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

Monitoring of bivalve mollusk harvesting areas: the relevance of Salmonella spp

The microbiological monitoring of bivalve mollusk harvesting areas in the Marche region is based on the parameters of Escherichia coli and Salmonella spp. However, Regulation EU/2019/627 stated criteria based on E. coli only to determine the health status of these areas. Therefore, the reason for Salmonella spp. monitoring, as provided in the Marche region, could be aimed at reducing the risk of placing on the market contaminated bivalve mollusks. This study, using the results of microbiological monitoring carried out in the Marche region from 2015 to 2022 and the methods based on Bayes' theorem and Poisson's distribution, evaluated the effectiveness and efficiency of Salmonella spp. monitoring in reducing the risk to the consumer. The results show that i) the use of a single sample unit significantly reduced the possibility of detecting non-compliance with the microbiological safety criterion; ii) the time taken to report positive results (average of approximately 10 days) did not allow the timely implementation of control measures; iii) the prevalence of positive outcomes was quite sporadic: a random trend of positivity is recognizable on a geographical and monthly basis for mussels and a geographical basis for striped clams; iv) considering the predictive value of E. coli against Salmonella spp., the specificity is very high and the negative predictive value versus Salmonella spp. would be >80%. In conclusion, the study shows that the monitoring of Salmonella spp. has a limited effect on reducing the risk to the consumer; however, in the cost/benefit assessment, other aspects not covered by this study should be considered.

Improving the Detection and Understanding of Infectious Human Norovirus in Food and Water Matrices: A Review of Methods and Emerging Models

Human norovirus (HuNoV) is a leading global cause of viral gastroenteritis, contributing to numerous outbreaks and illnesses annually. However, conventional cell culture systems cannot support the cultivation of infectious HuNoV, making its detection and study in food and water matrices particularly challenging. Recent advancements in HuNoV research, including the emergence of models such as human intestinal enteroids (HIEs) and zebrafish larvae/embryo, have significantly enhanced our understanding of HuNoV pathogenesis. This review provides an overview of current methods employed for HuNoV detection in food and water, along with their associated limitations. Furthermore, it explores the potential applications of the HIE and zebrafish larvae/embryo models in detecting infectious HuNoV within food and water matrices. Finally, this review also highlights the need for further optimization and exploration of these models and detection methods to improve our understanding of HuNoV and its presence in different matrices, ultimately contributing to improved intervention strategies and public health outcomes.

Comprehensive analysis and assessment of exposure to enteric viruses and bacteria in shellfish

Shellfish species, including oysters, clams, and mussels, are extensively cultured in coastal waters. Its location is determined by factors such as nutrient availability, water temperature, tidal cycle, and the presence of contaminants such as Escherichia coli and enteric viruses. With the expansion and intensification of human activities at vicinities, the presence of anthropogenic contaminants has increased, threatening shellfish farms and consumer safety give the prevalent consumption of raw shellfish. This literature review aims to provide a comprehensive analysis of the dietary exposure and assess the risk associated with enteric viruses and bacteria detected in shellfish. The predominant bacteria and viruses detected in shellfish are reported, and the potential interrelation is discussed. The main characteristics of each contaminant and shellfish were reviewed for a more comprehensive understanding. To facilitate a direct estimation of exposure, the estimated daily intake (EDI) of bacteria was calculated based on the average levels of E. coli in shellfish, as reported in the literature. The mean daily ingestion of seafood in each of the five continents was considered. Asia exhibited the highest intake of contaminants, with an average of ±5.6 E. coli units/day.kg body weight in cockles. Simulations were conducted using recommended shellfish consumption levels established by state agencies, revealing significantly lower (p < 0.01) EDI for all continents compared to estimations based on recommended levels. This indicates a higher risk associated with healthy shellfish ingestion, potentially leading to increased intoxication incidents with a change in dietary habits. To promote a healthier lifestyle through increased shellfish consumptions, it is imperative to reduce the exposure of shellfish species to bacteria and enteric viruses. The conventional use of E. coli as the sole indicator for consumption safety and water quality in shellfish farms has been deemed insufficient. Instances where shellfish met E. coli limits established by state agencies were often found to be contaminated with human enteric viruses. Therefore, a holistic approach considering the entire production chain is necessary to support the shellfish industry and ensure food safety.

Research Progress on Biological Accumulation, Detection and Inactivation Technologies of Norovirus in Oysters

Noroviruses (NoVs) are major foodborne pathogens that cause acute gastroenteritis. Oysters are significant carriers of this pathogen, and disease transmission from the consumption of NoVs-infected oysters occurs worldwide. The review discusses the mechanism of NoVs bioaccumulation in oysters, particularly the binding of histo-blood group antigen-like (HBGA-like) molecules to NoVs in oysters. The review explores the factors that influence NoVs bioaccumulation in oysters, including temperature, precipitation and water contamination. The review also discusses the detection methods of NoVs in live oysters and analyzes the inactivation effects of high hydrostatic pressure, irradiation treatment and plasma treatment on NoVs. These non-thermal processing treatments can remove NoVs efficiently while retaining the original flavor of oysters. However, further research is needed to reduce the cost of these technologies to achieve large-scale commercial applications. The review aims to provide novel insights to reduce the bioaccumulation of NoVs in oysters and serve as a reference for the development of new, rapid and effective methods for detecting and inactivating NoVs in live oysters.

