A highly prevalent and specific cryptic plasmid pBI143 for human fecal pollution tracking in a subtropical urban river.

Microbial source tracking (MST) is a critical tool for identifying sources of human and animal fecal pollution in aquatic environments. To enhance human fecal pollution tracking, this study evaluated the performance characteristics of pBI143, a cryptic plasmid recently identified for potential MST applications. Nucleic acid samples from ten animal species were screened for pBI143, revealing its presence in a small number of pigs, cows, dogs, cats, and flying fox fecal samples.

Determinants of antimicrobial resistance in biosolids: A systematic review, database, and meta-analysis.

Biosolids can provide a nutrient rich soil amendment, particularly for poor soils and semi-arid or drought-prone areas. However, there are concerns that sludge and biosolids could be a source of propagation and exposure to AMR determinants such as antibiotic resistant bacteria (ARB), and antibiotic resistance genes (ARGs). To inform risk assessment efforts, a systematic literature review was performed to build a comprehensive spreadsheet database of ARB and ARG concentrations in biosolids (and some sludges specified as intended for land application), along with 69 other quantitative and qualitative meta-data fields from 68 published studies describing sampling information and processing methods that can be used for modeling purposes.

Comparison of adsorption-extraction workflows for improved measurements of viruses and bacteria in untreated wastewater.

The lack of standardized methods and large differences in virus concentration and extraction workflows have hampered severe acute respiratory syndrome (SARS-CoV-2) wastewater surveillance and data reporting practices. Numerous studies have shown that adsorption-extraction (AE) method holds promise, yet several uncertainties remain regarding the optimal AE workflow. Several procedural components that may influence the recovered concentrations of target DNA/RNA, including membrane types, homogenization instruments, speed and duration, and lysis buffer.

Development of a triplex RT-qPCR assay for simultaneous quantification of Japanese encephalitis, Murray Valley encephalitis, and West Nile viruses for environmental surveillance.

The co-circulation of mosquito-borne Japanese encephalitis virus (JEV), Murray Valley encephalitis virus (MVEV), and West Nile virus (WNV) has impacted human and animal health in multiple countries worldwide. To facilitate early warnings and surveillance of the presence of these viral infectious agents in the environment, a triplex reverse transcription-quantitative PCR (RT-qPCR) was developed for simultaneous quantification of JEV, MVEV, and WNV in potential hotspots such as piggery and urban wastewater and environmental water samples. The performance of the developed triplex RT-qPCR assay was compared with that of simplex counterparts, all using the same primer and probe sequences.

Development and comparative assessment of RT-qPCR and duplex RT-LAMP assays for the monitoring of Aichi virus A (AiV-A) in untreated wastewater samples.

Diverse enteric pathogens, transmitted through human and animal feces, can cause gastroenteritis. Enteric viruses, such as human Aichi virus, specifically genotype A (AiV-A), are emerging pathogens that cause illnesses even at low doses and are spreading globally. This research developed a reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay targeting the 3CD junction and a reverse transcription colorimetric loop-mediated isothermal amplification (RT-cLAMP) duplex assay targeting junctions 2BC and 3CD of the AiV-A genome for rapid and sensitive detection of this virus in metropolitan and regional wastewater samples in Queensland, Australia.

Development and evaluation of a colorimetric LAMP based-assay targeting the Bacteroides HF183 marker for tracking sewage pollution in environmental waters.

Surface waters are vulnerable to contamination by human and animal feces, posing risks to human health due to potential exposure to enteric pathogens. This research developed a colorimetric loop-mediated isothermal amplification (cLAMP) assay to detect sewage associated Bacteroides dorei HF183/BacR287 (HF183) marker in wastewater and environmental water samples. The host sensitivity and host specificity of the assay were evaluated, and their performance was compared to the Bacteroides HF183 qPCR assay using control materials (gBlocks), environmental water samples seeded with untreated sewage, and ambient environmental water samples.

