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Frontiers in Bacteriology ·

Volume 5 - 2026 | https://doi.org/10.3389/fbrio.2026.1876999

Microbiological and genomic surveillance of WHO critical priority pathogens along the oyster supply chain: water quality as a driver of persistence and depuration as a mitigating strategy in a One Health context

  • Gustavo Rocha1*corresponding author
  • Mateus Rocha Ribas1
  • Izadora Borgmann Frizzo de Assunção1
  • Juliana Lemos Dal Pizzol1
  • Victor Felipe Wolleck1
  • Julia Raimundo de Jesus1
  • Gabriel Sanabria da Silva1
  • Jussara Kasuko Palmeiro1
  • Thais Cristine Marques Sincero1*corresponding author
  1. Laboratório de Microbiologia Molecular Aplicada, Departamento de Análises Clínicas, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis, Brazil
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Abstract

Oysters are widely consumed worldwide, often raw, which raises food safety concerns. These filter-feeding bivalves can accumulate contaminants, including antimicrobial-resistant bacteria (ARB), posing a public health risk. This study aimed to investigate the presence of ARB in the oyster supply chain, evaluating the impact of production, commercialization and depuration processes on ARB contamination. Samples were collected from six oyster farms and commercial establishments supplied by them in the North and South Bays of Florianópolis, Brazil. Seawater, farmed oysters, commercially available oysters, depurated oysters, and larval-stage oysters were analyzed. A total of 167 antimicrobial-resistant isolates were identified, with Escherichia coli and Klebsiella pneumoniae being the most prevalent, many of which are classified as WHO critical-priority pathogens. Whole genome sequencing of selected isolates revealed a high diversity of sequence types, including globally distributed lineages, and the presence of shared clones across seawater and oysters, indicating bacterial circulation along the supply chain. Genomic analysis also identified a wide range of resistance genes, including extended-spectrum β-lactamases (ESBL), as well as determinants conferring resistance to quinolones, aminoglycosides, tetracyclines, sulfonamides, and trimethoprim, many of which were associated with plasmids. A similarity was observed between the antimicrobial resistance profiles of oysters collected from the marine environment and those commercially available. Sites with higher ARB contamination in the seawater showed increased resistance levels in oysters sold for human consumption. In some cases, identical resistance profiles and sequence types were detected across different stages of the supply chain, indicating persistence and dissemination along the supply chain. Additionally, the depuration process effectively reduced resistant bacteria and the prevalence of resistance genes in oysters. These findings demonstrate that contaminated seawater is a key driver of ARB dissemination throughout the oyster supply chain, while depuration is an effective microbiological control measure that reduces resistant bacteria and resistance genes, thereby contributing to improved food safety.

Keywords

1 Introduction

Oysters are bivalve mollusks widely consumed worldwide, valued for both their nutritional benefits and gastronomic prestige. Their raw consumption is particularly appreciated, as they are considered a delicacy (Botta et al., 2020). However, this practice poses significant public health risks, as oysters feed by filtering large volumes of water (Gawde et al., 2024). This filtration mechanism allows them to accumulate contaminants such as pathogenic microorganisms, heavy metals, and persistent organic compounds, which can compromise food safety and the quality of the consumed product (Patra et al., 2021; Vásquez-Ponce et al., 2025). Due to this ability to bioaccumulate environmental pollutants, oysters are widely recognized as bioindicators of water quality. By accumulating suspended particles, including nutrients, chemical pollutants, and antimicrobial-resistant bacteria (ARB), oysters directly reflect the environmental conditions of their ecosystem (Sun et al., 2023). Therefore, their microbiological analysis serves as an essential tool for monitoring environmental contamination and assessing potential health risks associated with their consumption. Given these factors, strict sanitary control and continuous water quality monitoring in aquaculture settings are critical to ensuring both environmental safety and public health.

Major oyster-producing countries, including the United States, France, China, and Australia, have established comprehensive frameworks to monitor and control microbial contamination in farmed and commercially distributed oysters. In the United States, the National Shellfish Sanitation Program sets microbiological standards and mandates routine water quality monitoring, focusing on Escherichia coli and fecal coliforms, with depuration required in some areas (FDA, 2023). The European Union, with France as a leading producer, enforces Regulation No 853/2004, which classifies harvesting areas based on Escherichia coli levels, requiring depuration for more contaminated areas (European Parliament and Council, 2004). China, the world’s largest oyster producer, has implemented the National Food Safety Standards (GB standards) to regulate microbial contaminants, including fecal coliforms, among other parameters (China, 2011). In Australia, the Shellfish Quality Assurance Program governs the industry, ensuring compliance with strict depuration and testing requirements, adopting Escherichia coli as a key indicator and conducting additional testing for enteric viruses, such as norovirus and hepatitis A, in certain situations (ASQAP, 2023). In Brazil, the current legislation is governed by Portaria SDA/MAPA No. 884, of September 6, 2023, which establishes requirements and procedures for the quality control of bivalve mollusks, such as oysters. It regulates food safety aspects from production to commercialization, including microbiological criteria and conditions for the classification of cultivation areas, measuring Escherichia coli concentration (Brasil, 2023). These regulatory frameworks play a crucial role in mitigating health risks associated with oyster consumption, yet differences in monitoring strategies, microbiological indicators, and enforcement practices may influence the effectiveness of contamination control across different regions.

Aquaculture environments used for oyster farming are generally located in anthropized coastal regions influenced by various pollution sources, including urban sewage, agricultural activities, and industrial effluents (Deng et al., 2024; Desdouits et al., 2023). These factors contribute to the degradation of water quality, favoring the spread of pathogenic microorganisms and the accumulation of toxic substances in filter-feeding organisms (Diner et al., 2023). Moreover, these environments frequently act as reservoirs for multidrug-resistant bacteria, representing considerable health risks for individuals who consume raw or inadequately cooked seafood (Mohammed et al., 2024).

Among the microorganisms present in these ecosystems, those classified as critical priority by the World Health Organization (WHO) stand out, including multidrug-resistant bacteria such as ESBL-producing Enterobacterales (World Health Organization, 2024). The presence of these organisms in oysters represents a public health threat (Guedes et al., 2023), as it can facilitate the transmission of antimicrobial resistance genes to other pathogens, exacerbating the problem of bacterial resistance (Li and Zhang, 2022). Furthermore, the ingestion of contaminated oysters can result in severe infections, especially in immunocompromised individuals, the elderly, and children (Yeh et al., 2020).

