Faecal-indicator bacteria and sedimentary processes in estuarine mudflats (Seine, France)

Origin, fluxes, and reservoirs of Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa in aquatic ecosystems of a French floodplain

The release and spread of opportunistic pathogens - some of which are resistant to antibiotics - in the environment is a major public health challenge worldwide. In this study, we found evidence of the origin of such microorganisms and characterized their dispersal and survival in floodplain ecosystems to understand their fate in the environment. We determined the concentrations of Escherichia coli, extended-spectrum β-lactamases (ESBL)-producing E. coli, Klebsiella pneumoniae, ESBL-producing K. pneumoniae, and Pseudomonas aeruginosa in a floodplain of Eastern France using a culture-based method. Furthermore, we assessed the population structure of E. coli isolates by quadruplex PCR, their plasmid replicon content by PCR-based replicon typing, and the nature of their bla_ESBL genes by PCR and sequencing. The main aquatic ecosystems of the floodplain (river, tributaries, riverine wetlands, and groundwater) were sampled monthly over a one-year cycle. The majority of E. coli isolates retrieved in the studied floodplain were likely of human origin. Moreover, contamination of floodplain aquatic ecosystems by opportunistic pathogens mainly resulted from hydrological fluxes during high-flow periods, suggesting that dispersal and dilution predominated. During low-flow periods, E. coli may be able to survive for several months in isolated ecosystems in which it may find favourable conditions to thrive. The most nutrient-rich and isolated wetlands are consequently potential pathogen reservoirs. The production of ESBL was not a disadvantage for E. coli in low-anthropized floodplain ecosystems.

Depth-Dependent Response of Fecal Indicator Bacteria in Sediments to Changes in Water Column Nutrient Levels

Concentrations of in bottom sediments can influence the assessment of microbial stream water quality. Runoff events bring nutrients to streams that can support the growth of in sediments. The objective of this work was to evaluate depth-dependent changes in populations after nutrients are introduced to the water column. Bovine feces were collected fresh and mixed into sediment. Studies were performed in a microcosm system with continuous flow of synthetic stream water over inoculated sediment. Dilutions of autoclaved bovine manure were added to water on Day 16 at two concentrations, and KBr tracer was introduced into the water column to evaluate ion diffusion. Concentrations of , total coliforms, and total aerobic heterotrophic bacteria, along with orthophosphate-P and ammonium N, were monitored in water and sediment for 32 d. Sediment samples were analyzed in 0- to 1-cm and 1- to 3-cm sectioned depths. Concentrations of and total coliforms in top sediments were approximately one order of magnitude greater than in bottom sediments throughout the experiment. Introduction of nutrients to the water column triggered an increase of nutrient levels in both top and bottom sediments and increased concentrations of bacteria in the water. However, the added nutrients had a limited effect on in sediment where bacterial inactivation continued. Vertical gradients of concentrations in sediments persisted during the inactivation periods both before and after nutrient addition to the water column.

Distinct Aeromonas Populations in Water Column and Associated with Copepods from Estuarine Environment (Seine, France)

Aeromonas spp. are ubiquitous bacteria primarily recovered from aquatic ecosystems. They are found in fresh water as well as estuarine and marine waters, and in association with numerous autochthonous aquatic organisms in these environments. However, aeromonads are also etiologic agents of fish diseases and are now recognized as emerging pathogens in humans. The estuary is therefore a key environment, harboring autochthonous aeromonads, and aeromonads originating from humans and animals, mainly released by treated WWTP effluent or watershed run-off via tributaries. The present study compares the abundance and the diversity of Aeromonas populations. Over 2 years of monitoring (eight campaigns from February 2013 to November 2015), the occurrence of Aeromonas was investigated within the water column (water and fluid mud) and in association with copepods. Moreover, the diversity of Aeromonas populations was ascertained by analyzing gyrB and radA sequences, and the antibiotic-resistance phenotypes were determined using the disk diffusion method. This study shows, for the first time, the presence of Aeromonas spp. in water (1.1 × 10² to 1.2 ± 0.3 × 10³ CFU.100 mL^-1), fluid mud (2.6 ± 2.6 × 10² to 9.8 ± 0.9 × 10³ CFU.g^-1) and in association with living copepods (1.9 ± 0.7 × 10² to >1.1 × 10⁴ CFU.g^-1) in the Seine estuary. Moreover, the diversity study, conducted on 36 strains isolated from the water column and 47 strains isolated from copepods, indicates distinct populations within these two compartments. Strains distributed in five clusters corresponding to A. bestiarum (n = 6; 5.45%), A. encheleia (n = 1; 0.91%), A. media (n = 22; 20.0%), A. rivipollensis (n = 34; 30.91%) and A. salmonicida (n = 47; 42.73%). A. salmonicida is the most abundant species associated with Eurytemora affinis (n = 35; 74.47%). In contrast, A. salmonicida accounts for only 30.56% (n = 11) of isolates in the water column. This study shows the coexistence of distinct populations of Aeromonas in the oligohaline area of an anthropized estuary. Moreover, A. media, a putative human pathogen, present in the water column and abundant in the WWTP samples, was not detected in association with living copepods.

