Viral and bacterial contamination in recreational waters: a case study in the Lisbon bay area

Unraveling the influence of human fecal pollution on antibiotic resistance gene levels in different receiving water bodies using crAssphage indicator gene

Discharged wastewater treatment plant (WWTP) effluents can contaminate receiving water bodies with human feces and alter the abundance of antibiotic resistance genes (ARGs). In this study, we examined the co-occurrence of ARGs, human fecal pollution indicator crAssphage, and antibiotics in human feces and a series of connected receiving water bodies affected by human feces, including water from different treatment units of a WWTP, river, lake, and tap waters. Results showed that crAssphage was detected in 68.2 % of the studied water bodies, confirming widespread human fecal contamination. Both ARG and crAssphage abundances exhibited a distance-decay effect from the emission source to the receiving environment. Interestingly, the detected ARG abundance in the water bodies was significantly correlated with crAssphage abundance but not with the residual antibiotic concentration, demonstrating that the presence of ARG could largely be explained by the extent of fecal pollution, with no clear signs of antibiotic selection. In addition, 14 ARGs co-shared by human feces and water bodies were significantly correlated with crAssphage. Furthermore, a close evolutionary relationship was observed between the bla_TEM-1 gene from human feces and aquatic environments. These results imply a potential ARG exchange between human feces and receiving water bodies. Overall, this study provides important insights into the distribution and sources of ARGs in water bodies affected by human fecal contamination.

Evaluating the potential for exposure to organisms of public health concern in naturally occurring bathing waters in Europe: A scoping review

Globally, water-based bathing pastimes are important for both mental and physical health. However, exposure to waterborne organisms could present a substantial public health issue. Bathing waters are shown to contribute to the transmission of illness and disease and represent a reservoir and pathway for the dissemination of antimicrobial resistant (AMR) organisms. Current bathing water quality regulations focus on enumeration of faecal indicator organisms and are not designed for detection of specific waterborne organisms of public health concern (WOPHC), such as antimicrobial resistant (AMR)/pathogenic bacteria, or viruses. This investigation presents the first scoping review of the occurrence of waterborne organisms of public health concern (WOPHC) in identified natural bathing waters across the European Union (EU), which aimed to critically evaluate the potential risk of human exposure and to assess the appropriateness of the current EU bathing water regulations for the protection of public health. Accordingly, this review sought to identify and synthesise all literature pertaining to a selection of bacterial (Campylobacter spp., Escherichia coli, Salmonella spp., Shigella spp., Vibrio spp., Pseudomonas spp., AMR bacteria), viral (Hepatitis spp., enteroviruses, rotavirus, adenovirus, norovirus), and protozoan (Giardia spp., and Cryptosporidium spp.) contaminants in EU bathing waters. Sixty investigations were identified as eligible for inclusion and data was extracted. Peer-reviewed investigations included were from 18 countries across the EU, totalling 87 investigations across a period of 35 years, with 30% published between 2011 and 2015. A variety of water bodies were identified, with 27 investigations exclusively assessing coastal waters. Waterborne organisms were classified into three categories; bacteria, viruses, and protozoa; amounting to 58%, 36% and 17% of the total investigations, respectively. The total number of samples across all investigations was 8,118, with detection of one or more organisms in 2,449 (30%) of these. Viruses were detected in 1281 (52%) of all samples where WOPHC were found, followed by bacteria (865(35%)) and protozoa (303(12%)). Where assessed (442 samples), AMR bacteria had a 47% detection rate, emphasising their widespread occurrence in bathing waters. Results of this scoping review highlight the potential public health risk of exposure to WOPHC in bathing waters that normally remain undetected within the current monitoring parameters.