The oyster depuration process is a strategy used to reduce the microbial load accumulated during the farming phase, improving the microbiological safety of the final product. This procedure involves immersing oysters in tanks with treated and monitored water for a specific period, allowing the elimination of contaminants, including potentially pathogenic bacteria. During depuration, oysters continue their natural filtration activity in a controlled environment, gradually expelling accumulated microorganisms and chemical pollutants, thereby mitigating health risks associated with raw oyster consumption (Campbell et al., 2022; Liu et al., 2023).

This study aims to investigate the presence of ARB through microbiological surveillance in the oyster supply chain, evaluating the influence of production, storage, human handling, and the depuration process on the occurrence of these microorganisms. Since current regulations focus on Escherichia coli levels but do not address the circulation of ARB, these microorganisms may still be present even when oysters are cultivated in waters classified as suitable for farming.

2 Materials and methods

2.1 Study settings and sample collection

Three oyster farmers from the north bay and three from the south bay of Florianópolis, (27°35′49″S, 48°32′56″W) were selected for our study (Figure 1). Moreover, we traced and included in this study the businesses (restaurants/fish markets) to which these producers supplied oysters. Additionally, to evaluate the benefits of the depuration process on the presence of resistant microorganisms in oysters, depurated oysters were included in this study. However, only two commercial establishments in the region perform this depuration process, both of which were included in the study. These facilities operate as licensed depuration units under the sanitary requirements established by the Brazilian National Program for Safe Bivalve Molluscs (MoluBiS; SDA/MAPA Ordinance No. 884/2023). Oysters were maintained in filtered seawater subjected to ultraviolet disinfection and complementary water treatment procedures for a minimum of 12 h prior to commercialization, with depuration periods extending up to approximately 36 h depending on operational conditions. In order to investigate a possible common origin of ARB contamination, we collected samples of larval stage oysters (3mm) provided by the Marine Mollusk Laboratory of the Federal University of Santa Catarina, which is responsible for supplying larval oysters to all producers selected in this study.

Study location and sample collection sites (1 to 6). Each collection site is associated with a business (restaurants/fish markets) to which these producers supplied oysters. Businesses from sampling sites 5 and 6 carry out the depuration process.
Figure 1. Study location and sample collection sites (1 to 6). Each collection site is associated with a business (restaurants/fish markets) to which these producers supplied oysters. Businesses from sampling sites 5 and 6 carry out the depuration process.

Samples of 15 adult oysters (Magallana gigas) were collected from each producer, along with one liter of seawater from their respective marine farms. Additionally, 15 ready-to-eat oysters were collected from a commercial business supplied by each respective producer, and 15 oysters and one liter of water from the depuration tanks of the establishments that carry out the oyster depuration process. In relation to the larval stage oysters, provided by the Marine Mollusk Laboratory of the Federal University of Santa Catarina, 100g of these larval oysters (3mm), along with one liter of cultivation tank water, were collected. All samples were collected during the summer and winter of 2023.

2.2 Sample processing and bacterial culture

To evaluate the occurrence of antimicrobial-resistant bacteria associated with oyster shells at the retail stage, commercially available oysters were initially washed in 1 L of sterile 0.9% saline. For each producer and supplied business, 15 oyster samples were removed from their shells, weighed, and transferred to bottles containing an equal weight-to-volume ratio of sterile 0.9% saline. The samples were homogenized using an ULTRA-TURRAX® disperser. Subsequently, 50 mL of the homogenized samples were transferred to enrichment medium bottles containing 450 mL of tryptic soy broth (TSB) and incubated at 37 °C with agitation for 6 hours. For larval-stage oysters, 100 g of the sample was weighed and processed similarly to adult oysters, except that the step of removing the oysters from their shells was not performed. For seawater samples collected from cultivation farms, cultivation and depuration tanks, and water used for washing the commercially available oysters, 1 L of water was filtered through nitrocellulose membranes with 0.45 μm pore size to capture the bacterial content. Each membrane was then transferred to a bottle containing 200 mL of TSB medium and incubated at 37 °C with agitation for 6 hours.

From each enrichment medium, 500 µL was transferred to tubes containing 4.5 mL of TSB, with each tube supplemented individually with cefotaxime (2 µg/mL), ertapenem (0.5 µg/mL), gentamicin (2 µg/mL), ciprofloxacin (0.5 µg/mL), polymyxin (1 µg/mL), cefoxitin (4 µg/mL), or vancomycin (4 µg/mL). The tubes were incubated overnight at 37 °C. Subsequently, 10 µL aliquots from each tube were streaked onto selective agar media as follows: MacConkey agar for Gram-negative bacilli, under selective pressure of cefotaxime, ertapenem, gentamicin, ciprofloxacin, or polymyxin; mannitol salt agar for Staphylococcus under cefoxitin selective pressure; and bile esculin agar for Enterococcus under vancomycin selective pressure. For each respective selective pressure, an antimicrobial disk identical to the initial selective agent was placed on the agar (cefotaxime 30 µg, ertapenem 10 µg, gentamicin 10 µg, ciprofloxacin 5 µg, polymyxin B 300 IU, cefoxitin 30 µg, and vancomycin 5 µg). The plates were incubated at 37 °C for 24 hours. Each morphologically distinct colony that grew near the antimicrobial disk, were selected and subcultured on tryptic soy agar (TSA) at 37 °C for 24 h. Bacteria isolated on TSA medium were used for bacterial species identification, antimicrobial susceptibility testing, and DNA extraction.

2.3 Bacterial species identification and antimicrobial susceptibility testing

The bacterial isolates were identified using the VITEK® MS system (bioMérieux), which utilizes MALDI-TOF (Matrix Assisted Laser Desorption Ionization Time-of-Flight) technology, following the manufacturer’s instructions. For equipment calibration, the bacterial strain Escherichia coli ATCC 8739 was used.

The antimicrobial resistance profile of the isolates was assessed using the disk diffusion method. For Gram-negative bacilli, the following antimicrobial disks were used: cefotaxime (30 µg), ceftazidime (30 µg), aztreonam (30 µg), cefepime (30 µg), cefoxitin (30 µg), meropenem (10 µg), ertapenem (10 µg), imipenem (10 µg), ciprofloxacin (5 µg), tetracycline (30 µg), gentamicin (10 µg), and amikacin (30 µg). For Staphylococcus, only the cefoxitin disk (30 µg) was tested to identify methicillin-resistant Staphylococcus. For isolates belonging to the genus Enterococcus, only the vancomycin disk (5 µg) was tested to detect vancomycin-resistant Enterococcus. Data were interpreted based on the clinical breakpoint table from the Brazilian Committee on Antimicrobial Susceptibility Testing (BrCAST, 2025), which is based on the European Committee on Antimicrobial Susceptibility breakpoints. Phenotypic confirmation of Extended-Spectrum β-Lactamase (ESBL) production was performed using the combined disk method according to CLSI recommendations (CLSI, 2023), employing ceftazidime (30 µg) and cefotaxime (30 µg) disks alone and in combination with clavulanic acid [ceftazidime-clavulanic acid (40 µg; 30 µg ceftazidime + 10 µg clavulanic acid) and cefotaxime-clavulanic acid (40 µg; 30 µg cefotaxime + 10 µg clavulanic acid)]. Isolates showing an increase of ≥5 mm in the inhibition zone diameter for either antimicrobial in the presence of clavulanic acid were classified as ESBL producers. The evaluation of polymyxin resistance was performed using the Colistin Drop Test (Pasteran et al., 2020). A Gram-negative isolate was considered multidrug-resistant when it showed resistance to at least three different classes of tested antimicrobials (Magiorakos et al., 2012).