Toward better monitoring of human noroviruses and F-specific RNA bacteriophages in aquatic environments using bivalve mollusks and passive samplers: A case study

Monitoring pathogenic enteric viruses in continental and marine water bodies is essential to control the viral contamination of human populations. Human Noroviruses (NoV) are the main enteric viruses present in surface waters and foodstuff. In a context of global change, it is currently a challenge to improve the management of viral pollutions in aquatic environments and thereby limit the contamination of vulnerable water bodies or foodstuffs. The aim of this study is to evaluate the potential of specific accumulation systems for improving the detection of NoV in water bodies, compared to direct water analyses. Passive samplers (Zetapor filters) and three species of bivalve molluscan shellfish (BMS) (Dreissena polymorpha, Mytilus edulis and Crassostreas gigas) were used as accumulation systems to determine their performance in monitoring continental and marine waters for viruses. F-specific RNA bacteriophages (FRNAPH) were also analyzed since they are described as indicators of NoV hazard in many studies. During a one-year study in a specific area frequently affected by fecal pollution, twelve campaigns of exposure of passive samplers and BMS in continental and coastal waters were conducted. Using suitable methods, NoV (genome) and FRNAPH (infectious and genome) were detected in these accumulation systems and in water at the same time points to determine the frequency of detection but also to gain a better understanding of viral pollution in this area. The reliability of FRNAPH as a NoV indicator was also investigated. Our results clearly showed that BMS were significantly better than passive samplers and direct water analyses for monitoring NoV and FRNAPH contamination in water bodies. A dilution of viral pollution between the continental and the coastal area was observed and can be explained by the distance from the source of the pollution. Viral pollution is clearly greater during the winter period, and stakeholders should take this into consideration in their attempts to limit the contamination of food and water. A significant correlation was once again shown between NoV and FRNAPH genomes in BMS, confirming the reliability of FRNAPH as a NoV indicator. Moreover, a strong correlation was observed between NoV genomes and infectious FRNAPH, suggesting recent viral pollution since infectious particles had not been inactivated at sufficient levels in the environment. More generally, this study shows the value of using BMS as an active method for improving knowledge on the behavior of viral contamination in water bodies, the ranking of the contamination sources, and the vulnerability of downstream water bodies.

A Comprehensive Review for the Surveillance of Human Pathogenic Microorganisms in Shellfish

Bivalve molluscan shellfish have been consumed for centuries. Being filter feeders, they may bioaccumulate some microorganisms present in coastal water, either naturally or through the discharge of human or animal sewage. Despite regulations set up to avoid microbiological contamination in shellfish, human outbreaks still occur. After providing an overview showing their implication in disease, this review aims to highlight the diversity of the bacteria or enteric viruses detected in shellfish species, including emerging pathogens. After a critical discussion of the available methods and their limitations, we address the interest of technological developments using genomics to anticipate the emergence of pathogens. In the coming years, further research needs to be performed and methods need to be developed in order to design the future of surveillance and to help risk assessment studies, with the ultimate objective of protecting consumers and enhancing the microbial safety of bivalve molluscan shellfish as a healthy food.

Inactivation of Human Norovirus GII.4 and Vibrio parahaemolyticus in the Sea Squirt (Halocynthia roretzi) by Floating Electrode-Dielectric Barrier Discharge Plasma

Human norovirus (HNoV) GII.4 and Vibrio parahaemolyticus may be found in sea squirts. Antimicrobial effects of floating electrode-dielectric barrier discharge (FE-DBD) plasma (5-75 min, N₂ 1.5 m/s, 1.1 kV, 43 kHz) treatment were examined. HNoV GII.4 decreased by 0.11-1.29 log copy/μL with increasing duration of treatment time, and further by 0.34 log copy/μL when propidium monoazide (PMA) treatment was added to distinguish infectious viruses. The decimal reduction time (D₁) of non-PMA and PMA-treated HNoV GII.4 by first-order kinetics were 61.7 (R² = 0.97) and 58.8 (R² = 0.92) min, respectively. V. parahaemolyticus decreased by 0.16-1.5 log CFU/g as treatment duration increased. The D₁ for V. parahaemolyticus by first-order kinetics was 65.36 (R² = 0.90) min. Volatile basic nitrogen showed no significant difference from the control until 15 min of FE-DBD plasma treatment, increasing after 30 min. The pH did not differ significantly from the control by 45-60 min, and Hunter color in "L" (lightness), "a" (redness), and "b" (yellowness) values reduced significantly as treatment duration increased. Textures appeared to be individual differences but were not changed by treatment. Therefore, this study suggests that FE-DBD plasma has the potential to serve as a new antimicrobial to foster safer consumption of raw sea squirts.