Change in the Structure of Escherichia coli Population and the Pattern of Virulence Genes along a Rural Aquatic Continuum

The aim of this study was to investigate the diversity of the Escherichia coli population, focusing on the occurrence of pathogenic E. coli, in surface water draining a rural catchment. Two sampling campaigns were carried out in similar hydrological conditions (wet period, low flow) along a river continuum, characterized by two opposite density gradients of animals (cattle and wild animals) and human populations. While the abundance of E. coli slightly increased along the river continuum, the abundance of both human and ruminant-associated Bacteroidales markers, as well as the number of E. coli multi-resistant to antibiotics, evidenced a fecal contamination originating from animals at upstream rural sites, and from humans at downstream urban sites. A strong spatial modification of the structure of the E. coli population was observed. At the upstream site close to a forest, a higher abundance of the B2 phylogroup and Escherichia clade strains were observed. At the pasture upstream site, a greater proportion of both E and B1 phylogroups was detected, therefore suggesting a fecal contamination of mainly bovine origin. Conversely, in downstream urban sites, A, D, and F phylogroups were more abundant. To assess the occurrence of intestinal pathogenic strains, virulence factors [afaD, stx1, stx2, eltB (LT), estA (ST), ipaH, bfpA, eae, aaiC and aatA] were screened among 651 E. coli isolates. Intestinal pathogenic strains STEC O174:H21 (stx2) and EHEC O26:H11 (eae, stx1) were isolated in water and sediments close to the pasture site. In contrast, in the downstream urban site aEPEC/EAEC and DAEC of human origin, as well as extra-intestinal pathogenic E. coli belonging to clonal group A of D phylogroup, were sampled. Even if the estimated input of STEC (Shiga toxin-producing E. coli) - released in water at the upstream pasture site - at the downstream site was low, we show that STEC could persist in sediment. These results show that, the run-off of small cattle farms contributed, as much as the wastewater effluent, in the dissemination of pathogenic E. coli in both water and sediments, even if the microbiological quality of the water was good or to average quality according to the French water index.

Abundance and Distribution of Enteric Bacteria and Viruses in Coastal and Estuarine Sediments-a Review

The long term survival of fecal indicator organisms (FIOs) and human pathogenic microorganisms in sediments is important from a water quality, human health and ecological perspective. Typically, both bacteria and viruses strongly associate with particulate matter present in freshwater, estuarine and marine environments. This association tends to be stronger in finer textured sediments and is strongly influenced by the type and quantity of clay minerals and organic matter present. Binding to particle surfaces promotes the persistence of bacteria in the environment by offering physical and chemical protection from biotic and abiotic stresses. How bacterial and viral viability and pathogenicity is influenced by surface attachment requires further study. Typically, long-term association with surfaces including sediments induces bacteria to enter a viable-but-non-culturable (VBNC) state. Inherent methodological challenges of quantifying VBNC bacteria may lead to the frequent under-reporting of their abundance in sediments. The implications of this in a quantitative risk assessment context remain unclear. Similarly, sediments can harbor significant amounts of enteric viruses, however, the factors regulating their persistence remains poorly understood. Quantification of viruses in sediment remains problematic due to our poor ability to recover intact viral particles from sediment surfaces (typically <10%), our inability to distinguish between infective and damaged (non-infective) viral particles, aggregation of viral particles, and inhibition during qPCR. This suggests that the true viral titre in sediments may be being vastly underestimated. In turn, this is limiting our ability to understand the fate and transport of viruses in sediments. Model systems (e.g., human cell culture) are also lacking for some key viruses, preventing our ability to evaluate the infectivity of viruses recovered from sediments (e.g., norovirus). The release of particle-bound bacteria and viruses into the water column during sediment resuspension also represents a risk to water quality. In conclusion, our poor process level understanding of viral/bacterial-sediment interactions combined with methodological challenges is limiting the accurate source apportionment and quantitative microbial risk assessment for pathogenic organisms associated with sediments in aquatic environments.

Sediment composition influences spatial variation in the abundance of human pathogen indicator bacteria within an estuarine environment

Faecal contamination of estuarine and coastal waters can pose a risk to human health, particularly in areas used for shellfish production or recreation. Routine microbiological water quality testing highlights areas of faecal indicator bacteria (FIB) contamination within the water column, but fails to consider the abundance of FIB in sediments, which under certain hydrodynamic conditions can become resuspended. Sediments can enhance the survival of FIB in estuarine environments, but the influence of sediment composition on the ecology and abundance of FIB is poorly understood. To determine the relationship between sediment composition (grain size and organic matter) and the abundance of pathogen indicator bacteria (PIB), sediments were collected from four transverse transects of the Conwy estuary, UK. The abundance of culturable Escherichia coli, total coliforms, enterococci, Campylobacter, Salmonella and Vibrio spp. in sediments was determined in relation to sediment grain size, organic matter content, salinity, depth and temperature. Sediments that contained higher proportions of silt and/or clay and associated organic matter content showed significant positive correlations with the abundance of PIB. Furthermore, the abundance of each bacterial group was positively correlated with the presence of all other groups enumerated. Campylobacter spp. were not isolated from estuarine sediments. Comparisons of the number of culturable E. coli, total coliforms and Vibrio spp. in sediments and the water column revealed that their abundance was 281, 433 and 58-fold greater in sediments (colony forming units (CFU)/100g) when compared with the water column (CFU/100ml), respectively. These data provide important insights into sediment compositions that promote the abundance of PIB in estuarine environments, with important implications for the modelling and prediction of public health risk based on sediment resuspension and transport.