2.4 Detection of resistance genes by PCR

Isolates that exhibited phenotypic resistance to any class of antibiotics tested using the disk diffusion assay or the drop test for polymyxins were genotypically characterized for resistance genes associated with the corresponding antibiotic class. For carbapenem resistance, the genes blaNDM, blaKPC, blaIMP, blaVIM, blaSPM, blaOXA-23, blaOXA-48, blaOXA-51, blaOXA-58, and blaOXA-143 were tested. ESBL detection included blaTEM, blaGES, blaSHV, blaCTX-M-1, blaCTX-M-2, blaCTX-M-8, blaCTX-M-9, and blaCTX-M-25. Isolates with non-intrinsic resistance to cefoxitin were tested for the presence of AmpC β-lactamase genes, including blaCMY-1-like/MOX, blaCMY-2-like/LAT, blaDHA, blaACC, blaMIR/ACT, and blaFOX. Quinolone resistance was assessed by screening for qnrA, qnrB, qnrC, qnrD, qnrS, and qnrVC, while aminoglycoside resistance was evaluated by detecting rmtA, rmtB, rmtC, rmtD, rmtE, rmtF, rmtG, rmtH, armA, and npmA. Polymyxin resistance was determined through the presence of mcr-1, mcr-2, mcr-3, mcr-4, and mcr-5, whereas tetracycline resistance was investigated by testing for tetA, tetB, tetC, tetD, tetE, and tetG.

2.5.1 Genomic DNA extraction and whole-genome sequencing

Genomic DNA was extracted by enzymatic and chemical lysis, followed by organic extraction with chloroform:isoamyl alcohol and alcohol precipitation. Whole-genome sequencing was performed using both short- and long-read platforms. Illumina sequencing was carried in paired-end mode (2 × 150 bp), using the Nextera DNA Library Prep Kit. Long-read sequencing was performed on an Oxford Nanopore Technologies MinION Mk1B using an R10 (v10) flow cell, with libraries prepared using the Rapid Barcoding Kit 96. All procedures followed the manufacturers’ protocols.

2.5.2 Read processing, quality assessment, genome assembly, and functional annotation

Raw sequencing read quality was assessed using FASTQC (Galaxy version 0.74+galaxy1; Andrews, 2010). Read trimming and filtering were performed with FASTP (Galaxy version 1.0.1+galaxy3; Chen et al., 2018). Short-read genome assemblies were generated using Unicycler (Galaxy version 0.5.1+galaxy0; Wick et al., 2017), while long-read assemblies were constructed using Flye (Galaxy version 2.9.6+galaxy0; Lin et al., 2016). Hybrid genome assemblies were produced by mapping short reads to long-read assemblies using BWA-MEM2 (Galaxy version 2.3+galaxy0; Li, 2013), followed by iterative polishing with Pilon (Galaxy version 1.20; Walker et al., 2014). The quality and completeness of the final assemblies were evaluated using CheckM2 (Galaxy version 1.1.0+galaxy0; Chklovski et al., 2023). Functional annotation was performed using the Solu platform (Saratto et al., 2025). The presence of antimicrobial resistance genes within plasmid-associated contigs was further confirmed using the Proksee platform (Grant et al., 2023).

2.6 Statistical analysis

Statistical analyses were performed to evaluate differences in ARB isolate counts among sampling sites and to assess the association between ARB contamination in environmental matrices and commercial oysters. Given the discrete, non-normally distributed nature of the count data and the small sample size (n = 6 sampling sites), non-parametric tests were applied throughout. Differences in ARB isolate counts among sampling sites were assessed using the Kruskal-Wallis test, with all six measurements per site (three sample types across two seasons) treated as within-site observations. When a significant result was detected, pairwise comparisons were performed using the Dunn post-hoc test with Bonferroni correction for multiple comparisons. The relationship between ARB contamination levels in seawater and sea oysters and those recorded in commercial oysters was evaluated using Spearman’s rank correlation coefficient (rs), calculated separately for each season and for both sampling periods combined. All statistical analyses were performed using R (version 4.6.0) in RStudio (version 2025.05.0). A significance level of p < 0.05 was adopted for all tests.

3 Results

3.1 Resistant bacterial selection

A total of 802 bacterial isolates were screened on MacConkey agar, 13 on mannitol salt agar, and 8 on bile esculin agar. After excluding isolates without defined antimicrobial breakpoints, those sensible to tested antimicrobials and those with intrinsic resistance to the selective antimicrobials, 167 antimicrobial-resistant bacterial isolates remained. All of these resistant isolates were recovered from MacConkey agar. Consequently, no methicillin-resistant Staphylococcus or vancomycin-resistant Enterococcus were identified. Although selected resistance determinants were investigated by PCR, some phenotypic resistance profiles were not associated with the targeted genes screened. For instance, despite the detection of polymyxin-resistant phenotypes, none of the isolates carried the mobile colistin resistance genes mcr-1 to mcr-5.

In total, the following species of antimicrobial-resistant isolates were identified: Acinetobacter baumannii (n=2), Acinetobacter calcoaceticus (n=1), Acinetobacter haemolyticus (n=1), Acinetobacter junii (n=1), Acinetobacter pittii (n=2), Acinetobacter seifertii (n=3), Acinetobacter venetianus (n=1), Acinetobacter vivianni (n=1), Aeromonas spp. (n=4), Aeromonas hydrophila (n=3), Aeromonas punctata (n=7), Citrobacter freundii (n=8), Enterobacter kobei (n=1), Enterobacter cloacae (n=1), Escherichia coli (n=96), Klebsiella pneumoniae (n=10), Morganella morganii (n=4), Providencia alcalifaciens (n=1), Providencia rettgeri (n=2), Pseudomonas spp. (n=1), Pseudomonas aeruginosa (n=4), Pseudomonas putida (n=8), Vibrio fluvialis (n=4), and Vibrio parahemolyticus (n=1). Additionally, resistance genes distributed across these species included blaCTX-M-1 (n=13), blaCTX-M-2 (n=1), blaCTX-M-8 (n=6), blaTEM (n=21), blaGES (n=1), blaCMY-1/MOX (n=5), blaCMY-2/LAT (n=2), blaDHA-1 (n=1), qnrB (n=9), qnrS (n=9), tetA (n=45), tetB (n=19) and tetD (n=1) (Figure 2).