The comparison of decay rates of infectious SARS-CoV-2 and viral RNA in environmental waters and wastewater.

Understanding the decay characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater and ambient waters is important for multiple applications including assessment of risk of exposure associated with handling wastewater samples, public health risk associated with recreation in wastewater polluted ambient waters and better understanding and interpretation of wastewater-based epidemiology (WBE) results. We evaluated the decay rates of infectious SARS-CoV-2 and viral RNA in wastewater and ambient waters under temperature regimes representative of seasonal fluctuations. Infectious virus was seeded in autoclaved primary wastewater effluent, final dechlorinated wastewater effluent, lake water, and marine water at a final concentration of 6.

Key considerations for pathogen surveillance in wastewater.

Wastewater surveillance (WWS) has received significant attention as a rapid, sensitive, and cost-effective tool for monitoring various pathogens in a community. WWS is employed to assess the spatial and temporal trends of diseases and identify their early appearances and reappearances, as well as to detect novel and mutated variants. However, the shedding rates of pathogens vary significantly depending on factors such as disease severity, the physiology of affected individuals, and the characteristics of pathogen.

Assessment of nucleic acid extraction protocols for antibiotic resistance genes (ARGs) quantification in aircraft wastewater.

This study evaluated ten nucleic acid extraction protocols (EP1 to EP10) for measuring five endogenous antibiotic resistance genes (ARGs) in four aircraft wastewater samples (AWW1 to AWW4). The targeted ARGs, including bla, bla, ermB, qnrS, and tetA, encompassed highly and minimally abundant ARGs. TetA and ermB were consistently detected across four aircraft wastewater samples using the DNeasy Blood and Tissue Kit and the AllPrep PowerViral DNA/RNA kit.

Leveraging wastewater surveillance to detect viral diseases in livestock settings.

Wastewater surveillance has evolved into a powerful tool for monitoring public health-relevant analytes. Recent applications in tracking severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection highlight its potential. Beyond humans, it can be extended to livestock settings where there is increasing demand for livestock products, posing risks of disease emergence.

Site-specific risk-based threshold (RBT) concentrations for sewage-associated markers in estuarine swimming waters.

This study establishes site-specific risk-based threshold (RBT) concentrations for sewage-associated markers, including Bacteroides HF183 (HF183), Lachnospiraceae Lachno3 (Lachno3), cross-assembly phage (CrAssphage), and pepper mild mottle virus (PMMoV), utilizing quantitative microbial risk assessment (QMRA) for recreational estuarine waters (EW). The QMRA model calculates a RBT concentration corresponding to a selected target illness risk for ingestion of EW contaminated with untreated sewage. RBT concentrations were estimated considering site-specific decay rates and concentrations of markers and reference pathogen (human norovirus; HNoV), aiding in the identification of high-risk days during the swimming season.

Microbial source tracking of fecal pollution to coral reef lagoons of Norfolk Island, Australia.

Fecal pollution contributes to global degradation of water quality and requires identification of the source(s) for predicting human health risk, tracking disease, and developing management strategies. While fecal indicator bacteria are commonly used to detect fecal pollution, they cannot identify sources. Novel approaches, such as microbial source tracking (MST), can be applied to evaluate the origin of fecal pollution.

Comparing the decay of human wastewater-associated markers and enteric viruses in laboratory microcosms simulating estuarine waters in a temperate climatic zone using qPCR/RT-qPCR assays.

This study investigated the decay rates of wastewater-associated markers and enteric viruses in laboratory microcosms mimicking estuarine water environments in temperate Sydney, NSW, Australia using qPCR and RT-qPCR assays. The results demonstrated the reduction in concentrations of Bacteroides HF183, Lachnospiraceae Lachno3, cross-assembly phage (crAssphage), pepper mild mottle virus (PMMoV), human adenovirus (HAdV 40/41), and enterovirus (EV) over a span of 42 days under spring/summer temperatures, presence/absence of microbiota, and different light conditions. The study found that HF183, Lachno3, crAssphage, PMMoV, HAdV 40/41, and EV exhibited varying decay rates depending on the experimental conditions.