Assessment of the Presence of Hepatitis E virus in Surface Water and Drinking Water in Portugal

Hepatitis E virus (HEV) is a non-enveloped single-stranded positive-sense RNA virus, belonging to the Hepeviridae family, resistant to environmental conditions, and transmitted by the consumption of contaminated water. This virus is responsible for both sporadic and epidemic outbreaks, leading to thousands of infections per year in several countries, and is thus considered an emerging disease in Europe and Asia. This study refers to a survey in Portugal during 2019, targeting the detection and eventual quantification of enteric viruses in samples from surface and drinking water. Samples positive for HEV RNA were recurrently found by reverse transcription quantitative PCR (RT-qPCR), in both types of matrix. The infectivity of these samples was evaluated in cultured Vero E6 cells and RNA from putative viruses produced in cultures evidencing cytopathic effects and was subjected to RT-qPCR targeting HEV genomic RNA. Our results evidenced the existence of samples positive either for HEV RNA (77.8% in surface water and 66.7% in drinking water) or for infectious HEV (23.0% in surface water and 27.7% in drinking water). These results highlight the need for effective virological control of water for human consumption and activities.

Environmental and Adaptive Changes Necessitate a Paradigm Shift for Indicators of Fecal Contamination

Changes in the occurrence, distribution, and seasonal variation of waterborne pathogens due to global climate change may increase the risk of human exposure to these microorganisms, thus heightening the need for more reliable surveillance systems. Routine monitoring of drinking water supplies and recreational waters is performed using fecal indicator microorganisms, such as Escherichia coli , Enterococcus spp., and coliphages. However, the presence and numbers of these indicators, especially E. coli and Enterococcus spp., do not correlate well with those of other pathogens, especially enteric viruses, which are a major cause of waterborne outbreaks associated with contaminated water and food, and recreational use of lakes, ponds, rivers, and estuarine waters. For that reason, there is a growing need for a surveillance system that can detect and quantify viral pathogens directly in water sources to reduce transmission of pathogens associated with fecal transmission. In this review, we present an updated overview of relevant waterborne enteric viruses that we believe should be more commonly screened to better evaluate water quality and to determine the safety of water use and reuse and of epidemiological data on viral outbreaks. We also discuss current methodologies that are available to detect and quantify these viruses in water resources. Finally, we highlight challenges associated with virus monitoring. The information presented in this review is intended to aid in the assessment of human health risks due to contact with water sources, especially since current environmental and adaptive changes may be creating the need for a paradigm shift for indicators of fecal contamination.

Molecular epidemiology and host genetics of norovirus and rotavirus infections in Portuguese elderly living in aged care homes

Norovirus (NoV) and rotavirus group A (RVA) are major agents of acute gastroenteritis worldwide. This study aimed to investigate their epidemiological profile in Portuguese elderly living in long-term care facilities and to assess the host genetic factors mediating infection susceptibility. From November 2013 to June 2015, 636 faecal specimens from 169 elderly, mainly asymptomatic, living in nursing homes in Greater Lisbon and Faro district, Portugal, were collected. NoV and RVA were detected by real-time polymerase chain reaction and NoV genotyped by phylogenetic analysis. NoV detection rate was 7.1% (12 of 169). Three GI.3 and one GII.6 strains were genotyped. RVA detection rate was 3.6% (6 of 169), exclusively in asymptomatic individuals. Host genetic factors associated with infection susceptibility were described on 250 samples by saliva-based enzyme-linked immunosorbent assays. The Lewis-negative phenotype was 8.8% (22 of 250) and the rate of nonsecretors was 16.8% (42 of 250). Association to NoV and RVA infection was performed in the subgroup of individuals (n = 147) who delivered both faecal and saliva samples. The majority of NoV- and RVA-positive individuals (90.9% and 83.3%, respectively) were secretor-positive, with Lewis B phenotype. In a subset of individuals, FUT2 and FUT3 genes were genotyped to assess mutations and validate the secretor and Lewis phenotypes. All sequenced nonsecretors were homozygous for FUT2 nonsense mutation G428A. In this study, low detection rates of NoV and RVA infections were found during two winter seasons. However, even in the absence of any outbreak, the importance of finding these infections in a nonepidemic situation in long-term care facilities may have important implications for infection control.