Isolates characterized by resistance phenotype and genotype at each sampling site.
Figure 2. Isolates characterized by resistance phenotype and genotype at each sampling site.

3.2 Antimicrobial resistant bacteria in the oyster supply chain

Regarding the larval-stage oysters, which are distributed to all producers included in this study, only two antimicrobial-resistant isolates were identified: Vibrio fluvialis, with no detected resistance genes, from the oysters themselves, and Acinetobacter seifertii, carrying only the tetB gene, from the water in the tank where these oysters develop. This finding suggests that ARB contamination does not originate from a single common source.

Throughout the study, a correlation was observed between ARB contamination levels in seawater or oysters from the sea and the persistence of ARB in ready-to-eat oysters. Statistical analysis confirmed significant differences in ARB isolate counts among sampling sites (Kruskal-Wallis, H = 21.30, p < 0.001), with Site 4 presenting significantly higher contamination than Sites 1 and 6 (Dunn post-hoc test with Bonferroni correction, p < 0.05). During the summer period, sites with lower ARB contamination levels, such as sites 1, 2, 3, and 6, showed a corresponding low ARB contamination in oysters (Figure 3). At these sites, only six resistant isolates were identified in seawater, and five in oysters from the sea, with the blaTEM and tetA genes detected in these samples. Commercial oysters from these sites followed the same trend, exhibiting minimal ARB contamination, with just five resistant isolates identified, carrying only the blaCTX-M-1 and tetA genes. In contrast, the sites 4 and 5, displayed significantly higher ARB contamination levels, with oysters showing considerably greater ARB contamination (Figure 3). At site 4, a high level of ARB contamination was observed, where nine resistant isolates were detected in seawater, harboring the blaCTX-M-1, blaCTX-M-8, blaTEM, qnrS, and tetA genes. Oysters collected directly from the sea at this site contained 19 resistant isolates, carrying blaCTX-M-1, blaTEM, blaCMY-1/MOX, qnrB, qnrS, tetA, and tetB genes. This elevated ARB contamination was also evident in commercialized oysters supplied by this producer, where 11 resistant isolates were identified, carrying blaTEM, qnrB, tetA, and tetB genes. At site 5, resistance was similarly prevalent, with seven resistant isolates from seawater, harboring blaCTX-M-1, tetA, and tetB genes, and six resistant isolates from oysters collected directly from the sea, containing blaTEM, qnrB, and tetA genes. In market-ready oysters from this producer, 10 resistant isolates were identified, carrying blaCTX-M-1, blaCTX-M-2, blaTEM, blaCMY-1/MOX, blaCMY-2/LAT, tetA, tetB, and tetD genes. Overall, seawater ARB counts were perfectly correlated with commercial oyster contamination across sites during summer (Spearman rs = 1.000, p < 0.001), supporting the hypothesis that environmental contamination directly predicts ARB levels in ready-to-eat oysters.

Distribution of antibiotic-resistant bacteria isolates in seawater, sea oysters, and commercial oysters across sampling sites in North Bay and South Bay during summer and winter.
Figure 3. Distribution of antibiotic-resistant bacteria isolates in seawater, sea oysters, and commercial oysters across sampling sites in North Bay and South Bay during summer and winter.

During the winter sampling period, a similar trend was observed, with sites 1 and 6 displaying low ARB contamination levels, which was reflected in the low ARB contamination of oysters from these areas (Figure 3). At these sites only two resistant isolates were detected in seawater, which did not carry any resistance genes, and commercial oysters showed minimal ARB contamination with only three resistant isolates found, also with no resistance genes detected. In contrast, sites 2, 3, 4, and 5 exhibited higher ARB contamination levels, resulting in a greater number of resistant isolates found in commercial oysters (Figure 3). At site 2, five resistant isolates were detected in seawater, carrying blaCTX-M-8, blaTEM, and tetA genes, with an equivalent number of resistant isolates found in oysters, harboring the tetB gene. Commercial oysters from this site displayed six resistant isolates with the blaTEM gene. Site 3 showed a similar trend, with one resistant isolate in seawater carrying the tetB gene and three resistant isolates in oysters. Commercial oysters from this site displayed higher resistance, with five resistant isolates carrying blaCMY-1/MOX, and tetA genes. Site 4 maintained a high level of ARB contamination in seawater, with five resistant isolates carrying blaCTX-M-1, qnrS, tetA, and tetB. Similarly, oysters collected directly from the sea contained three resistant isolates harboring blaCTX-M-8, blaTEM, qnrB, qnrS, and tetA. This high degree of ARB contamination persisted in commercialized oysters, where seven resistant isolates were identified, carrying blaCTX-M-1, blaCTX-M-8, blaTEM, qnrB, tetA, and tetB. Notably, nearly all resistance genes detected in seawater and marine oysters were also found in commercial oysters, indicating that ARB contamination acquired at sea persists through to the final consumer. Site 5 exhibited a moderate level of ARB contamination, with two resistant isolates in seawater carrying blaCTX-M-1, blaTEM, tetA, and tetB, while oysters from the same location harbored two isolates containing blaGES and qnrS. In commercial establishments supplied by this producer, five resistant isolates were found in oysters, carrying blaTEM, qnrS, and tetB. This pattern was further supported statistically, with sea oyster ARB counts significantly correlated with commercial oyster contamination in winter (Spearman rs = 0.851, p = 0.032), and strong associations observed when seasons were pooled (seawater vs commercial oyster: rs = 0.846, p < 0.001; sea oyster vs commercial oyster: rs = 0.837, p < 0.001).

3.3 Benefits of oyster depuration process

Depuration demonstrated a notable benefit in reducing the load of resistant microorganisms and, consequently, the reduction of detected resistance genes At site 5, during the summer, 10 resistant isolates were detected in ready-to-eat oysters, containing the genes blaCTX-M-1, blaCTX-M-2, blaTEM, blaCMY-1/MOX, blaCMY-2/LAT, tetA, tetB, and tetD. After depuration, only two isolates remained in the oysters and one in the depuration tank water, all without antimicrobial resistance genes. In winter, the same collection site revealed five resistant isolates carrying the genes blaTEM, qnrS, and tetB, but after depuration, only one resistant isolate remained in both the oysters and the depuration tank water, neither carrying any resistance genes. Additionally, the winter collection at point 6, which initially showed low ARB contamination with only one resistant isolate and no identified resistance genes, resulted in the complete elimination of resistant isolates after the depuration process, both in the oysters and in the depuration tank water (Figure 2).