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. lari isolates from Australia, Denmark, France, and Germany, which included 82 isolates from human stool and blood, 12 from food, 14 from domestic animal, 19 from waterbirds, and 31 from the environment were analyzed. Genome-wide analysis of the genetic diversity, virulence, and antimicrobial resistance (AMR) traits was carried-out. Most of the isolates belonged to C. lari subsp. lari (Cll; 98, 62.0%), while C. lari subsp. concheus and C. lari urease-positive thermotolerant Campylobacter (UPTC) were represented by 12 (7.6%) and 15 (9.5%) isolates, respectively. Furthermore, 33 (20.9%) isolates were not assigned a subspecies and were thus attributed to distant Campylobacter spp. clades. Whole-genome sequence-derived multilocus sequence typing (MLST) and core-genome MLST (cgMLST) analyses revealed a high genetic diversity with 97 sequence types (STs), including 60 novel STs and 14 cgMLST clusters (≤10 allele differences), respectively. The most prevalent STs were ST-21, ST-70, ST-24, and ST-58 (accounting for 13.3%, 4.4%, 3.8%, and 3.2% of isolates, respectively). A high prevalence of the 125 examined virulence-related loci (from 76.8 to 98.4% per isolate) was observed, especially in Cll isolates, suggesting a probable human pathogenicity of these strains. IMPORTANCE Currently, relatedness between bacterial isolates impacting human health is easily monitored by molecular typing methods. These approaches rely on discrete loci or whole-genome sequence (WGS) analyses. Campylobacter lari is an emergent human pathogen isolated from diverse ecological niches, including fecal material from humans and animals, aquatic environments, and seafood. The presence of C. lari in such diverse sources underlines the importance of adopting an integrated One Health approach in studying C. lari population structure for conducting epidemiological risk assessment. This retrospective study presents a comparative genomics analysis of C. lari isolates retrieved from two different continents (Europe and Australia) and from different sources (human, domestic animals, waterbirds, food, and environment). It was designed to improve knowledge regarding C. lari ecology and pathogenicity, important for developing effective surveillance and disease prevention strategies.

First Data on Campylobacter spp. Presence in Shellfish in Croatia

This study aimed to assess the presence of thermotolerant Campylobacter spp., as one of the most important foodborne zoonotic pathogens, in three shellfish species: mussels (Mytilus galloprovincialis), oysters (Ostrea edulis) and queen scallops (Aequipecten opercularis). The samples were collected from nine locations in the Istrian aquatory, Croatia. Isolation of Campylobacter was done according to standard ISO method, and species were identified using multiplex PCR. Isolates identified as C. jejuni and C. lari were genotyped using multilocus sequence typing (MLST) to determine the potential source of contamination. Among 108 examined samples of bivalve molluscs, mussels dominated and were the only ones found positive for the presence of Campylobacter (25.6%). In total, 19 C. lari and 1 C. jejuni strains were isolated. C. lari isolates found in this study belong to 13 sequence types (STs), and 9 of them are newly described in this paper. Two out of the four previously described C. lari STs that were found in this study were previously found in human stool. The only C. jejuni isolate was found to be sequence type 1268, which belongs to ST-1275 clonal complex that is almost exclusively found in seabirds and can sporadically cause infection in humans. Regarding the obtained results, introducing surveillance of thermotolerant Campylobacter in shellfish in the Republic of Croatia is advised as an improvement for public health safety.

Assessment of Microbiological Quality of Fresh Vegetables and Oysters Produced in Buenos Aires Province, Argentina

Fresh vegetables and shellfish are prone to microbial contamination through irrigation or breeding with sewage-polluted waters, as well as by infected food handlers. In this work, we studied the presence of human and bovine polyomaviruses and human norovirus in fresh lettuces, strawberries and oysters produced in Buenos Aires province, Argentina. In oysters, we also investigated F-specific RNA bacteriophages, indicator Escherichia coli (E. coli) and pathogen bacteria of concern (Salmonella spp., Vibrio spp.). Within vegetables, we found viral contamination of human origin given the presence of human-associated polyomaviruses -MCPyV, HPyV6, JCPyV, and SV40- in lettuce and strawberry samples (16 and 10%, respectively), probably coming from irrigation waters and food handling. Among oysters, human (MCPyV, 4.2%) and bovine (BPyV1, 8.4%) polyomaviruses were detected even with low counts of E. coli. Bacteriophages (n = 3) and Salmonella spp. (n = 1) were also found, while Vibrio spp. was not detected. These results may indicate that the contamination in oysters comes from human and animal excreta, probably present in breeding waters. Norovirus was not detected in any food sample. To our knowledge, this is the first description of SV40 in lettuces and MCPyV and BPyV1 in oysters. The detection of different viral contaminants encourages further studies to evaluate the need for including viral indicators in microbiological standards. The identification of possible sources and routes of contamination using viral markers during routine microbiological controls, such as the polyomaviruses used in this work, would be useful to focus attention on the most hazardous stages of the food production chain.

