACTRN12618000633280; Pre-results.

Salmonella from a Microtidal Estuary Are Capable of Invading Human Intestinal Cell Lines

Faecal contamination poses health risks for the recreational users of urban estuaries. However, our understanding of the potential pathogenicity of faecal microbes in these environments is limited. To this end, a study was conducted to understand the spatial and seasonal distribution of Salmonella in water and sediments of the Yarra River estuary, Melbourne, Australia. Among 210 samples in total, culturable Salmonella were recovered from 27%, 17%, and 19% of water, bank, and bed sediment samples, respectively. The combined detection increased from 15% in winter to 32% in summer (p < 0.05) indicating seasonal variation as potential part of public health risk assessments. Further, pathogenic potential of the Salmonella isolates was characterised via the quantification of attachment and invasion capacity using human epithelial colorectal cell line Caco-2 on a subset of isolates (n = 62). While all of these isolates could attach and invade Caco-2 cells, 52% and 13% of these showed greater attachment and invasiveness, respectively, than the corresponding mean values for S. Typhimurium ATCC14028 control. Isolates from winter were on average more invasive (seven out of eight isolates with the highest invasiveness recovered from the colder sampling period) than the isolates from summer, and Salmonella collected during summer showed lower invasion (p < 0.05) compared with the control. Similar low invasion compared with the same control was observed for isolates recovered from bank sediment (p < 0.05). While the higher prevalence in summer may imply higher risks during these peak recreational periods, it is essential that this information is used in combination with quantitative microbial risk assessments to fully understand the health risks posed by Salmonella in microtidal estuaries.

Campylobacter in an Urban Estuary: Public Health Insights from Occurrence, HeLa Cytotoxicity, and Caco-2 Attachment Cum Invasion

Aquatic recreation in urban estuaries worldwide is often restricted by fecal pollution. Variability in the occurrence of fecal pathogens and their differential virulence potentials within these estuaries may result in variable public health risks. To address this hypothesis, Campylobacter were isolated from the Yarra River estuary, Australia and then characterized via HeLa cell cytotoxicity and attachment to and the invasion of Caco-2 monolayers. Overall, 54% (n=216) of estuarine samples (water and sediment combined) yielded biochemically confirmed culturable Campylobacter; higher detection was recorded in water (92%, n=90) than in the bank and bed sediments combined (27%, n=126). The seasonality of occurrence was not significant. HeLa cell cytotoxicity revealed that estuarine Campylobacter had low cytotoxin titers; the 95% confidence interval (CI) ranged between 61 and 85, which was markedly lower than the mean value (~386) for the C. jejuni 11168 reference pathogenic strain. The Caco-2 attachment of estuarine Campylobacter isolates (n=189) revealed that the 95%CI for the attachment efficiency of the test strains ranged between 0.09 and 0.1%, with only 3.7% having a higher efficiency than the 5^th percentile value for C. jejuni 11168. None of the estuarine strains exhibited Caco-2 invasion capabilities. In contrast to the common assumption during quantitative microbial/risk assessments (QMRAs) that all environmental strains are pathogenic, the present results revealed that Campylobacter within the Yarra River estuary had very low virulence potential. Since this is the first study to use human epithelial cell lines to characterize estuary-borne pathogens, these results generate valuable insights for a better understanding of the public health risks in urban estuaries that will underpin more robust QMRAs.

Human campylobacteriosis: A public health concern of global importance

Campylobacter species are among the leading cause of bacterial foodborne and waterborne infections. In addition, Campylobacter is one of the major causative agent of bacterial gastrointestinal infections and the rise in the incidence of Campylobacter infections have been reported worldwide. Also, the emergence of some Campylobacter species as one of the main causative agent of diarrhea and the propensity of these bacteria species to resist the actions of antimicrobial agents; position them as a serious threat to the public health. This paper reviews Campylobacter pathogenicity, infections, isolation and diagnosis, their reservoirs, transmission pathways, epidemiology of Campylobacter outbreaks, prevention and treatment option, antibiotics resistance and control of antibiotics use.

Electrochemical oxidation disinfects urban stormwater: Major disinfection mechanisms and longevity tests

Although electrochemical oxidation (ECO) has shown excellent potential for disinfecting wastewater and surface waters, its application on urban stormwater has been rarely tested. In order to improve stormwater ECO design, this paper explores the major inactivation processes using Boron Doped Diamond (BDD) and titanium Dimensional Stable Anodes (DSA). Both BDD and DSA showed comparable disinfection rates. The mechanism study suggested that BDD relied on hydroxyl radical and the presence of chloride ions, while DSA disinfected stormwater mainly via the production of free‑chlorine. A deterioration study carried out at a catchment in Melbourne, showed a steady performance for BDD and revealed that DSA's performance degraded with time, likely linked to the high operational voltage required for specific chemistry of stormwater. Scanning Electron Microscopes and an Energy Dispersive X-ray Detector tests confirmed elemental losses occurred on the DSA surface, together with an aluminium/silicon coating layer potentially sourced from the stormwater clayish sediments. Furthermore, disinfection by-products in electrochemical disinfected stormwater using either BDD or DSA were at least one order of magnitude lower than the Australia Drinking Water Guidelines limits. The mechanism and long-term study demonstrated that careful anode selection is required as some anodes will deteriorate in stormwater matrices faster than others.