3.4 WHO priority bacteria circulating in ready-to-eat oysters

Of the 167 isolates screened in this study, 44 were classified as WHO critical priority pathogens (World Health Organization, 2024), specifically third-generation cephalosporin-resistant Enterobacterales. Among these, 33 were considered multidrug-resistant. The identified critical priority pathogens included Escherichia coli (n=32), Klebsiella pneumoniae (n=5), Citrobacter freundii (n=4), Enterobacter cloacae (n=1), and Morganella morganii (n=1), carrying the resistance genes blaTEM (n=31), blaCTX-M-1 (n=15), blaCTX-M-8 (n=6), blaCMY-1/MOX (n=5), blaCMY-2/LAT (n=2), and blaCTX-M-2 (n=1).

During the summer, establishments 2, 4, and 5, and during the winter, establishments 1, 2, 3, 4, and 5, harbored WHO critical priority pathogens in ready-to-eat oysters. With emphasis on collection sites 4 and 5, which, both in summer and winter, presented WHO critical priority pathogens in seawater, marine oysters, and oysters sold by establishments supplied by these producers.

Among these isolates, two cases stand out in demonstrating the transmission of environmental ARB contamination to the final consumer. The first is an Escherichia coli isolate carrying the genes blaCTX-M-1, blaTEM, tetA, and qnrS, collected at site 4 during the summer, which was traced in both seawater and the washing water of ready-to-eat oysters at the commercial establishment supplied by this producer. The second is a Klebsiella pneumoniae isolate carrying the genes blaCTX-M-8, blaTEM, qnrB, and tetA, collected also at site 4, but during the winter, which was identified in both marine oysters and ready-to-eat oysters at the corresponding commercial establishment. These findings suggest that ARB contamination present in the marine environment may persist through the production chain and reach the final consumer.

Additionally, it is important to highlight the presence of multidrug-resistant organisms in ready-to-eat oysters, such as Citrobacter freundii carrying the genes blaTEM, qnrB, and tetA, two Escherichia coli carrying the genes blaCTX-M-1, qnrS, and tetA, and blaCTX-M-1, blaTEM, qnrS, and tetA, and an Klebsiella pneumoniae isolate harboring blaCTX-M-8, blaTEM, qnrB, and tetA.

3.5 Genomic characterization of resistant isolates

Whole genome sequencing was performed on a subset of representative antimicrobial-resistant isolates recovered from oysters, seawater, and washing water along the oyster supply chain. In total, 17 isolates were sequenced, including Escherichia coli (n=12), Klebsiella pneumoniae (n=3), Citrobacter freundii (n=1), and Enterobacter cloacae (n=1). Most isolates (94%) were classified as multidrug-resistant, harboring resistance determinants to three or more antimicrobial classes. A diverse set of plasmid incompatibility groups was identified, including IncF, IncX, IncN, IncHI2, IncI, IncY, IncL/M, IncC, IncR, and Col-type plasmids (Table 1).

Table 1. Genomic features, sequence types, and plasmid profiles of selected antimicrobial-resistant isolates from the oyster supply chain.

IsolateSourceSpeciesSTGenome (Mb)PlasmidsMDR
60OysterEscherichia coli17225.11IncFIA/B/I; IncX1Yes
153Sea waterEscherichia coli904.99IncYYes
158OysterEscherichia coli695.24IncFIA/B/I; IncX1Yes
163OysterEscherichia coli2245.08IncFIA/B/I; IncX1Yes
174OysterEscherichia coli384.94IncNYes
193OysterEscherichia coli104.78IncN; IncFIA/I; IncFIB; IncQ; Col1561Yes
201Washing waterEscherichia coli104.72IncX1Yes
230OysterEscherichia coli4574.95IncFIANo
320Sea waterEscherichia coli7445.00IncI; IncFIA/I; IncQ1Yes
321Sea waterEscherichia coli105.07IncFIA/B/IYes
338Sea waterEscherichia coli32585.95IncFIA/B/I; IncHI2Yes
349OysterEscherichia coli104.90IncFIA/B/IYes
149Sea waterKlebsiella pneumoniae455.83IncFIB/IYes
327OysterKlebsiella pneumoniae456.04IncFIB; IncC; IncL/M; ColRNAIYes
357OysterKlebsiella pneumoniae455.84IncFIB; IncC; IncL/M; ColRNAIYes
204Washing waterCitrobacter freundii185.16IncFIB; IncRYes
369Washing waterEnterobacter cloacae–4.47IncNYes

Multilocus sequence typing (MLST) analysis revealed a high genetic diversity among E. coli isolates, which were assigned to multiple sequence types (STs), including ST10, ST38, ST69, ST90, ST224, ST457, ST744, ST1722, and ST3258. Notably, some sequence types were detected across different sources within the supply chain. For instance, ST10 was identified in isolates from oysters, seawater, and washing water, while ST45 was consistently found among K. pneumoniae isolates recovered from both seawater and oysters.

The plasmid content analysis demonstrated that most isolates carried multiple plasmid replicons, with IncF-type plasmids (IncFIA, IncFIB, IncFII) being the most prevalent. Additional plasmids such as IncX1, IncN, IncHI2, IncL/M, and IncC were also frequently detected. Several isolates harbored combinations of different plasmid types.

A comprehensive resistome analysis revealed the presence of a wide range of antimicrobial resistance genes associated with multiple antibiotic classes. Among β-lactam resistance genes, extended-spectrum β-lactamases (ESBLs) were predominant, particularly blaCTX-M variants, followed by other β-lactamase genes such as blaTEM and blaOXA. Additionally, AmpC-type enzymes, including blaCMY-2 and blaDHA-1, were also identified. Resistance to aminoglycosides was mainly associated with genes such as aadA, aph, and aac variants, while plasmid-mediated quinolone resistance genes (qnrB, qnrS, qnrE) were detected alongside chromosomal mutations in gyrA and parC. Additional resistance determinants included sulfonamide (sul1, sul2, sul3), tetracycline (tetA, tetB, tetD), trimethoprim (dfrA variants), phenicol (cat, floR), and macrolide resistance genes (mph, erm, msr) A large proportion of the detected resistance genes were associated with plasmids, including ESBL genes and determinants conferring resistance to quinolones, tetracyclines, sulfonamides, and aminoglycosides (Table 2). Manual inspection of the assemblies using Proksee confirmed that all resistance genes designated as plasmid-associated in Table 2 were located on plasmid-derived contigs carrying plasmid replicon sequences.