Occurrence and distribution of fecal indicators and pathogenic bacteria in seawater and Perna perna mussel in the Gulf of Annaba (Southern Mediterranean)

The identification of fecal contamination in coastal marine ecosystems is one of the main requirements for evaluation of potential risks to human health. The objective of this study was to investigate the occurrence and distribution of fecal indicators and pathogenic bacteria in seawaters and mussels collected monthly during a period of 1 year from four different sites in Northeastern Algeria (sites S1 to S4), through biochemical and molecular analyses. Our research is the first to use molecular analysis to unambiguously identify the potentially pathogenic bacteria present in Algerian Perna perna mussels. The obtained results revealed that the levels of fecal indicator bacteria (FIB) from both P. perna and seawater samples largely exceeded the permissible limits at S2 and S3. This is mainly related to their location close to industrial and coastal activity zones, which contain a mixture of urban, agricultural, and industrial pollutants. Besides, P. perna collected from all sites were severalfold more contaminated by FIB than seawater samples, primarily during the warm season of the study period. Biochemical and molecular analyses showed that isolated bacteria from both seawater and mussels were mainly potentially pathogenic species such as E. coli, Salmonella spp., Staphylococcus spp., Klebsiella spp., Pseudomonas spp., and Proteus spp.

Application of crAssphage, F-RNA phage and pepper mild mottle virus as indicators of human faecal and norovirus contamination in shellfish

Shellfish growing waters contaminated with inadequately treated human wastewater is a major source of norovirus in shellfish and poses a significant human health risk to consumers. Microbial source tracking (MST) markers have been widely used to identify the source (s) of faecal contamination in water but data are limited on their use for shellfish safety. This study evaluated the source specificity, sensitivity, occurrence and concentration of three viral MST markers i.e. cross-assembly phage (crAssphage), F-specific RNA bacteriophage genogroup II (F-RNA phage GII) and pepper mild mottle virus (PMMoV) using animal faeces (n = 119; 16 animal groups), influent wastewater (n = 12), effluent wastewater (n = 16) and shellfish (n = 33). CrAssphage, F-RNA phage GII and PMMoV had source specific values of 0.97, 0.99 and 0.91, respectively. The sensitivity of MST markers was confirmed by their 100% detection frequency in influent wastewaters. The frequency of detection in effluent wastewater ranged from 81.3% (F-RNA phage GII) to 100% (PMMoV). Concentration of F-RNA phage GII was one log₁₀ (influent wastewater) and 2-3 log₁₀ (effluent wastewater) lower than crAssphage and PMMoV, respectively. Despite lower prevalence of F-RNA phage GII in oysters and mussels compared to crAssphage and PMMoV, concentrations of the three MST markers were similar in mussels. As an indicator of norovirus contamination in shellfish, crAssphage and PMMoV had greater predictive sensitivity (100%; [95% CI; 81.5%-100%)]) and F-RNA phage GII had greater predictive specificity (93.3%; [95% CI; 68.1%-99.8%]). In contrast, crAssphage and F-RNA phage GII have similar accuracy for predicting norovirus in shellfish, however, PMMoV significantly overestimated its presence. Therefore, a combination of crAssphage and F-RNA phage GII analysis of shellfish could provide a robust estimation of the presence of human faecal and norovirus contamination.

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. Thus, by using 16S rRNA amplicon high-throughput sequencing, the aims of this study were (i) to explore and compare fecal bacterial communities from wild waterbirds (i.e., six families and 15 species, n = 275 samples) to that of poultry, cattle, pigs, and influent/effluent of wastewater treatment plants (n = 150 samples) and (ii) to develop new MST markers for waterbirds. Significant differences were observed between wild waterbirds and the four other groups. We identified 7,349 Amplicon Sequence Variants (ASVs) from the hypervariable V3–V4 region. Firmicutes and Proteobacteria and, in a lesser extent, Actinobacteria and Bacteroidetes were ubiquitous while Fusobacteria and Epsilonbacteraeota were mainly present in wild waterbirds. The clustering of samples in non-metric multidimensional scaling (NMDS) ordination indicated a by-group clustering shape, with a high diversity within wild waterbirds. In addition, the structure of the bacterial communities was distinct according to bird and/or animal species and families (Adonis R² = 0.13, p = 10^–4, Adonis R² = 0.11, p = 10^–4, respectively). The Analysis of Composition of Microbiomes (ANCOM) showed that the wild waterbird group differed from the others by the significant presence of sequences from Fusobacteriaceae (W = 566) and Enterococcaceae (W = 565) families, corresponding to the Cetobacterium (W = 1427) and Catellicoccus (W = 1427) genera, respectively. Altogether, our results suggest that some waterbird members present distinct fecal microbiomes allowing the design of qPCR MST markers. For instance, a swan- and an oystercatcher-associated markers (named Swan_2 and Oyscab, respectively) have been developed. Moreover, bacterial genera harboring potential human pathogens associated to bird droppings were detected in our dataset, including enteric pathogens, i.e., Arcobacter, Clostridium, Helicobacter, and Campylobacter, and environmental pathogens, i.e., Burkholderia and Pseudomonas. Future studies involving other wildlife hosts may improve gut microbiome studies and MST marker development, helping mitigation of yet unknown fecal pollution sources.