Evidence for coexistence of distinct Escherichia coli populations in various aquatic environments and their survival in estuary water

Escherichia coli, a commensal bacterium from the intestinal tracts of humans and vertebrate animals, has been used as one of two bacterial indicators of fecal contamination, along with intestinal enterococci, to monitor the microbiological quality of water. However, water environments are now recognized as a secondary habitat where some strains can survive. We investigated the survival of E. coli isolates collected from bodies of water in France exhibiting distinct profiles of contamination, defined according to the following criteria: vicinity of the point sources of contamination, land use, hydrology, and physicochemical characteristics of the receiving water. We selected 88 E. coli strains among a collection of 352 strains to carry out a microcosm experiment in filtered estuarine water for 14 days at 10°C. The relationship between the survival of E. coli strains and genotypic and phenotypic characteristics was analyzed. This work showed that distinct E. coli survival types, able to survive from between 7 and 14 days to less than 2 days, coexisted in the water. E. coli isolates that rapidly lost their culturability were more frequently isolated in water recently contaminated by fecal bacteria of human origin, and most were multiresistant to antibiotics and harbored several virulence factors. In contrast, persistent strains able to survive from 4 to 14 days were more often found in water with low levels of fecal bacteria, belonged mainly to the B1 phylogroup, often harbored only one virulence factor, kspE or ompT, and were able to grow at 7°C.

Evidence of methylmercury production and modification of the microbial community structure in estuary sediments contaminated with wastewater treatment plant effluents

The Seine's estuary (France) waters are the receptacle of effluents originating from wastewater treatment plants (WWTP). In this estuary, mudflats are deposition zones for sediments and their associated contaminants, and play an essential role in the mercury (Hg) biogeochemical cycle mainly due to indigenous microorganisms. Microcosms were used to assess the impact of WWTP-effluents on mercury methylation by monitoring Hg species (total dissolved Hg in porewater, methylmercury and total mercury) and on microbial communities in sediments. After effluent amendment, methylmercury (MeHg) concentrations increased in relation with the total Hg and organic matter content of the WWTP-effluents. A correlation was observed between MeHg and acid-volatile-sulfides concentrations. Quantification of sulfate-reducing microorganisms involved in Hg methylation showed no increase of their abundance but their activity was probably enhanced by the organic matter supplied with the effluents. WWTP-effluent spiking modified the bacterial community fingerprint, mainly influenced by Hg contamination and the organic matter amendment.

Fecal pollution in coastal marine sediments from a semi-enclosed deep embayment subjected to anthropogenic activities: an issue to be considered in environmental quality management frameworks development

Sewage discharge is a major source of pollution in marine environments. Urban wastewaters can directly enter marine environments carrying pathogen organisms, organic loads, and nutrients. Because marine sediments can act as the ultimate fate of a wide range of pollutants, environmental quality assessment in this compartment can help to identify pollution problems in coastal areas. In the present study, characterization of surficial marine sediments allowed assessment of fecal pollution in a semi-enclosed deep embayment that is subjected to anthropogenic activities. Physicochemical parameters and fecal indicators presented a great spatial heterogeneity. Fecal coliform and Clostridium perfringens showed accumulation in an extensive area, not only in proximity to sewage discharge points, but also in sediments at 100 meters depth. Results included herein demonstrated that, in coastal areas, urban wastewater discharge can affect the whole ecosystem through accumulation of fecal matter in bottom sediments. Application of multivariate techniques provided useful information with applicability for management of coastal areas in such complex systems. Environmental implications of wastewater discharge in coastal areas indicate the need to implement and include sediment quality control strategies in legislative frameworks.

Relationships between hydrosedimentary processes and occurrence of mercury-resistant bacteria (merA) in estuary mudflats (Seine, France)

The Seine estuary (France) is one of the world's macrotidal systems that is most contaminated with heavy metals. To study the mercury-resistant bacterial community in such an environment, we have developed a molecular tool, based on competitive PCR, enabling the quantification of Gram-negative merA gene abundance. The occurrence of the Gram-negative merA gene in relation with the topology (erosion/deposit periods) and the mercury contamination of three contrasted mudflats was investigated through a multidisciplinary approach and compared with a non-anthropized site (Authie, France). The higher abundance of the Gram-negative merA gene in the Seine estuary mudflats indicates a relationship between the degree of anthropization and the abundance of the merA gene in the mudflat sediments. In the Seine mudflats, the maxima of abundance are always located in fresh sediment deposits. Therefore, the abundance is closely related with the hydrosedimentary processes, which thus seem to be determining factors in the occurrence of the Gram-negative merA gene in the surface sediments of the Seine's mudflat.