Table 2. Resistome profiles of selected antimicrobial-resistant isolates from the oyster supply chain.

Isolateβ-lactamsAminoglycosidesQuinolonesSulfonamidesTetracyclinesTrimethoprimPhenicolsMLSFosfomycin
60bla<sub>CTX-M-15</sub> (P)aadA1 (P)aadA2 (P)gyrA_D87N gyrA_S83L parC_E84G parC_S80Isul3 (P)tet(A) (P)dfrA12 (P)dfrA51 (P)cmlA1 (P)-uhpT_E350Q cyaA_S352T
153bla<sub>TEM</sub> (P) bla<sub>CTX-M-15</sub> (P)aph(3'')-Ib (P)aph(6)-Id (P)gyrA_D87N gyrA_S83L parC_S80I parE_S458AqnrS (P)sul2 (P)tet(A) (P)dfrA14 (P)---
158bla<sub>CTX-M</sub>bla<sub>TEM-1</sub> (P)-gyrA_S83L-tet(A) (P)tet(B) (P)dfrA14 (P)-erm(B) (P)mph(A) (P)cyaA_S352T
163bla<sub>TEM-1</sub> (P) bla<sub>DHA-1</sub> (P)aadA2 (P)gyrA_D87N gyrA_S83L parC_S80I parE_S458AqnrB4 (P)sul1 (P)tet(B) (P)dfrA12 (P)catA1 (P)mph(A) (P)mph(E) (P)msr(E) (P)uhpT_E350Q
174bla<sub>TEM-1</sub> (P) bla<sub>CTX-M-14</sub>aac(3)-IIeaadA2 (P)aph(3'')-Ib (P)aph(6)-Id (P)gyrA_D87Y gyrA_S83L parC_S80I parE_S458Asul1 (P)sul2 (P)tet(D) (P)dfrA12 (P)-erm(B) (P)mph(A) (P)cyaA_S352T
193bla<sub>TEM-1</sub> (P)bla<sub>OXA-1</sub>aac(3)-IId (P) aac(6')-Ib-cr5 aph(3'')-Ib (P)aph(6)-Id (P)aadA5 (P)gyrA_D87N gyrA_S83L parC_S80I parE_S458Asul2 (P)tet(B) (P)dfrA17 (P)-mph(A)-
201bla<sub>TEM-1</sub> (P)bla<sub>CTX-M-15</sub>aph(3'')-Ib (P)aph(6)-Id (P)aadA1gyrA_S83AqnrS1 (P)sul2 (P)tet(A) (P)dfrA1---
230bla<sub>CMY-2</sub> (P)-------uhpT_E350QcyaA_S352T
320bla<sub>TEM</sub> (P) bla<sub>CTX-M-55</sub> (P)aph(3')-Ia (P)aadA5 (P)aph(3'')-Ib (P)aph(6)-Id (P)gyrA_D87N gyrA_S83L parC_A56T parC_S80Isul1 (P)sul2 (P)tet(B) (P)dfrA17 (P)catA1 (P)mph(A) (P)-
321bla<sub>TEM</sub> (P)bla<sub>CTX-M-15</sub>aac(3)-IId (P) aadA5 (P)aph(3'')-Ib (P)aph(6)-Id (P)gyrA_D87N gyrA_S83L parC_S80Isul2 (P)tet(A) (P)dfrA17 (P)-mph(A) (P)-
338bla<sub>CTX-M-55</sub> (P)16S_A794Taac(3)-IId (P) aac(3)-VIaaadA1 (P)aph(3')-Ia (P)aph(6)-Id (P)gyrA_D87N gyrA_S83L parC_S80RqnrS (P)sul1sul2sul3 (P)tet(A) (P)dfrA14 (P)floR (P)mph(A) (P)lnu(F) (P)cyaA_S352T
349bla<sub>TEM</sub> (P)bla<sub>CTX-M-15</sub>aac(3)-IId (P) aadA5 (P)aph(3'')-Ibaph(6)-IdgyrA_D87N gyrA_S83L parC_S80Isul2 (P)tet(A) (P)dfrA17 (P)-mph(A) (P)-
149bla<sub>CTX-M-15</sub> (P)bla<sub>OXA-1</sub> (P)bla<sub>TEM-1</sub> (P) bla<sub>SHV-1</sub>aac(3)-IIe (P) aac(6')-Ib-cr5 (P) aph(3'')-Ib (P)aph(6)-Id (P)aac(6')-Ib-cr5 (P) qnrB1 (P)oqxA11oqxB19sul2 (P)tet(A) (P)dfrA14 (P)catB3 (P)-fosA
327bla<sub>TEM</sub> (P) bla<sub>CTX-M</sub> (P, bla<sub>OXA</sub> (P) bla<sub>SHV</sub>aac(6')-Ib (P)aac(6')-Ib-cr5 (P)aadA1 (P)aph(3'')-Ib (P) aph(6)-Id (P)qnrB2 (P)qnrE (P)aac(6')-Ib-cr5 (P)oqxA11oqxB19sul1 (P)sul2 (P)tet(A) (P)-catB3 (P)floR (P) oqxA11oqxB19mph(A) (P)erm(B) (P)fosA
357bla<sub>TEM</sub> (P) bla<sub>CTX-M</sub> (P) bla<sub>OXA</sub> (P)bla<sub>SHV</sub>aph(6)-Id (P)aac(6')-Ib-cr5 (P) aadA1 (P)aph(3'')-Ib (P)aph(6)-Id (P)qnrB2 (P)qnrE1 (P)aac(6')-Ib-cr5 (P)oqxA11oqxB19sul1 (P)sul2 (P)tet(A) (P)-catB3 (P)floR, (P) oqxA11oqxB19mph(A) (P)erm(B) (P)fosA
204bla<sub>TEM-1</sub>bla<sub>CMY</sub>bla<sub>DHA-1</sub> (P)bla<sub>OXA-1</sub> (P)aac(6')-Ib-cr5 (P) aadA5gyrA_T83IqnrB4 (P)aac(6')-Ib-cr5 (P)sul1 (P)tet(A) (P)dfrA17dfrA51 (P)catB3 (P)mph(A) (P)-
369bla<sub>TEM-40</sub> (P)aph(3'')-Ib (P)aph(6)-Id (P)-sul2 (P)-dfrA8 (P)--fosA

Genes followed by (P) in bold are located on plasmids, whereas genes without this designation are chromosomally encoded.