Contamination, bioaccumulation mechanism, detection, and control of human norovirus in bivalve shellfish: A review

Human norovirus (HuNoV) is a major foodborne pathogen that causes acute viral gastroenteritis, and bivalve shellfish are one of the main carriers of HuNoV transmission. A comprehensive understanding of bivalve shellfish-related HuNoV outbreaks focusing on contamination factors, bioaccumulation mechanisms, and pre- and post-harvest interventions is essential for the development of effective strategies to prevent contamination of shellfish. This review comprehensively surveys the current knowledge on global contamination and non-thermal treatment of HuNoV in bivalve shellfish. HuNoV contamination in bivalve shellfish is significantly related to the season and water. While evaluating the water quality of shellfish-inhabited waters is a key intervention, the development of non-heat treatment technology to effectively inactivate the HuNoV in bivalve shellfish while maintaining the flavor and nutrition of the shellfish is also an important direction for further research. Additionally, this review explores the bioaccumulation mechanisms of HuNoV in bivalve shellfish, especially the mechanism underlying the binding of histo-blood group antigen-like molecules and HuNoV. The detection methods for infectious HuNoV are also discussed. The establishment of effective methods to rapidly detect infectious HuNoV and development of biological components to inactivate or prevent HuNoV contamination in shellfish also need to be studied further.

-Blue mussel (Mytilus spp.) cultivation in mesohaline eutrophied inner coastal waters: mitigation potential, threats and cost effectiveness

The EU-water framework directive (WFD) focuses on nutrient reductions to return coastal waters to the good ecological status. As of today, many coastal waters have reached a steady state of insufficient water quality due to continuous external nutrient inputs and internal loadings. This study focuses first on the current environmental status of mesohaline inner coastal waters to illustrate their needs of internal measures to reach demanded nutrient reductions and secondly, if mussel cultivation can be a suitable strategy to improve water quality. Therefore, nitrogen, phosphorus, chlorophyll a, and Secchi depth of nine mesohaline inner coastal waters in north east Germany were analyzed from 1990 to 2018. Two pilot mussel farms were used to evaluate their effectiveness as a mitigation measure and to estimate potential environmental risks, including the interactions with pathogenic vibrio bacteria. Further, estimated production and mitigation potential were used to assess economic profitability based on the sale of small sized mussels for animal feed and a compensation for nutrient mitigation. The compensation costs were derived from nutrient removal costs of a waste water treatment plant (WWTP). Results show that currently all nine water bodies do not reach the nutrient thresholds demanded by the WFD. However, coastal waters differ in nutrient pollution, indicating that some can reach the desired threshold values if internal measures are applied. The mitigation potential of mussel cultivation depends on the amount of biomass that is cultivated and harvested. However, since mussel growth is closely coupled to the salinity level, mussel cultivation in low saline environments leads to lower biomass production and inevitably to larger cultivation areas. If 50% of the case study area Greifswald Bay was covered with mussel farms the resulting nitrogen reduction would increase Secchi depth by 7.8 cm. However, high chlorophyll a values can hamper clearance rates (<20 mg m⁻³ = 0.43 l h⁻¹ dry weight g⁻¹) and therefore the mitigation potential. Also, the risk of mussel stock loss due to high summer water temperatures might affect the mitigation potential. The pilot farms had no significant effect on the total organic content of sediments beneath. However, increased values of Vibrio spp. in bio deposits within the pilot farm (1.43 10⁶ ± 1.10 10⁶CFU 100 ml⁻¹ (reference site: 1.04 10⁶ ± 1.45 10⁶ CFU 100 ml⁻¹) were measured with sediment traps. Hence, mussel farms might act as a sink for Vibrio spp. in systems with already high vibrio concentrations. However, more research is required to investigate the risks of Vibrio occurrence coupled to mussel farming. The economic model showed that mussel cultivation in environments below 12 PSU cannot be economic at current market prices for small size mussels and compensations based on nutrient removal cost of WWTPs.

