The continuous presence of antibiotics in bivalves may affect animals and bacterial microbiota living in and on water animals (Figure 1). Chiesa et al. (2018), using an HPLC–MS/MS multiclass method, developed a method for the determination of 29 antibiotics belonging to eight different chemical classes (penicillin, quinolones, tetracyclines, sulphonamides, macrolides, lincosamides, cephalosporins, and amphenicols), in mussels and clams, both wild and farmed, collected from various geographic areas of the world and, particularly, Italy. In 100 samples of Meretrix lyrata (the lyrate Asiatic hard clam), M. meretrix (the Asiatic hard clam), Venerupis decussata (the cross-cut carpet shell), V. philippinarum (the Manila clam), Paphia textile (the carpet clam), and Chamelea gallina (the Venus clam), they found four representatives of tetracycline group (49.45 ng g^–1 tetracycline, 125.03 ng g^–1 oxytetracycline, 60.45 ng g^–1 doxycycline, and 77.48 ng g^–1 chlortetracycline) in one pool of farmed clams obtained from the Italian side of the North Adriatic Sea. Considering the annual Per capita consumption of 0.33 kg clams (European Commission, data), the daily consumption is 0.91 g; the result of the multiplication of this value by the sum of the concentrations of the four tetracyclines (312.41 ng g^–1) found in the clam sample of North Adriatic Sea, is 0.29 μg per day. Molluscs from Bohai Sea (11 species of commercially available molluscs Crassostrea talienwhanensis, Chlamys farreri, Amussium, Scapharca subcrenata, Meretrix meretrix L., Mactra veneriformis, Mactra chinesis, Mya arenaria, Neverita didyma, Rapana venosa, and Mytilus edulis) were also analyzed for the presence of antibiotics in their flesh (Li et al., 2012). The authors found 22 antibiotics, including quinolones, sulfonamides and macrolides, in all samples of molluscs. The analysis of seawater from the Antarctic (Hernández et al., 2019) around South Shetland Island Fildes Peninsula, where are few scientific stations from several countries, showed the presence of antibiotics in seawater. The most prevalent antibiotics were two quinolones, ciprofloxacin, and norfloxacin, at average concentrations of 0.89 μg/L and 0.75 μg/L, respectively. Three macrolides were identified: Azithromycin and clarithromycin (average concentrations close to 0.4 μg/L), and erythromycin (average concentration 0.003 μg/L). González-Alonso et al. (2017) also found antibiotics in this area. Clarithromycin, ofloxacin, sulfadiazine, sulfamethazine, trimethoprim, and sulfamethoxazole were among the most consumed pharmaceuticals at all Antarctic stations nearby the sampling area. This datum could represent a risk mainly associated with the increase in antibiotic-resistance phenomenon. Continuous delivery of antibiotics to the marine environment strongly signals that anthropogenic activities are one of the primary sources of antibiotics in marine environments. The presence of antibiotics can lead to the conclusion that pharmaceuticals’ continuous pressure on microbial communities can lead to independent ways to develop resistance against the most concentrated or most effectively eliminating substances.

Even not targeted on environment purifying, bivalve farms perfectly fulfill their role in assessing AR spreading. In contrast to finfish aquaculture, bivalve aquaculture is fed with natural phytoplankton or detritus, and no additives such as antibiotics are added during their post-larval life (Wijsman et al., 2019). Moreover, the ecological importance of bivalve molluscs as filter feeders gives them a unique position in aquaculture systems as they are used to purify water from farming in multi-trophic aquaculture systems (MTA) (Sanz-Lazaro and Sanchez-Jerez, 2020). Thus they hold a particular position in AR distribution in marine environments (Figure 1). A field study comparing traditional and MTA aquaculture of fish Chanos chanos revealed that the latter system can prevent the shift in microbial communities and persistence of sulphonamide-resistant phenotypes (Ying et al., 2018). In the spatiotemporal study of bacterial resistance against florfenicol in the area of intense salmon farming, the microbiota of mussel M. chilensis revealed a striking influence depending on the distance to the next fish farm concerning water currents (Ramírez et al., 2022). Another study pinpoints AR against antibiotics used in aquaculture but against colistin–an antibiotic of last resort against multidrug-resistant Gram-negative bacteria in human medicine in Portuguese mussel farms (Salgueiro et al., 2021).

Similarly, a broad spectrum of AR genes was found in Ruditapes philippinarum clam (Dahanayake et al., 2019). Despite the importance of mussels in assessment and AR clearance, the products from mussels farms may become a public health threat for consumers. Selective pressures exerted by the overuse or misuse of antibiotics in primary food production, genetically modified crops with antibiotic-resistance marker genes, microorganisms added intentionally to the food chain (probiotic or technological) with potentially transferable antimicrobial resistance genes, food processing technologies used at sub-lethal doses (e.g., alternative non-thermal treatments), and the use of biocides are among the main driving forces behind the selection and spread of antimicrobial resistance throughout the food chains (Udoekong et al., 2021).