4 Discussion

Here we present a comprehensive study on the occurrence and characteristics of ARB among oyster samples, collected over the seasons of summer and winter from different production and commercialization sites of the oyster supply chain. This investigation assessed the presence of resistant microorganisms, the distribution of critical priority pathogens, and the prevalence of resistance genes, providing insights into the impact of environmental factors and depuration processes on the microbiological safety of oysters.

Oysters, as filter-feeding bivalves, have the intrinsic capacity to accumulate a variety of microorganisms present in their surrounding aquatic environment. This study identified several antimicrobial-resistant bacterial species associated with oysters, including Escherichia coli, Klebsiella pneumoniae, Citrobacter freundii, and Vibrio spp., among others. These bacteria can pose significant risks to public health, particularly when oysters are consumed raw (Campbell et al., 2022; Freire et al., 2023; Mohammed et al., 2024; Yeh et al., 2020).

The study revealed a diverse array of antimicrobial resistance genes circulating within the oyster supply chain. The most prevalent genes included blaTEM, blaCTX-M-1, qnrB, qnrS, tetA and tetB, with less common but clinically significant genes such as blaCTX-M-2, blaCTX-M-8, blaGES, blaCMY-1/MOX, blaCMY-2/LAT, blaDHA-1, and tetD also detected. The detection of such diversity from high prevalence to uncommon resistance genes highlights the role of aquatic environments as reservoirs and conduits for the dissemination of antimicrobial resistance (Grevskott et al., 2017; Jampani et al., 2024).

To further investigate the genomic context of antimicrobial resistance, whole genome sequencing of selected isolates revealed a high diversity of sequence types (STs), including globally distributed lineages such as ST10, ST38, ST69, and ST744. These sequence types have been frequently associated with human, animal, and environmental sources, suggesting that the resistant bacteria identified in this study are not confined to a single ecological niche but rather circulate across interconnected reservoirs (Beining et al., 2025; Gomi et al., 2017; Fuga et al., 2022). The presence of these lineages in oysters highlights the role of coastal environments as convergence points for bacteria originating from multiple sources, including wastewater discharge, agricultural runoff, and human activities, reinforcing the concept of a One Health interface in marine ecosystems.

The detection of identical sequence types across different stages of the oyster supply chain provides evidence of bacterial circulation between environmental and processing compartments. In particular, ST10 was identified in isolates from oysters, seawater, and washing water, while ST45 was consistently observed among Klebsiella pneumoniae isolates from both marine and oyster samples. This pattern supports the occurrence of dissemination along the production and handling chain, linking environmental contamination to the final food product (Mohammed et al., 2024). Such continuity suggests that contamination events are not isolated but may persist throughout multiple stages, potentially facilitating the maintenance and amplification of resistant populations from the aquatic environment to the point of consumption.

The detection of shared sequence types among seawater, oysters, and shell-washing water is consistent with the persistence and dissemination of antimicrobial-resistant bacteria throughout the oyster supply chain. In particular, ST10 Escherichia coli was identified in isolates from oysters, seawater, and washing water, while ST45 was consistently observed among Klebsiella pneumoniae isolates recovered from both marine and oyster samples. These findings support the hypothesis that antimicrobial-resistant bacteria present in the aquatic environment may persist through successive stages of production and handling, ultimately reaching the final food product (Mohammed et al., 2024). Such continuity suggests that contamination events may not be isolated and could persist throughout multiple stages of the supply chain, potentially facilitating the maintenance and spread of resistant populations from the marine environment to the point of consumption. However, MLST is based on a limited number of housekeeping genes and does not provide sufficient resolution to demonstrate direct transmission between isolates (Shropshire et al., 2025). In particular, widely distributed sequence types such as Escherichia coli ST10 encompass substantial genomic diversity and may also reflect independent contamination events originating from different environmental sources (Yu et al., 2018).

Plasmid analysis further demonstrated the presence of multiple incompatibility groups within individual isolates, with IncF-type plasmids being the most prevalent. These plasmids are widely recognized as major vectors of antimicrobial resistance genes, particularly those encoding extended-spectrum β-lactamases. In addition, other plasmid types such as IncX, IncN, IncHI2, IncL/M, and IncC were detected, frequently co-occurring within the same isolates. The coexistence of multiple plasmid replicons within single strains suggests an enhanced capacity for genetic exchange and recombination (Botts et al., 2023; Fang et al., 2024; Rozwandowicz et al., 2018; Yassara et al., 2025). Moreover, the widespread association of resistance genes with plasmids across multiple antimicrobial classes, including β-lactams, quinolones, tetracyclines, sulfonamides, and aminoglycosides, indicates that horizontal gene transfer may play a central role in structuring the resistome in this environment. These findings are consistent with the notion that marine ecosystems can act as reservoirs and mixing vessels for mobile genetic elements carrying clinically relevant resistance determinants.

The resistome profiles revealed the co-occurrence of multiple resistance determinants within the same isolates, including combinations of ESBL genes, AmpC enzymes, plasmid-mediated quinolone resistance genes, and chromosomal mutations (Hareza et al., 2025; Kurittu et al., 2021; Mansouri et al., 2024). This combination of resistance mechanisms is characteristic of multidrug-resistant phenotypes and reflects the cumulative effects of different selective pressures acting on bacterial populations. The simultaneous presence of chromosomal mutations and plasmid-mediated resistance genes, particularly for quinolones, suggests layered resistance strategies that may enhance bacterial survival under antimicrobial exposure (Kurittu et al., 2021). Additionally, the accumulation of diverse resistance determinants within single isolates raises concerns regarding co-selection, where the use of one antimicrobial class may indirectly select for resistance to others. Altogether, these genomic features may contribute to the persistence, adaptation, and dissemination of resistant bacteria in aquatic environments and along the oyster supply chain.

In our study, ESBL resistance genes were detected in oyster samples, with 28% of the isolates carrying these genes. The rates of ESBL-producing isolates in the present study were higher than those reported in bivalves from other countries. In a study investigating the presence of ESBL in Enterobacterales from commercially available clams in Tunisian markets, only 1.6% of the isolates harbored ESBL genes (Sola et al., 2022). A study on antimicrobial resistance in Escherichia coli isolated from marine bivalves collected in Norway identified the ESBL phenotype in just 7% of the isolates (Grevskott et al., 2017), while 8% of Escherichia coli isolates from Magallana gigas oysters in Portugal carried ESBL genes (Freire et al., 2023). However, our study found a lower proportion of ARB contamination compared to a study investigating fresh shellfish from retail markets in India, where 53% of Escherichia coli isolates exhibited ESBL production (Singh et al., 2020).