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

The European epidemic monophasic variant of Salmonella enterica serovar Typhimurium (S. 1,4,[5],12:i:-) characterized by the multi locus 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 Salmonella in Europe. The epidemic S. 1,4,[5],12:i:- ST34 emerged in the 1980s by an acquisition of the Salmonella Genomic Island (SGI)-4 at the 3' end of the phenylalanine phe tRNA locus conferring resistance to copper and arsenic toxicity. Subsequent integration of the Tn21 transposon into the fljAB locus gave resistance to mercury toxicity and several classes of antibiotics used in food-producing animals (ASSuT profile). The second step of the evolution occurred in the 1990s, with the integration of mTmV and mTmV-like prophages carrying the perC and/or sopE genes involved in the ability to reduce nitrates in intestinal contents and facilitate the disruption of the junctions of the host intestinal epithelial cells. Heavy metals are largely used as food supplements or pesticide for cultivation of seeds intended for animal feed so the expansion of the epidemic S. 1,4,[5],12:i:- ST34 was strongly related to the multiple-heavy metal resistance acquired by transposons, integrative and conjugative elements and facilitated by the escape until 2011 from the regulatory actions applied in the control of S. Typhimurium in Europe. The genomic plasticity of the epidemic S. 1,4,[5],12:i:- was demonstrated in our study by the analysis of the plasmidome. We were able to identify plasmids harboring genes mediating resistance to phenicols, colistin, and fluoroquinolone and also describe for the first time in six of the analyzed genomes the presence of two plasmids (pERR1744967-1 and pERR2174855-2) previously described only in strains of enterotoxigenic Escherichia coli and E. fergusonii.

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. Our objectives here were to assess the feasibility of this methodology for field detection. Different types of membrane were deployed in coastal waters over 2 years and the microorganisms tested using qPCR were: human norovirus (NoV) genogroups (G)I and II, sapovirus, Vibrio spp. and the species Vibrio alginolyticus, V. cholerae, V. vulnificus, and V. parahaemolyticus, OsHV-1 virus, and bacterial markers of fecal contamination. NoV GII, Vibrio spp., and the AllBac general Bacteroidales marker were quantified on the three types of membrane. NoV GII and OsHV-1 viruses followed a seasonal distribution. All membranes were favorable for NoV GII detection, while Zetapor was more adapted for OsHV-1 detection. Nylon was more adapted for detection of Vibrio spp. and the AllBac marker. The quantities of NoV GII, AllBac, and Vibrio spp. recovered on membranes increased with the duration of exposure. This first application of passive sampling in seawater is particularly promising in terms of an early warning system for the prevention of contamination in oyster farming areas and to improve our knowledge on the timing and frequency of disease occurence.

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. Our objectives here were to assess the feasibility of this methodology for field detection. Different types of membrane were deployed in coastal waters over 2 years and the microorganisms tested using qPCR were: human norovirus (NoV) genogroups (G)I and II, sapovirus, Vibrio spp. and the species Vibrio alginolyticus, V. cholerae, V. vulnificus, and V. parahaemolyticus, OsHV-1 virus, and bacterial markers of fecal contamination. NoV GII, Vibrio spp., and the AllBac general Bacteroidales marker were quantified on the three types of membrane. NoV GII and OsHV-1 viruses followed a seasonal distribution. All membranes were favorable for NoV GII detection, while Zetapor was more adapted for OsHV-1 detection. Nylon was more adapted for detection of Vibrio spp. and the AllBac marker. The quantities of NoV GII, AllBac, and Vibrio spp. recovered on membranes increased with the duration of exposure. This first application of passive sampling in seawater is particularly promising in terms of an early warning system for the prevention of contamination in oyster farming areas and to improve our knowledge on the timing and frequency of disease occurence.

Antibiotic-Resistant Enterococcus Species in Marine Habitats: A Review

Antibiotic-resistant Enterococcus (ARE) are among leading causes of nosocomial infections worldwide. Enterococcus spp. are ubiquitous in sewage, which can contaminate surface waters via many pathways, providing a route of exposure for humans. This review focuses on ARE in marine and estuarine habitats, including marine animals. Phylogenetic confirmation of the genus Enterococcus and intermediate or full resistance to clinically relevant antibiotics were inclusion criteria. The proportion of resistant isolates varied greatly among antibiotics, for example, 24.2% for ampicillin and 2.4% for vancomycin. The water column contained the highest proportion of ARE observations (18.8%), followed by animal feces and tissues (14.8%), sediment (9.4%), and sand (2.0%). The proportion of multidrug-resistant isolates was the greatest in animal tissue and fecal samples, followed by water and sediments. This review indicates that clinically relevant ARE are present in marine/estuarine habitats and that animals may be important reservoirs.

AB_SA: Accessory genes-Based Source Attribution - tracing the source of Salmonella enterica 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. soil and water), posing an additional public-health burden and major challenges in the identification of the source. Genomic data opens up new opportunities for the development of statistical models aiming to indicate the likely source of pathogen contamination. Here, we propose a computationally fast and efficient multinomial logistic regression source-attribution classifier to predict the animal source of bacterial isolates based on 'source-enriched' loci extracted from the accessory-genome profiles of a pangenomic dataset. Depending on the accuracy of the model's self-attribution step, the modeller selects the number of candidate accessory genes that best fit the model for calculating the likelihood of (source) category membership. The Accessory genes-Based Source Attribution (AB_SA) method was applied to a dataset of strains of Salmonella enterica Typhimurium and its monophasic variant (S. enterica 1,4,[5],12:i:-). The model was trained on 69 strains with known animal-source categories (i.e. poultry, ruminant and pig). The AB_SA method helped to identify 8 genes as predictors among the 2802 accessory genes. The self-attribution accuracy was 80 %. The AB_SA model was then able to classify 25 of the 29 S. enterica Typhimurium and S. enterica 1,4,[5],12:i:- isolates collected from the environment (considered to be of unknown source) into a specific category (i.e. animal source), with more than 85 % of probability. The AB_SA method herein described provides a user-friendly and valuable tool for performing source-attribution studies in only a few steps. AB_SA is written in R and freely available at https://github.com/lguillier/AB_SA.