In the supply chain, molluscs usually are subjected to several stressors during capture, depuration, storage, and transportation, including prolonged periods of air exposure and temperature fluctuation. The stressors strongly decrease the bivalves’ quality, cause some changes in the bivalves’ metabolism, and may favor the growth of bacteria, an inadvisable component of meat. According to Pan et al. (2018), depuration with UV light decreases the number of bacteria significantly but lowered temperature during the depuration process extends the number of surviving clams and lowers the observed bacteria number compared to molluscs depurated at higher temperature (2,630 vs. 1,090 CFU/ml (colony forming units). The temperature can also affect the glycogen content and pH of bivalve tissues. Unlike crustaceans and finfish, molluscs’ flesh contains an appreciable amount of glycogen. Thus, the spoilage of molluscs is primarily glycolytic (1–5% glycogen content) rather than proteolytic, which may lead to a pH decrease resulting in a lower pH than in the case of other seafood. Lower pH at later stages of spoilage may favor the growth of bacterial species preferring lower pH, like enterococci, lactobacilli, and yeasts. For this reason, animals are usually transported to the point of sale, where they undergo further processing (Kontominas et al., 2021).

The analysis of bacterial communities on flash during the storage process of Manila clams (R. philippinarum) confirmed that each day of storage changes the proportions of bacterial taxons significantly. Authors showed it in the example of Proteobacteriales, including the class of Gammaproteobacteria with, among other, pathogenic genera like Vibrio, Escherichia, Pseudomonas, and Aeromonas. Proteobacteria are considered typical spoilage organisms for fresh seafood (Liu et al., 2020) and, like Aeromonas hydrophila, A. sobria or Shewanella putrefaciens, Vibrio spp. dominate the bacterial communities in many seafoods (Madigan et al., 2014; Chen et al., 2019; Zhuang et al., 2021).

Both fresh and cooked immediately after collection, bivalves may be at risk of colonization caused by pathogenic bacteria (Ekanem, 1998; Baris Bingol et al., 2008; Ates et al., 2011). These bacteria can originate from the natural environment or result from human, animal or abiotic activities, e.g., rain washing out the organic pollution from lands into the water (Alegbeleye and Sant’Ana, 2020), wave action and rainfall (Hernandez et al., 2020; Udoekong et al., 2021). The marine ecosystem can be considered an extensive reservoir of ARB (Antibiotic Resistant Bacteria) and ARGs mainly acquired through fecal contamination of human and/or animal origin (Figure 1). Publications report the bacterial microbiota in coastal and marine ecosystems, including E. coli, Clostridium perfringens, Bacillus cereus, S. aureus, Salmonella spp. and others (Islam and Tanaka, 2004; Moreno Roldán et al., 2011; Grabowska et al., 2020; Verga et al., 2020; Silva dos Santos et al., 2022). Although global seafood production is growing yearly, systematic surveillance of AMR in this sector is mainly lacking or has only been at a pilot study level. One main reason for this gap is the difficulties of investigating AMR phenotypes of marine bacteria, which often have specific growth requirements, and often lack standardized antimicrobial susceptibility testing methods and interpretation criteria (Delannoy et al., 2022). Among the most frequently found bacteria in bivalve molluscs are those belonging to the Proteobacteria phylum (Pierce and Ward, 2019). In this phylum, there are found commensal bacteria (e.g., Bacillus spp., Vibrio spp., and Aeromonas spp.) and non-commensal bacteria (e.g., Shewanella algae). Most bacterial species’ prevalence in bivalves corresponds to the beach’s pollution degree (Silva dos Santos et al., 2022) and general water bacteriological quality (Verga et al., 2020). However, there are much more bacteria than “most interesting” human and animal pathogens. We observe bacterial genera being narrow pathogens of animals like Francisella spp. (Duodu et al., 2012; Charles et al., 2021; Seong et al., 2021) and species like F. halioticida, which is a dangerous pathogen of giant abalone (Haliotis gigantea) and Yesso scallops (Mizuhopecten yessoensis) (Charles et al., 2021). This particular species is now known as endangering the mussel cultures (Cano et al., 2022), causing economic losses and a decline in mussels. Some bacteria may also break the barrier between the animal and human-animal species and cause disease symptoms and outbreaks like Vibrio fluvialis (Ramamurthy et al., 2014; Onohuean et al., 2022).

