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.

Tuberculosis (TB) remains broadly present in the Americas despite intense global efforts for its control and elimination. Starting from a large dataset comprising spoligotyping (n = 21183 isolates) and 12-loci MIRU-VNTRs data (n = 4022 isolates) from a total of 31 countries of the Americas (data extracted from the SITVIT2 database), this study aimed to get an overview of lineages circulating in the Americas. A total of 17119 (80.8%) strains belonged to the Euro-American lineage 4, among which the most predominant genotypic family belonged to the Latin American and Mediterranean (LAM) lineage (n = 6386, 30.1% of strains). By combining classical phylogenetic analyses and Bayesian approaches, this study revealed for the first time a clear genetic structuration of LAM9 sublineage into two subpopulations named LAM9C1 and LAM9C2, with distinct genetic characteristics. LAM9C1 was predominant in Chile, Colombia and USA, while LAM9C2 was predominant in Brazil, Dominican Republic, Guadeloupe and French Guiana. Globally, LAM9C2 was characterized by higher allelic richness as compared to LAM9C1 isolates. Moreover, LAM9C2 sublineage appeared to expand close to twenty times more than LAM9C1 and showed older traces of expansion. Interestingly, a significant proportion of LAM9C2 isolates presented typical signature of ancestral LAM-RD^Rio MIRU-VNTR type (224226153321). Further studies based on Whole Genome Sequencing of LAM strains will provide the needed resolution to decipher the biogeographical structure and evolutionary history of this successful family.

Between April 2018 and August 2019, a total of 135 strains of Enterobacter cloacae complex (ECC) were randomly collected at the University Hospital Center of Guadeloupe to investigate the structure and diversity of the local bacterial population. These nosocomial isolates were initially identified genetically by the hsp60 typing method, which revealed the clinical relevance of E. xiangfangensis (n = 69). Overall, 57/94 of the third cephalosporin-resistant strains were characterized as extended-spectrum-β-lactamase (ESBL) producers, and their whole-genome was sequenced using Illumina technology to determine the clonal relatedness and diffusion of resistance genes. We found limited genetic diversity among sequence types (STs). ST114 (n = 13), ST1503 (n = 9), ST53 (n = 5) and ST113 (n = 4), which belong to three different Enterobacter species, were the most prevalent among the 57 ESBL producers. The bla_CTXM-15 gene was the most prevalent ESBL determinant (56/57) and was in most cases associated with IncHI2/ST1 plasmid replicon carriage (36/57). To fully characterize this predominant bla_CTXM-15/IncHI2/ST1 plasmid, four isolates from different lineages were also sequenced using Oxford Nanopore sequencing technology to generate long-reads. Hybrid sequence analyses confirmed the circulation of a well-conserved plasmid among ECC members. In addition, the novel ST1503 and its associated species (ECC taxon 4) were analyzed, in view of its high prevalence in nosocomial infections. These genetic observations confirmed the overall incidence of nosocomial ESBL Enterobacteriaceae infections acquired in this hospital during the study period, which was clearly higher in Guadeloupe (1.59/1000 hospitalization days) than in mainland France (0.52/1,000 hospitalization days). This project revealed issues and future challenges for the management and surveillance of nosocomial and multidrug-resistant Enterobacter in the Caribbean.

Periodically, the French West Indies receive dust originating from North Africa (NA). Microorganisms associated with desert dust can be transported over long distances through the atmosphere and could represent a means for the remote colonization of new habitats by putatively pathogenic microorganisms. The aim of this study was to determine the diversity and frequency of microbial agents (bacteria, eukaryotes) in NA dusts and the potential threat toward human and/or animal health by comparing microbial air composition during dust events and in control samples. In 2017 and 2018, 16 samples were collected during seven NA dust episodes and there were 9 controls. The microbial composition of the samples was characterized using a cultivable approach and by metabarcoding analyses (16S and 18S). A greater bacterial load and greater diversity were observed during the dust events, and some genera were significantly associated with the events. Some, such as Geodermatophilus, can be considered signature species of NA dust. No pathogenic species were found with the cultivable approach, whereas the metabarcoding analyses highlighted the presence of several potentially pathogenic species or known human pathogens such as Naegleria fowleri.

Background: Environmental DNA (eDNA) has revolutionized biodiversity monitoring by enabling species detection from microbes to megafauna without direct observation or capture. Yet most marine eDNA collection systems remain expensive and labor-intensive, limiting their deployment at scale or by non-specialists. To address these challenges, we developed TorpeDNA, a compact, low-cost, and user-friendly eDNA sampler designed to operate under diverse marine conditions, including high-speed towing and citizen-science use. This proof-of-concept study evaluates its performance, scalability, and limitations across three contrasting marine environments encompassing different trophic levels, taxa, and user contexts. Methods: Three case studies were conducted. (1) In Northern Brittany (France), TorpeDNA (20 µm filters) was compared with large-capacity filtration capsule (0.45 µm) for characterising eukaryotic and vertebrates’ communities using metabarcoding. (2) Along the French Atlantic coast, TorpeDNA was benchmarked against serial laboratory filtration (10–0.45 µm fraction) to assess bacterial assemblages near aquaculture and wastewater gradients. (3) In the South-West Pacific, TorpeDNA was deployed aboard a Citizens of the Sea vessel to sample open-ocean plankton communities from microbes to vertebrates along a 2,000 km transect between Aotearoa-New Zealand and Fiji. Results: Across all studies, TorpeDNA generated biodiversity profiles broadly comparable to those from fine-pore or serial filtration methods. However, some notable differences were observed between methods, largely attributable to the different filter pore sizes and water volumes processed, which influenced the preferential capture or exclusion of host-associated or sediment-bound microbes, larger plankton forms, and/or rare taxa. TorpeDNA effectively recovered dominant microbial, phytoplankton, and zooplankton assemblages, reproducing known ecological and biogeographic gradients, from temperate to tropical plankton turnover and coastal-to-offshore transitions. Vertebrate DNA detection was limited in both methods, likely reflecting low natural eDNA concentrations, insufficient water volume processed, or marker inefficiency and highlighting the need for further optimization of sampling duration, flow rate, and assay sensitivity. Conclusion: TorpeDNA achieves a practical balance between usability, versatility across trophic levels, and integration across spatial and methodological scales. Its robust, low-cost design and compatibility with different filter types and standard molecular workflows make it scalable across platforms, from small to large research vessels to citizen-science initiatives and offering a fit-for-purpose tool for global, inclusive, and scalable ocean biodiversity sampling.