Rapid identification and detection of Vibrio parahaemolyticus via different types of modus operandi with LAMP method in vivo

Purpose

Vibrio parahaemolyticus, an easy-ignored food-borne pathogen, can cause bacterial outbreaks and human disease during early-stage infection. In this study, we aimed to evaluate the detection efficiency of loop-mediated isothermal amplification (LAMP) as an emerging technique to directly detect V. parahaemolyticus infection in mammalian hosts and assess its potential in clinical applications.

Methods

A LAMP assay was used for rapid identification of V. parahaemolyticus in a variety of mouse models in which animals were infected via the digestive tract, wounds, or through general infection, and the results were compared with routine analytical methods.

Results

Our results confirmed that the LAMP assay was capable of detecting V. parahaemolyticus in different mouse organs independent of the source of bacteria, although its sensitivity depended on the route of infection and the organ affected. Foodborne-derived V. parahaemolyticus was the most sensitive route, with the small intestine being the most sensitive organ. The LAMP assay indicated that V. parahaemolyticus that spread through the blood stream had the most serious consequences during early-stage infection. Positive LAMP results were identified in all blood samples from i.v. injected mice. Furthermore, the LAMP method could directly detect trace quantities of V. parahaemolyticus in fresh peripheral blood while conventional methods failed to do so, thereby shortening the time-to-result from days to minutes.

Conclusions

In this study, we demonstrated that the LAMP assay was effective in speeding up the detection of V. parahaemolyticus. Instead of being a secondary method to assist in the clinic, the LAMP assay has potential for use as the primary technique for rapid detection of V. parahaemolyticus in the future.

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. Source attribution methods for Salmonella have so far been based on traditional wet-lab typing methods. With the change to whole genome sequencing there is a need to develop new methods for source attribution based on sequencing data. Four European datasets collected in Denmark (DK), Germany (DE), the United Kingdom (UK) and France (FR) are presented in this descriptor. The datasets contain sequenced samples of Salmonella Typhimurium and its monophasic variants isolated from human, food, animal and the environment. The objective of the datasets was either to attribute the human salmonellosis cases to animal reservoirs or to investigate contamination of the environment by attributing the environmental isolates to different animal reservoirs.

Complete Genome Sequence of Campylobacter armoricus 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, Campylobacter armoricus 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 28.45%, respectively.

As determined by a hybrid approach combining Oxford Nanopore MinION and Illumina MiniSeq sequence data, Campylobacter armoricus 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 28.45%, respectively.

Enumeration and Survival of Salmonella enterica in Live Oyster Shellstock Harvested from Canadian Waters

Since 2015, 11 recalls of live oyster shellstock have been issued in Canada due to the presence of Salmonella enterica. Six of those recalls took place in 2018. To understand this increase, fundamental information is needed on the relationship between S. enterica and oysters. The aims of this study were to address important data gaps concerning the levels of Salmonella in naturally contaminated oysters and the ability of this pathogen to survive in live oyster shellstock. Enumeration data were evaluated for five oyster and clam samples collected from the east coast of Canada from 2015 to 2018. The reported levels were <0.0015 to 0.064 most probable number per g of oyster tissue. The S. enterica isolates recovered from these animals belonged to serovars Typhimurium, Infantis, Enteritidis, and I 4,5:i:-. Filter feeding by the oysters was exploited to assess the Salmonella accumulation that would occur following a natural contamination event. Detectable levels of the pathogen were observed after 30 min of exposure and began to plateau at 60 min. A survival study in live oyster shellstock indicated that after 4 days of storage at ambient temperatures, the Salmonella level declined slightly from 4.3 to 3.7 log CFU/g. These data indicate that the levels of Salmonella found in naturally contaminated oysters are low and are not expected to increase between the point of harvest and the point of consumption. The changing ecology of shellfish environments requires continued monitoring and testing to safeguard public health. The data presented here will be useful for the evaluation and design of sampling plans and risk management approaches for the control of Salmonella in live oyster shellstock.