Relationships between Microbial Indicators and Pathogens in Recreational Water Settings

Fecal pollution of recreational waters can cause scenic blight and pose a threat to public health, resulting in beach advisories and closures. Fecal indicator bacteria (total and fecal coliforms, Escherichia coli, and enterococci), and alternative indicators of fecal pollution (Clostridium perfringens and bacteriophages) are routinely used in the assessment of sanitary quality of recreational waters. However, fecal indicator bacteria (FIB), and alternative indicators are found in the gastrointestinal tract of humans, and many other animals and therefore are considered general indicators of fecal pollution. As such, there is room for improvement in terms of their use for informing risk assessment and remediation strategies. Microbial source tracking (MST) genetic markers are closely associated with animal hosts and are used to identify fecal pollution sources. In this review, we examine 73 papers generated over 40 years that reported the relationship between at least one indicator and one pathogen group or species. Nearly half of the reports did not include statistical analysis, while the remainder were almost equally split between those that observed statistically significant relationships and those that did not. Statistical significance was reported less frequently in marine and brackish waters compared to freshwater, and the number of statistically significant relationships was considerably higher in freshwater (p < 0.0001). Overall, significant relationships were more commonly reported between FIB and pathogenic bacteria or protozoa, compared to pathogenic viruses (p: 0.0022⁻0.0005), and this was more pronounced in freshwater compared to marine. Statistically significant relationships were typically noted following wet weather events and at sites known to be impacted by recent fecal pollution. Among the studies that reported frequency of detection, FIB were detected most consistently, followed by alternative indicators. MST markers and the three pathogen groups were detected least frequently. This trend was mirrored by reported concentrations for each group of organisms (FIB > alternative indicators > MST markers > pathogens). Thus, while FIB, alternative indicators, and MST markers continue to be suitable indicators of fecal pollution, their relationship with waterborne pathogens, particularly viruses, is tenuous at best and influenced by many different factors such as frequency of detection, variable shedding rates, differential fate and transport characteristics, as well as a broad range of site-specific factors such as the potential for the presence of a complex mixture of multiple sources of fecal contamination and pathogens.

Toward a better guard of coastal water safety-Microbial distribution in coastal water and their facile detection

Prosperous development in marine-based tourism has raised increasing concerns over the sanitary quality of coastal waters with potential microbial contamination. The World Health Organization has set stringent standards over a list of pathogenic microorganisms posing potential threats to people with frequent coastal water exposure and has asked for efficient detection procedures for pathogen facile identification. Inspection of survey events regarding the occurrence of marine pathogens in recreational beaches in recent years has reinforced the need for the development of a rapid identification procedure. In this review, we examine the possibility of recruiting uniform molecular assays to identify different marine pathogens and the feasibility of appropriate biomarkers, including enterochelin biosynthetic genes, for general toxicity assays. The focus is not only on bacterial pathogens but also on other groups of infectious pathogens. The ultimate goal is the development of a handy method to more efficiently and rapidly detect marine pathogens.

Microbial quality and physical-chemical characteristics of thermal springs

Microbial quality and physical-chemical properties of recreational spas were surveyed to investigate the health aspect of the spas' water. A total of 195 samples were collected from pools and springs of the spas in five sites from Ardebil Province of Iran. The effects of an independent factor defined as 'condition' and its component sub-factors (i.e., sampling point, location, and sampling date) on microbial quality and physical-chemical properties of the spas were studied by applying path analysis. The influence of physical-chemical properties on microbial quality was also considered. The percentage of samples exceeding the ISIRI (Swimming pool water microbiological specifications (vol 9412), Institute of Standards and Industrial Research of Iran, Tehran, 2007) limits for Staphylococcus (spp.) was up to 55.8 in the springs and 87.8 in the pools, 58.1 and 99.2 for HPC, 90.7 and 97.8 for total coliform and fecal coliform, and 9.3 and 34.4 for Pseudomonas aeruginosa, respectively. There were significant differences between the pools and springs for both physical-chemical properties and microbial quality. From the path analysis, sampling point was the most effective sub-factor of 'condition' on both the physical-chemical properties and microbial quality. Among the physical-chemical properties, water color had the most enhancing or additive influence on microbial pollution, while EC indicated a reducing or subtractive effect.