Evaluation of colorimetric RT-LAMP for screening of SARS-CoV-2 in untreated wastewater.

This study compared reverse transcription-loop-mediated isothermal amplification (RT-LAMP) and three reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays targeting the N and E genes of the SARS-CoV-2 genome for detecting RNA in untreated wastewater samples. RT-qPCR assays exhibited consistent amplification down to 2 × 10 GC/reaction, with greater analytical sensitivity at 2 × 10 GC/reaction by US CDC N1 and US CDC N2 assays. In contrast, RT-LAMP exhibited lower sensitivity, detecting SARS-CoV-2 only at or above 2 × 10 GC/reaction.

Tracking the effects of the COVID-19 pandemic on viral gastroenteritis through wastewater-based retrospective analyses.

The COVID-19 pandemic possibly disrupted the circulation and seasonality of gastroenteritis viruses (e.g., Norovirus (NoV), Sapovirus (SaV), group A rotavirus (ARoV), and Aichivirus (AiV)).

Decay of Cryptosporidium parvfum DNA in cowpats in subtropical environments determined using qPCR.

Cryptosporidium oocysts pose a significant threat to public health due to its ability to contaminate environmental waters, leading to outbreaks of waterborne diseases and emphasizing the crucial need for effective water treatment and monitoring systems. This study aimed to investigate the decay of Cryptosporidium oocyst DNA in cow fecal matter under different environmental conditions prevalent in sub-tropical Southeast Queensland (SEQ) during summer and winter seasons. The effects of ambient sunlight and shaded conditions on the decay rates of C.

Reduction of human fecal markers and enteric viruses in Sydney estuarine waters receiving wet weather overflows.

The current microbial source tracking (MST) study tracked the reduction of the culturable fecal indicator bacteria enterococci, four human fecal markers (Bacteroides HF183, Lachnospiraceae Lachno3, cross-assembly phage (CrAssphage) and pepper mild mottle virus (PMMoV)) along with four enteric viruses - human adenovirus 40/41 (HAdV 40/41), enterovirus (EV), human norovirus GI (HNoV GI) and GII (HNoV GII) post wet weather overflows (WWOs) at two estuarine water sites from two depths under separate six-day sampling campaigns over seven and 12 days in Sydney, NSW, Australia. Neither HNoV GI nor GII was detected, while 13.9 % (10/72) of estuarine water samples had detections of EV.

Show us the data: global COVID-19 wastewater monitoring efforts, equity, and gaps.

A year since the declaration of the global coronavirus disease 2019 (COVID-19) pandemic, there were over 110 million cases and 2.5 million deaths. Learning from methods to track community spread of other viruses such as poliovirus, environmental virologists and those in the wastewater-based epidemiology (WBE) field quickly adapted their existing methods to detect SARS-CoV-2 RNA in wastewater.

Have genetic targets for faecal pollution diagnostics and source tracking revolutionized water quality analysis yet?

The impacts of nucleic acid-based methods - such as PCR and sequencing - to detect and analyze indicators, genetic markers or molecular signatures of microbial faecal pollution in health-related water quality research were assessed by rigorous literature analysis. A wide range of application areas and study designs has been identified since the first application more than 30 years ago (>1100 publications). Given the consistency of methods and assessment types, we suggest defining this emerging part of science as a new discipline: genetic faecal pollution diagnostics (GFPD) in health-related microbial water quality analysis.

Wastewater Surveillance Can Function as an Early Warning System for COVID-19 in Low-Incidence Settings.

Introduction: During the first two years of the COVID-19 pandemic, Australia implemented a series of international and interstate border restrictions. The state of Queensland experienced limited COVID-19 transmission and relied on lockdowns to stem any emerging COVID-19 outbreaks. However, early detection of new outbreaks was difficult.