Notably, in our study 44 bacterial isolates were classified as critical priority pathogens by the WHO, including multidrug-resistant strains of Enterobacterales resistant to third-generation cephalosporins. These pathogens, such as Escherichia coli and Klebsiella pneumoniae, exhibited resistance profiles involving genes like blaTEM, blaCTX-M, and blaCMY variants. The persistence of these critical pathogens in oysters destined for human consumption represents a public health concern, as it facilitates the potential transfer of antimicrobial resistance genes to human microbiota (Despotovic et al., 2023). In a similar study conducted in Egypt on commercially sold oysters, Escherichia coli was detected in 72% of the 33 samples. Among these isolates, 91.7% carried blaTEM, 54.2% blaCMY-2 and 20.8% blaCTX-M (Mohammed et al., 2024).

In our study the quality of the aquatic environment was correlated with the microbiological safety of oysters. Sites with higher ARB contamination levels in seawater, such as South Bay sites 4 and 5, exhibited a corresponding increase in resistant bacteria and genes in both marine and commercial oysters. Conversely, cleaner sites showed reduced ARB contamination levels, emphasizing the critical importance of maintaining high water quality standards in aquaculture practices to ensure the safety of the final product. Even though it is within the acceptable coliform limits set by Brazilian legislation (Brasil, 2023), studies that analyzed the correlation between total coliforms and the abundance of antimicrobial resistance genes highlighted a positive correlation between these two variables, emphasizing the anthropogenic factor in the higher abundance of total coliforms and antimicrobial resistance genes (Brandão et al., 2017; Wu et al., 2020). This would justify the high prevalence of resistant isolates and resistance genes at sampling sites 4 and 5, as they are in a densely populated bay with known deficient wastewater treatment. Oysters serve as effective bioindicators of environmental contamination due to their filter-feeding behavior, which enables them to accumulate microorganisms and pollutants from their habitats (Sun et al., 2023). The presence of multidrug-resistant bacteria and resistance genes in oysters reflects the antimicrobial resistance burden of their surrounding environment. This bioindicator role underscores the importance of using oysters in environmental monitoring programs to assess and manage ecosystem health.

Commercial oysters can be affected by various handling processes, including transportation, storage, and manipulation, which expose them to factors such as refrigeration conditions, improper handling practices, and microbial contamination. However, oysters, when removed from water, close their shells, trapping seawater inside. This retained water continues to circulate within the oyster, creating a semi-closed system that limits the entry of external contaminants and helps preserve the internal microbiota. This unique biological trait may contribute to reducing the impact of external contamination during the supply chain, enhancing food safety for consumers (Yeh et al., 2020). This phenomenon can explain why oysters from more contaminated marine environments tend to remain highly contaminated until they reach the final consumer, whereas those from less contaminated waters generally maintain lower contamination levels throughout the supply chain.

The depuration process demonstrated substantial efficacy in reducing both the load of resistant bacteria and the prevalence of resistance genes in oysters. Establishments that employed depuration showed marked decreases in ARB contamination levels, with some instances of complete elimination of resistant isolates. These findings corroborate the benefits of depuration as a critical control measure in enhancing the microbiological safety of oysters, thereby mitigating public health risks associated with the consumption of raw shellfish. Previous studies have demonstrated the benefits of depuration in reducing the load of pathogenic microorganisms (Campbell et al., 2022; Jeong et al., 2021). Additionally, it has been shown that commercially sold oysters subjected to the depuration process carry a lower load of antimicrobial resistance genes compared to those that did not undergo depuration (Guedes et al., 2023).

5 Conclusion

Our findings demonstrate that water quality at oyster farming sites is the primary factor influencing the presence of ARB throughout the supply chain, with higher contamination levels in oysters from more polluted waters persisting until commercialization. The presence of ESBL-producing and multidrug-resistant Enterobacterales in ready-to-eat oysters highlights the potential public health risks associated with their consumption. Genomic analyses further revealed the circulation of shared bacterial lineages across different stages of the supply chain, as well as the widespread presence of plasmid-associated resistance genes across multiple antimicrobial classes. Additionally, the study confirms that depuration is an effective strategy to reduce bacterial contamination and antimicrobial resistance genes in oysters, reinforcing its importance as a microbiological control measure. Altogether, these results emphasize the need for stricter water quality management, improved sanitary handling practices, and broader implementation of depuration to mitigate the risks of antimicrobial resistance dissemination in the oyster supply chain.

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Footnotes

Edited by: Flávia Lúcia Piffano Costa Pellegrino, Rio de Janeiro State University, Brazil

Reviewed by: Alex Odoom, University of Ghana, Ghana

Rubens Dias, Federal University of the State of Rio de Janeiro, Brazil

Statements

Conflict of interest

The author(s) declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Funding

The author(s) declared that financial support was received for this work and/or its publication. This work was supported by research grants from Fundação de Amparo à Pesquisa e Inovação do Estado de Santa Catarina [FAPESC 2021TR1717 and SGP-e FAPESC N°: 3003/2021], and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES). This study also received support from the AquaticAMR project managed by the Agence Nationale de la Recherche (ANR) as part of the investment programme France 2030 under the reference “ANR-21-EXES-0005”; from the Occitanie Region; and from the ExposUM Institute of the University of Montpellier.

Data availability

The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/genbank/, PRJNA1426971.

Author contributions

GR: Conceptualization, Data curation, Investigation, Methodology, Supervision, Validation, Visualization, Writing – original draft. MR: Conceptualization, Investigation, Methodology, Validation, Writing – review & editing. Id: Investigation, Validation, Writing – review & editing. JLD: Investigation, Writing – review & editing. VW: Investigation, Writing – review & editing. Jd: Investigation, Writing – review & editing. Gd: Investigation, Writing – review & editing. JP: Conceptualization, Investigation, Funding acquisition, Methodology, Supervision, Writing – review & editing. TS: Conceptualization, Funding acquisition, Methodology, Supervision, Writing – review & editing.

Acknowledgements

We would like to thank all the oyster farmers and the Marine Mollusk Laboratory of the Federal University of Santa Catarina for making the analyzed samples viable.

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Citation

Rocha, G., et al. (2026). Microbiological and genomic surveillance of WHO critical priority pathogens along the oyster supply chain: water quality as a driver of persistence and depuration as a mitigating strategy in a One Health context. Frontiers in Bacteriology, Volume 5. https://doi.org/
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5 - 2026

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Copyright © 2026 Rocha, Ribas, de Assunção, Dal Pizzol, Wolleck, de Jesus, da Silva, Palmeiro and Sincero.

License: https://creativecommons.org/licenses/by/4.0/

*Correspondence: Gustavo Rocha; Thais Cristine Marques Sincero

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