Grey and harbor seals in France (mainland and Saint-Pierre et Miquelon): microbial communities and identification of a microbial source tracking seal marker.

Introduction: Seals, protected wild marine mammals, are widely found in waters around the world. However, rising concerns about their increasing numbers in some areas have led to potential worries regarding microbiological contamination of coastal areas by their feces, which could impact bathing and shellfish-harvesting activities. To the best of our knowledge, no study has been conducted on the bacterial and RNA viral communities present in the feces of both grey and harbor seals, which are the two main seal species observed in mainland France and overseas.

Comparative Analysis of and Isolated from Livestock Animals to and Isolated from Surface Water Using DNA Sequencing and MALDI-TOF.

This study evaluated the contribution of cattle, sheep, poultry and pigs to the contamination of surface water from rivers by and using MLST, cgMLST and considered MALDI-TOF MS as an alternative technique. The 263 strains isolated from cattle (n = 61), sheep (n = 42), poultry (n = 65), pigs (n = 60) and surface water (n = 35) were distributed across 115 sequence types (STs), 49 for and 66 for Considering MLST data, 14.2%, 11.

Genomic Diversity of Campylobacter lari Group Isolates from Europe and Australia in a One Health Context.

Members of the Campylobacter lari group are causative agents of human gastroenteritis and are frequently found in shellfish, marine waters, shorebirds, and marine mammals. Within a One Health context, we used comparative genomics to characterize isolates from a diverse range of sources and geographical locations within Europe and Australia and assess possible transmission of food, animal, and environmental isolates to the human host. A total of 158 C.

Free-living and particle-attached bacterial community composition, assembly processes and determinants across spatiotemporal scales in a macrotidal temperate estuary.

Bacteria play an important role in biogeochemical cycles as they transform and remineralize organic matter. Particles are notable hotspots of activity, hosting particle-attached (PA) communities that can differ largely from their free-living (FL) counterparts. However, long-standing questions remain concerning bacterial community assembly processes and driving factors.

Quorum sensing disruption regulates hydrolytic enzyme and biofilm production in estuarine bacteria.

Biofilms of heterotrophic bacteria cover organic matter aggregates and constitute hotspots of mineralization, primarily acting through extracellular hydrolytic enzyme production. Nevertheless, regulation of both biofilm and hydrolytic enzyme synthesis remains poorly investigated, especially in estuarine ecosystems. In this study, various bioassays, mass spectrometry and genomics approaches were combined to test the possible involvement of quorum sensing (QS) in these mechanisms.

Comparative Analysis of Fecal Microbiomes From Wild Waterbirds to Poultry, Cattle, Pigs, and Wastewater Treatment Plants for a Microbial Source Tracking Approach.

Fecal pollution in coastal areas is of a high concern since it affects bathing and shellfish harvesting activities. Wild waterbirds are non-negligible in the overall signal of the detectable pollution. Yet, studies on wild waterbirds' gut microbiota focus on migratory trajectories and feeding impact on their shape, rare studies address their comparison to other sources and develop quantitative PCR (qPCR)-based Microbial Source Tracking (MST) markers to detect such pollution.

The Spatiotemporal Dynamics and Microevolution Events That Favored the Success of the Highly Clonal Multidrug-Resistant Monophasic Circulating in Europe.

The European epidemic monophasic variant of enterica serovar (. 1,4,[5],12:i:-) characterized by the multi sequence type ST34 and the antimicrobial resistance ASSuT profile has become one of the most common serovars in Europe (EU) and the United States (US). In this study, we reconstructed the time-scaled phylogeny and evolution of this in Europe.

Passive Samplers, a Powerful Tool to Detect Viruses and Bacteria in Marine Coastal Areas.

The detection of viruses and bacteria which can pose a threat either to shellfish health or shellfish consumers remains difficult. The current detection methods rely on point sampling of water, a method that gives a snapshot of the microorganisms present at the time of sampling. In order to obtain better representativeness of the presence of these microorganisms over time, we have developed passive sampling using the adsorption capacities of polymer membranes.

AB_SA: Accessory genes-Based Source Attribution - tracing the source of Typhimurium environmental strains.

The partitioning of pathogenic strains isolated in environmental or human cases to their sources is challenging. The pathogens usually colonize multiple animal hosts, including livestock, which contaminate the food-production chain and the environment (e.g.

Four European Salmonella Typhimurium datasets collected to develop WGS-based source attribution methods.

Zoonotic Salmonella causes millions of human salmonellosis infections worldwide each year. Information about the source of the bacteria guides risk managers on control and preventive strategies. Source attribution is the effort to quantify the number of sporadic human cases of a specific illness to specific sources and animal reservoirs.

Complete Genome Sequence of CA639, Which Carries Two Plasmids, Compiled Using Oxford Nanopore and Illumina Sequencing Technologies.

As determined by a hybrid approach combining Oxford Nanopore MinION and Illumina MiniSeq sequence data, strain CA639 harbored a circular chromosome of 1,688,169 bp with a G+C content of 28.47% and two plasmids named pCA639-1 and pCA639-2, with lengths of 51,123 and 28,139 bp, and G+C contents of 26.5% and 28.

sp. nov., a novel member of the group isolated from surface water and stools from humans with enteric infection.