Campylobacter armoricus sp. nov., a novel member of the Campylobacter lari 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 Campylobacter in a shellfish-harvesting area and its catchment in Brittany, France, six urease-positive isolates of members of the genus Campylobacter 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 Campylobacter lari group by MALDI-TOF mass spectrometry and placed into a distinct group in the genus Campylobacter, following atpA gene sequence analysis based on whole-genome sequencing data. This taxonomic position was confirmed by phylogenetic analysis of the 16S rRNA, rpoB and hsp60 (groEL) loci, and an analysis of the core genome that provided an improved phylogenetic resolution. The average nucleotide identity between the representative strain CA656^T (CCUG 73571^T=CIP 111675^T) and the type strain of the most closely related species Campylobacter ornithocola WBE38^T was 88.5 %. The strains were found to be microaerobic and anaerobic, motile, non-spore-forming, Gram-stain-negative, spiral-shaped bacteria that exhibit catalase, oxidase and urease activities but not nitrate reduction. This study demonstrates clearly that the nine isolates represent a novel species within the C. lari group, for which the name Campylobacter armoricus is proposed. Here, we present phenotypic and morphological features of the nine strains and the description of their genome sequences. The proposed type strain CA656^T has a 1.589 Mbp chromosome with a DNA G+C content of 28.5 mol% and encodes 1588 predicted coding sequences, 38 tRNAs, and 3 rRNA operons.

Substratum-associated microbiota

This survey of 2018 literature on substratum-associated microbiota presents brief highlights on research findings from primarily freshwaters, but includes those from a variety of aquatic ecosystems. Coverage of topics associated with benthic algae and cyanobacteria, though not comprehensive, includes new methods, taxa new to science, nutrient dynamics, trophic interactions, herbicides and other pollutants, metal contaminants, nuisance, bloom-forming and harmful algae, bioassessment, and bioremediation. Coverage of bacteria, also not comprehensive, focused on methylation of mercury, metal contamination, toxins, and other environmental pollutants, including oil, as well as the use of benthic bacteria as bioindicators, in bioassessment tools and in biomonitoring. Additionally, we cover trends in recent and emerging topics on substratum-associated microbiota of relevance to the Water Environment Federation. PRACTITIONER POINTS: This review of literature from 2018 on substratum-associated microbiota presents highlights of findings on algae, cyanobacteria, and bacteria from primarily freshwaters. Topics covered that focus on algae and cyanobacteria include findings on new methods, taxa new to science, nutrient dynamics, trophic interactions, herbicides and other pollutants, metal contaminants, nuisance, bloomforming and harmful algae, bioassessment, and bioremediation. Topics covered that focus on bacteria include findings on methylation of mercury, metal contamination, toxins and other environmental pollutants, including oil, as well as the us e of benthic bacteria as bioindicators, in bioassessment tools and in biomonitoring. A brief presentation of new, noteworthy and emerging topics on substratum-associated microbiota, build on those from 2017, to highlight those of particular relevance to the Water Environment Federation.

Oyster eaters: From consumer practices to the representation of risks

This article focuses on a study of the representation of the health risks associated with oyster consumption. The research was initially part of an interdisciplinary project looking at the differences between diploid and triploid oysters. The triploid oyster has been genetically modified to stem reproduction, the process responsible for milt, in order that it can be consumed all year round. According to biologists, however, this modification can be a source of risks. Based on this premise, we sought to determine first the overall perception of risks in oyster consumption and second whether or not these risks were reflected in the consumers' representation, most notably through a study of their practices. The theoretical framework adopted was therefore social representations. To achieve our objective, we questioned different people on how they viewed this seafood product. A longitudinal study of practices was conducted over an eight-month period (July 2015-February 2016) in 29 households in France. These regular consumers were asked to record in a consumption log all their practices of intention, purchasing/fishing and consumption as they related to oysters during this period. Regular interviews were conducted based on this consumption log. In total, 86 interviews were conducted and transcribed in full, and a computer-assisted lexical analysis (Alceste) was performed on the data. The results showed that, although the consumers were aware of the risks identified by the experts, they were in control of them, particularly in relation to the trust they placed in intermediary bodies. These results were interpreted according to the relationships between beliefs and practices.

Source attribution of Campylobacter jejuni shows variable importance of chicken and ruminants reservoirs in non-invasive and invasive French clinical isolates

Campylobacter jejuni is the most common cause of bacterial gastroenteritis worldwide. Mainly isolated from stool samples, C. jejuni can also become invasive. C. jejuni belongs to the commensal microbiota of a number of hosts, and infection by this bacterium can sometimes be traced back to exposure to a specific source. Here we genome sequenced 200 clinical isolates (2010–2016) and analyzed them with 701 isolate genomes from human infection, chicken, ruminants and the environment to examine the relative contribution of different reservoirs to non-invasive and invasive infection in France. Host-segregating genetic markers that can discriminate C. jejuni source were used with STRUCTURE software to probabilistically attribute the source of clinical strains. A self-attribution correction step, based upon the accuracy of source apportionment within each potential reservoir, improved attribution accuracy of clinical strains and suggested an important role for ruminant reservoirs in non-invasive infection and a potentially increased contribution of chicken as a source of invasive isolates. Structured sampling of Campylobacter in the clinic and from potential reservoirs provided evidence for variation in the contribution of different infection sources over time and an important role for non-poultry reservoirs in France. This provides a basis for ongoing genomic epidemiology surveillance and targeted interventions.