Electrochemical oxidation for stormwater disinfection: How does real stormwater chemistry impact on pathogen removal and disinfection by-products level?

Preliminary laboratory work has shown that electrochemical oxidation (ECO) is a promising technology for disinfection of harvested stormwater. This paper focuses on understanding how stormwater chemistry (e.g. pH, chloride, bicarbonate, ammonia and total organic carbon - that can vary substantially between sites) impacts the disinfection performance of ECO. Real stormwater samples from four different urban catchments were collected and tested for ECO performance in disinfecting stormwater pathogens using a boron doped diamond anode under the current density of 4.2 mA/cm². Results showed that total disinfection of indigenous Escherichia coli (E. coli), as well as three different stormwater pathogens (Enterococci, Campylobacter and C. perfringens) was achievable for all four tested stormwater within 30 min. Compared to the synthetic stormwater, lower disinfection rates were observed in real stormwater which has more complex chemistry. Stormwater chloride concentration was the only tested parameter that had significant impact on the treatment performance, with higher initial stormwater chloride concentration leading to an increased disinfection rate. Disinfection by-products in the treated stormwater were well below the Australian Drinking Water Guideline value for health, with its production level positively correlated to the pH values of stormwater.

Salmonella enterica Serovar Typhimurium and Escherichia coli Survival in Estuarine Bank Sediments

Estuarine bank sediments have the potential to support the survival and growth of fecal indicator organisms, including Escherichia coli. However, survival of fecal pathogens in estuarine sediments is not well researched and therefore remains a significant knowledge gap regarding public health risks in estuaries. In this study, simultaneous survival of Escherichia coli and a fecal pathogen, Salmonella enterica serovar Typhimurium, was studied for 21 days in estuarine bank sediment microcosms. Observed growth patterns for both organisms were comparable under four simulated scenarios; for continuous-desiccation, extended-desiccation, periodic-inundation, and continuous-inundation systems, logarithmic decay coefficients were 1.54/day, 1.51/day, 0.14/day, and 0.20/day, respectively, for E. coli, and 1.72/day, 1.64/day, 0.21/day, and 0.24/day for S. Typhimurium. Re-wetting of continuous-desiccated systems resulted in potential re-growth, suggesting survival under moisture-limited conditions. Key findings from this study include: (i) Bank sediments can potentially support human pathogens (S. Typhimurium), (ii) inundation levels influence the survival of fecal bacteria in estuarine bank sediments, and (iii) comparable survival rates of S. Typhimurium and E. coli implies the latter could be a reliable fecal indicator in urban estuaries. The results from this study will help select suitable monitoring and management strategies for safer recreational activities in urban estuaries.

Stormwater constructed wetlands: A source or a sink of Campylobacter spp

Stormwater constructed wetlands are not well characterised for their ability to remove pathogens which can pose public health risks during stormwater harvesting activities. This study investigated the behaviour of faecal indicator organism Escherichia coli (E. coli) and reference pathogen Campylobacter spp. in stormwater constructed wetlands, using a case study system located in Melbourne, Australia. Grab sampling and event-based monitoring revealed influent concentrations of E. coli were typical of other urban stormwater studies, yet Campylobacter concentrations were orders of magnitude above those urban stormwater studies used to develop the Australian Guidelines for Water Recycling, reached levels typical of raw domestic wastewater. The wetland consistently removed E. coli from stormwater (mean log removal 0.96, range 0.19-1.79), while Campylobacter spp. concentrations were often higher in outflow than inflow (mean log removal 0.05, range -0.9-1.25). These results indicate that E. coli is a poor indicator for this reference pathogen. The log reductions of both organisms also failed to meet the criteria specified for any end-use, as listed in the Australian Guidelines for Water Recycling, suggesting further treatment is required prior to harvesting. Finally, this study proposed that direct faecal deposition by waterfowl faeces was a microbial source to stormwater wetlands and that this was partly responsible for the varied microbial removal rates observed. Overall, this work validates the need for further characterisation of pathogens in raw urban stormwater, and the ability for water sensitive urban design features, such as wetlands, to remove both indicator and pathogenic microorganisms.