Characterization, validation and application of a DNA microarray for the detection of mandatory and other waterborne pathogens

Culture methods for the detection of indicator bacteria are currently used for detection of waterborne bacteria. The need for an increased range of analyzed bacteria coupled with the obtainment of rapid and early results justify the development of a DNA microarray for the identification of waterborne pathogens. This DNA microarray has 16 implanted probes with a median size of 147 bases, targeting 12 different parameters, including all mandatory indicator microorganisms, such as Escherichia coli, Clostridium perfringens, Pseudomonas aeruginosa, Staphylococcus aureus, total and fecal coliforms and enterococci. The validation performed with DNA extracted from pure microbial cultures showed the suitability of the probes for detection of the target microorganism. To overcome the high dilution of water samples it was included either a prior culture step of bacterial contaminants retained after filtering 100 ml of water, or a 10-fold increase in the volume of filtered water, that resulted in the increase of the detected bacteria. The analysis of complex environmental water samples using culture methods and the DNA microarray revealed that the latter detected the same parameters plus other bacteria tested only in the DNA microarray. The results show that this DNA microarray may be a useful tool for water microbiological surveillance.

Occurrence of human enteric viruses in commercial mussels at retail level in three European countries

In this study, the prevalence of different enteric viruses in commercial mussels was evaluated at the retail level in three European countries (Finland, Greece and Spain). A total of 153 mussel samples from different origins were analysed for human norovirus (NoV) genogroups I and II, hepatitis A virus (HAV) and hepatitis E virus (HEV). Human adenovirus (HAdV) was also tested as an indicator of human faecal contamination. A full set of controls (such as sample process control, internal amplification controls, and positive and negative controls) were implemented during the process. The use of a sample process control allowed us to calculate the efficiencies of extraction, which ranged from 79 to 0.5 %, with an average value of 10 %. Samples were positive in 41 % of cases, with HAdV being the most prevalent virus detected (36 %), but no significant correlation was found between the presence of HAdV and human NoV, HAV and HEV. The prevalences of human norovirus genogroup II, HEV and human NoV genogroup I were 16, 3 and 0.7 %, respectively, and HAV was not detected. The estimated number of PCR detectable units varied between 24 and 1.4 × 10(3) g(-1) of digestive tract. Interestingly, there appeared to be a significant association between the type of mussel species (M. galloprovincialis) and the positive result of samples, although a complete overlap between country and species examined required this finding to be confirmed including samples of both species from all possible countries of origin.

Environmental survey to assess viral contamination of air and surfaces in hospital settings

The presence of pathogenic viruses in healthcare settings represents a serious risk for both staff and patients. Direct viral detection in the environment poses significant technical problems and the indirect indicators currently in use suffer from serious limitations. The aim of this study was to monitor surfaces and air in hospital settings to reveal the presence of hepatitis C virus, human adenovirus, norovirus, human rotavirus and torque teno virus by nucleic acid assays, in parallel with measurements of total bacterial count and haemoglobin presence. In total, 114 surface and 62 air samples were collected. Bacterial contamination was very low (<1 cfu/cm²) on surfaces, whereas the ‘medium’ detected value in air was 282 cfu/m³. Overall, 19 (16.7%) surface samples tested positive for viral nucleic acids: one for norovirus, one for human adenovirus and 17 (14.9%) for torque teno virus (TTV). Only this latter virus was directly detected in 10 air samples (16.1%). Haemoglobin was found on two surfaces. No relationship was found between viral, biochemical or bacterial indicators. The data obtained confirm the difficulty of assessing viral contamination using bacterial indicators. The frequent detection of TTV suggests its possible use as an indicator for general viral contamination of the environment.