During a study on the prevalence and diversity of members of the genus r in a shellfish-harvesting area and its catchment in Brittany, France, six urease-positive isolates of members of the genus were recovered from surface water samples, as well as three isolates from stools of humans displaying enteric infection in the same period. These strains were initially identified as members of the group by MALDI-TOF mass spectrometry and placed into a distinct group in the genus , following gene sequence analysis based on whole-genome sequencing data. This taxonomic position was confirmed by phylogenetic analysis of the 16S rRNA, and () loci, and an analysis of the core genome that provided an improved phylogenetic resolution.

Occurrence of Bacterial Pathogens and Human Noroviruses in Shellfish-Harvesting Areas and Their Catchments in France.

During a 2-year study, the presence of human pathogenic bacteria and noroviruses was investigated in shellfish, seawater and/or surface sediments collected from three French coastal shellfish-harvesting areas as well as in freshwaters from the corresponding upstream catchments. Bacteria isolated from these samples were further analyzed. isolates classified into the phylogenetic groups B2, or D and enterococci from and species were tested for the presence of virulence genes and for antimicrobial susceptibility.

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

The aim of this study was to investigate the diversity of the population, focusing on the occurrence of pathogenic , 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 slightly increased along the river continuum, the abundance of both human and ruminant-associated markers, as well as the number of multi-resistant to antibiotics, evidenced a fecal contamination originating from animals at upstream rural sites, and from humans at downstream urban sites.

Human-Driven Microbiological Contamination of Benthic and Hyporheic Sediments of an Intermittent Peri-Urban River Assessed from MST and 16S rRNA Genetic Structure Analyses.

Rivers are often challenged by fecal contaminations. The barrier effect of sediments against fecal bacteria was investigated through the use of a microbial source tracking (MST) toolbox, and by Next Generation Sequencing (NGS) of V5-V6 16S rRNA gene () sequences. Non-metric multi-dimensional scaling analysis of V5-V6 16S rRNA gene sequences differentiated bacteriomes according to their compartment of origin i.

Molecular Profiling of Shiga Toxin-Producing Escherichia coli and Enteropathogenic E. coli Strains Isolated from French Coastal Environments.

Unlabelled: Shiga toxin-producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) strains may be responsible for food-borne infections in humans. Twenty-eight STEC and 75 EPEC strains previously isolated from French shellfish-harvesting areas and their watersheds and belonging to 68 distinguishable serotypes were characterized in this study.

Prevalence and Characterization of Shiga Toxin-Producing and Enteropathogenic Escherichia coli in Shellfish-Harvesting Areas and Their Watersheds.

more strains formed a strong biofilm at 18 than at 30°C. Finally, more than 85% of analyzed strains were found to be sensitive to the 16 tested antibiotics. These data suggest the low risk of human infection by STEC if shellfish from these shellfish-harvesting areas were consumed.

Successful detection of pathogenic Shiga-toxin-producing Escherichia coli in shellfish, environmental waters and sediment using the ISO/TS-13136 method.

Unlabelled: The presence of highly pathogenic Shiga-toxin-producing Escherichia coli (STEC) in shellfish, upstream waters and sediment from coastal shellfish sites was evaluated using the ISO/TS-13136 method. Shellfish (oysters, mussels and cockles), water and sediment samples were collected monthly over a period of 1 year. The method used real-time PCR detection of stx1, stx2 and eae genes and genetic markers corresponding to the five major serogroups (O157, O26, O103, O111 and O145) on enrichment broths and the identification of STEC when these genes and markers were detected.

Performance of human fecal anaerobe-associated PCR-based assays in a multi-laboratory method evaluation study.

A number of PCR-based methods for detecting human fecal material in environmental waters have been developed over the past decade, but these methods have rarely received independent comparative testing in large multi-laboratory studies. Here, we evaluated ten of these methods (BacH, BacHum-UCD, Bacteroides thetaiotaomicron (BtH), BsteriF1, gyrB, HF183 endpoint, HF183 SYBR, HF183 Taqman(®), HumM2, and Methanobrevibacter smithii nifH (Mnif)) using 64 blind samples prepared in one laboratory. The blind samples contained either one or two fecal sources from human, wastewater or non-human sources.

Multi-laboratory evaluations of the performance of Catellicoccus marimammalium PCR assays developed to target gull fecal sources.

Here we report results from a multi-laboratory (n = 11) evaluation of four different PCR methods targeting the 16S rRNA gene of Catellicoccus marimammalium originally developed to detect gull fecal contamination in coastal environments. The methods included a conventional end-point PCR method, a SYBR(®) Green qPCR method, and two TaqMan(®) qPCR methods. Different techniques for data normalization and analysis were tested.

Evaluation of the repeatability and reproducibility of a suite of qPCR-based microbial source tracking methods.

Many PCR-based methods for microbial source tracking (MST) have been developed and validated within individual research laboratories. Inter-laboratory validation of these methods, however, has been minimal, and the effects of protocol standardization regimes have not been thoroughly evaluated. Knowledge of factors influencing PCR in different laboratories is vital to future technology transfer for use of MST methods as a tool for water quality management.

Performance of viruses and bacteriophages for fecal source determination in a multi-laboratory, comparative study.

An inter-laboratory study of the accuracy of microbial source tracking (MST) methods was conducted using challenge fecal and sewage samples that were spiked into artificial freshwater and provided as unknowns (blind test samples) to the laboratories. The results of the Source Identification Protocol Project (SIPP) are presented in a series of papers that cover 41 MST methods. This contribution details the results of the virus and bacteriophage methods targeting human fecal or sewage contamination.