Current Stormwater Harvesting Guidelines Are Inadequate for Mitigating Risk from Campylobacter During Nonpotable Reuse Activities

Campylobacter is a pathogen frequently detected in urban stormwater worldwide. It is one of the leading causes of enteric disease in many developed countries and is the leading cause of enteric disease in Australia. Prior to harvesting stormwater, adequate treatment is necessary to mitigate risks derived from such harmful pathogens. The goal of this research was to estimate the health risks associated with the exposure to Campylobacter when harvesting urban stormwater for toilet flushing and irrigation activities, and the role treatment options play in limiting risks. Campylobacter data collected from several urban stormwater systems in Victoria, Australia, were the inputs of a Quantitative Microbial Risk Assessment model. The model included seven treatment scenarios, spanning wetlands, biofilters, and more traditional treatment trains including those recommended by the Australian Guidelines for Water Recycling. According to our modeling and acceptable risk thresholds, only two treatment scenarios could supply water of sufficient quality for toilet flushing and irrigation end-uses: (1) using stormwater biofilters coupled with UV-treatment and (2) a more conventional coagulation, filtration, UV, and chlorination treatment plant. Importantly, our modeling results suggest that current guidelines in place for stormwater reuse are not adequate for protecting against exposure to Campylobacter. However, more research is required to better define whether the Campylobacter detectable in stormwater are pathogenic to humans.

Source tracking using microbial community fingerprints: Method comparison with hydrodynamic modelling

Urban estuaries around the world are experiencing contamination from diffuse and point sources, which increases risks to public health. To mitigate and manage risks posed by elevated levels of contamination in urban waterways, it is critical to identify the primary water sources of contamination within catchments. Source tracking using microbial community fingerprints is one tool that can be used to identify sources. However, results derived from this approach have not yet been evaluated using independent datasets. As such, the key objectives of this investigation were: (1) to identify the major sources of water responsible for bacterial loadings within an urban estuary using microbial source tracking (MST) using microbial communities; and (2) to evaluate this method using a 3-dimensional hydrodynamic model. The Yarra River estuary, which flows through the city of Melbourne in South-East Australia was the focus of this study. We found that the water sources contributing to the bacterial community in the Yarra River estuary varied temporally depending on the estuary's hydrodynamic conditions. The water source apportionment determined using microbial community MST correlated to those determined using a 3-dimensional hydrodynamic model of the transport and mixing of a tracer in the estuary. While there were some discrepancies between the two methods, this investigation demonstrated that MST using bacterial community fingerprints can identify the primary water sources of microorganisms in an estuarine environment. As such, with further optimization and improvements, microbial community MST has the potential to become a powerful tool that could be practically applied in the mitigation of contaminated aquatic systems.

Presence and survival of culturable Campylobacter spp. and Escherichia coli in a temperate urban estuary

Urban estuaries throughout the world typically contain elevated levels of faecal contamination, the extent of which is generally assessed using faecal indicator organisms (FIO) such as Escherichia coli. This study assesses whether the bacterial FIO, E. coli is a suitable surrogate for Campylobacter spp., in estuaries. The presence and survival dynamics of culturable E. coli and Campylobacter spp. are compared in the water column, bank sediments and bed sediments of the Yarra River estuary (located in Melbourne, Australia). The presence of E. coli did not necessarily indicate detectable levels of Campylobacter spp. in the water column, bed and bank sediments, but the inactivation rates of the two bacteria were similar in the water column. A key finding of the study is that E. coli and Campylobacter spp. can survive for up to 14days in the water column and up to 21days in the bed and bank sediments of the estuary. Preliminary data presented in this study also suggests that the inactivation rates of the two bacteria may be similar in bed and bank sediments. This undermines previous hypotheses that Campylobacter spp. cannot survive outside of its host and indicates that public health risks can persist in aquatic systems for up to three weeks after the initial contamination event.

Evaluation of Techniques for Measuring Microbial Hazards in Bathing Waters: A Comparative Study

Recreational water quality is commonly monitored by means of culture based faecal indicator organism (FIOs) assays. However, these methods are costly and time-consuming; a serious disadvantage when combined with issues such as non-specificity and user bias. New culture and molecular methods have been developed to counter these drawbacks. This study compared industry-standard IDEXX methods (Colilert and Enterolert) with three alternative approaches: 1) TECTA™ system for E. coli and enterococci; 2) US EPA’s 1611 method (qPCR based enterococci enumeration); and 3) Next Generation Sequencing (NGS). Water samples (233) were collected from riverine, estuarine and marine environments over the 2014–2015 summer period and analysed by the four methods. The results demonstrated that E. coli and coliform densities, inferred by the IDEXX system, correlated strongly with the TECTA™ system. The TECTA™ system had further advantages in faster turnaround times (~12 hrs from sample receipt to result compared to 24 hrs); no staff time required for interpretation and less user bias (results are automatically calculated, compared to subjective colorimetric decisions). The US EPA Method 1611 qPCR method also showed significant correlation with the IDEXX enterococci method; but had significant disadvantages such as highly technical analysis and higher operational costs (330% of IDEXX). The NGS method demonstrated statistically significant correlations between IDEXX and the proportions of sequences belonging to FIOs, Enterobacteriaceae, and Enterococcaceae. While costs (3,000% of IDEXX) and analysis time (300% of IDEXX) were found to be significant drawbacks of NGS, rapid technological advances in this field will soon see it widely adopted.