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Recreational bathing waters are complex systems with diverse inputs from multiple anthropogenic and zoogenic sources of faecal contamination. Faecal contamination is a substantial threat to water quality and public health. Here we present a comprehensive strategy to estimate the contribution of faecal indicator bacteria (FIB) from different biological sources on two at-risk beaches in Dublin, Ireland. The daily FIB loading rate was determined for three sources of contamination: a sewage-impacted urban stream, dog and wild bird fouling. This comparative analysis determined that the stream contributed the highest daily levels of FIB, followed by dog fouling. Dog fouling may be a significant source of FIB, contributing approximately 20 % of E. coli under certain conditions, whereas wild bird fouling contributed a negligible proportion of FIB (<3 %). This study demonstrates that source-specific quantitative microbial source apportionment (QMSA) strategies are vital to identify primary public health risks and target interventions to mitigate faecal contamination. [Display omitted] • Source-specific QMSA is vital to quantify diverse biological sources of faeces. • Sewage-impacted stream contributed the highest daily FIB loading onto beaches. • Dogs were estimated to load 0.6 –h 2.2 kg of faeces and 20 % of E. coli daily. • Wild bird fouling contributed a negligible proportion of FIB. [ABSTRACT FROM AUTHOR]

• T 90 of infectious SARS-CoV-2 at 4°C was 3.8 and 2.2 days in river and seawater • T 90 of infectious SARS-CoV-2 at 20°C was 2.3 and 1.1 days in river and seawater • SARS-CoV-2 RNA is more stable than the infectious particle in river and seawater • Infectious MS2 persisted longer than infectious SARS-CoV-2 in aquatic environments • The decay rate of MS2 and PMMoV RNA differed from the decay rate of SARS-CoV-2 RNA The introduction of SARS-CoV-2 containing human stool and sewage into water bodies may raise public health concerns. However, assessment of public health risks by faecally contaminated water is limited by a lack of knowledge regarding the persistence of infectious SARS-CoV-2 in water. In the present study the decay rates of viable infectious SARS-CoV-2 and SARS-CoV-2 RNA were determined in river and seawater at 4 and 20°C. These decay rates were compared to S. typhimurium bacteriophage MS2 and pepper mild mottle virus (PMMoV). Persistence of viable SARS-CoV-2 was temperature dependent, remaining infectious for significantly longer periods of time in both freshwater and seawater at 4°C than at 20°C. T 90 for infectious SARS-CoV-2 in river water was 2.3 days and 3.8 days at 20°C and 4°C, respectively. The T 90 values were 1.1 days and 2.2 days in seawater at 20°C and 4°C, respectively. In contrast to the rapid inactivation of infectious SARS-CoV-2 in river and sea water, viral RNA was relatively stable. The RNA decay rates were increased in non-sterilised river and seawater, presumably due to the presence of microbiota. The decay rates of infectious MS2, MS2 RNA and PMMoV RNA differed significantly from the decay rate of SARS-CoV-2 RNA, suggesting that their use as surrogate markers for the persistence of SARS-CoV-2 in the environment is limited. [Display omitted] [ABSTRACT FROM AUTHOR]

Antibiotic resistance represents the greatest challenge to healthcare systems around the world. As antibiotic resistance genes (ARGs) are shed in faeces, many studies have focused on how wastewater effluent contributes to ARG pollution in rivers. However, small urban streams and bathing waters not impacted by treated wastewater have received little attention though they may be important reservoirs of ARGs. The main objective of this study was to assess the extent to which ARG and faecal pollution impact small urban streams and bathing waters and to determine if there is a relationship between these contaminants. For one year, bi-monthly water samples were collected from two urban streams and Dublin city's three designated bathing waters. The Liffey Estuary, that receives treated wastewater, was also sampled. The sul1 , tet (O), qnrS , bla TEM , bla SHV and bla CTX-M ARGs were quantified. E. coli and intestinal enterococci levels were determined and the source of faecal pollution (human, dog, gull) quantified by microbial source tracking. Our results show that the Liffey Estuary, the urban streams and the bathing waters are highly impacted by ARGs and human faeces. There were clear correlations between all of the studied faecal indicators and ARGs in the Liffey Estuary. In the urban streams relationships were observed for only some of the ARGs and faecal indicators, which is likely a result of non-continuous sewage leaks and overflows to the streams. Similarly, only some ARGs correlated with faecal indicators in the urban bathing waters. The source of ARGs in the bathing waters is likely to be multifaceted as we detected sporadic dog and gull faecal markers. This study demonstrates that small urban streams and bathing waters are reservoirs of ARGs and that they may pose a previously unrecognised public health risk as they have the potential to transmit enteric pathogens and antibiotic resistance determinants. Unlabelled Image • All faecal indicators and ARGs correlated in the wastewater impacted Liffey Estuary • Urban streams were intermittently impacted by high levels of faecal indicators. • ARGs and faecal indicators sporadically correlate in small urban streams. • Faecal indicators and ARGs sporadically correlated in urban bathing waters. • Human, gull and dog source tracking markers were quantified in urban bathing waters. [ABSTRACT FROM AUTHOR]

• Faecal indicators should be based on the hydrodynamic properties of water systems. • FIB are appropriate in advection dominant waterbodies. • crAssphage and PMMoV are appropriate in dispersion/advection dominant waterbodies. The EU Bathing Water Directive (BWD) requires member states to assess bathing water quality according to the levels of faecal indicator bacteria (FIB) in designated bathing areas. However, this criterion has two significant limitations given that the BWD does not; (i) account for differences in hydrodynamic properties of bathing waters and, (ii) assumes that all faecal pathogens decay equally in aquatic environments. This study simulated sewage discharge events in three hypothetical aquatic environments characterised by different advection and dispersion parameters in the solute transport equation. Temporal changes in the downstream concentration of six faecal indicators were determined in simulations that utilised measured decay rates of each faecal indicator from a programme of controlled microcosm experiments in fresh and seawater environments. The results showed that the decay rates of faecal indicators are not a critical parameter in advection dominant water bodies, such as in fast-flowing rivers. Therefore, faecal indicator selection is less important in such systems and for these, FIB remains the most cost-effective faecal indicator to monitor the public health impacts of faecal contamination. In contrast, consideration of faecal indicator decay is important when assessing dispersion and advection/dispersion dominant systems, which would pertain to transitional (estuarine) and coastal waterbodies. Results suggest that the inclusion of viral indicators, such as crAssphage and PMMoV, could improve the reliability of water quality modelling and minimise the risk of waterborne illnesses from faecal contamination. [Display omitted] [ABSTRACT FROM AUTHOR]