The magnitude of antimicrobial resistance in many parts of the world has reached alarming levels and suggests that a “post-antibiotic era” may be a real possibility for the 21st century (Vidovic and Vidovic, 2020). Monitoring the pathogenic bacteria in seafood still needs more detailed and accessible programs. Table 1 presents programs that directly or indirectly refer to microbiota monitoring in the food/seafood in European countries or USA, only sometimes mentioning worldwide regulations (Food and Agriculture Organization [FAO], and World Health Organization [WHO], 2020a). The fundamental problem of most of these programs is the limited time of operation or incomplete data with a relatively small geographical coverage. Apart from those programs, there were also found regulations and directions aiming to control the quality of the seafood that included regulations of safety checks of microbiota, e.g., Europe Commission implementing regulation regarding imports of live, chilled, frozen, or processed bivalve molluscs, echinoderms, tunicates, marine gastropods for human consumption from USA (last updated 2022). Pathogenic bacteria species that were more likely reported and/or required to be reported by all sorts of programs and conventions in different countries were: E. coli, V. vulnificus, V. parahaemolyticus, and V. cholerae.

Nevertheless, some countries have developed programs to control seafood safety and quality (Table 1). The Food and Drug Administration (FDA) in the USA holds several large programs on microbiota presence and resistance in seafood directed explicitly at bivalves, e.g., NSSP (National Shellfish Sanitation Program run since 1925, available revisions from 2007-2019 every 2 years).¹ This program aims to promote and improve molluscs and other shellfish sanitation. In Europe, the leading organization contributing to the collection and awareness of the need for the collection of microbiota data is European Center for Disease Prevention and Control (ECDC, run since 1988, changed its name to recent one in 2010). ECDC holds programs such as EARS-Net (collect, and compare AMR data, analyze temporal trends in Europe, and provide AMR data for policy decisions) and monitors the Vibrio spp. growth in the Baltic Sea during the summer seasons (since 2013) (Table 1).

Bacterial communities are selected and suppressed by antibiotics delivered from other natural producers—microorganisms and antibiotics produced by humans. These last ones may affect marine and freshwater bacteria and might be a selective factor for antibiotic-resistance developed by many strains individually or acquired by HGT (horizontal gene transfer), conjugation and transformation mechanisms. Previous studies have reported that ARGs might be horizontally transferred by the facilitation of class 1 integron-integrase gene (intI1) on urban beaches by conjugating bacterial plasmids (Jang et al., 2021).

Heavy use of antibiotics in aquaculture may highly contaminate the water bodies; hence, detecting antimicrobial residues in the water environment is also significant. Similarly, producing sewages may result in AR genes’ pollution and introduce new variants of these genes into the marine environment. The importance of this growing problem can be illustrated by the emergence of plasmid-mediated colistin-resistance among human, animal, and zoonotic pathogens (Vidovic and Vidovic, 2020). The presence of the mcr-1 gene responsible for the resistance to colistin was observed by Valdez et al. (2022) (Table 2) in undefined Vibrio species and coliforms (E. coli and Citrobacter freundii) isolated from clams (Ruditapes decussatus and R. philippinarum). Samples were collected in Óbidos Lagoon (Caldas da Rainha, Portugal) in 2019, and other R. decussatus samples were collected in Ria Formosa (Algarve, Portugal). Antimicrobial susceptibility tests were performed by the disk diffusion method, according to the EUCAST guidelines against the antimicrobial: Colistin (10 μg), cefotaxime (30 μg), imipenem (10 μg), ciprofloxacin (5 μg), and meropenem (10 μg). The colistin-resistance gene was carried in the Vibrio spp. chromosomes. The mcr-2 gene was previously found by Lei et al. (2019) in V. parahaemolyticus VP181, which was obtained from a shrimp sample collected from Hong Kong, China. The gene of colistin-resistance was carried on a plasmid. Cherak et al. (2021) expressed concern that antibiotic-resistance is widely distributed in the aquatic environment. The authors collected data concerning the colistin-resistance data and proved that mcr genes are widely distributed in many geographical regions, types of environments and many Gram-negative bacterial species. Khedher et al. (2020) published work that analyzed 64,628 genome sequences belonging to 1,050 bacterial species and had 6′651 significant positive hits indicating the presence of mcr genes. Among others, MCR-1, 2 and 6 reveal that the putative progenitors of these MCR variants would be bacteria belonging to Moraxella, Enhydrobacter, Dichelobacter, Psychrobacter, Methylophilaceae, Limnobacter, and Vibrio genera. It is interesting to note that all these bacteria originate from water and/or soil environments. Also, a considerable number of mcr-9-like sequences were identified with 3′056 hits. Most of these bacterial genera, including, Stenotrophomonas, Vibrio, Aeromonas, Shewanella, Moraxella, Buttiauxella, and Salmonella, are bacteria from environmental sources (Vidovic and Vidovic, 2020).

A work published in 2022 by Delannoy et al. (2022) concerned the presence of ARGs and mobile genetic elements (MGE) in the marine environment, including seafood. The team tested 268 seafood isolates of the bacterial microflora for the presence of 41 ARGs and 33 MGEs, including plasmid replicons, integrons, and insertion sequences in Gram-negative bacteria. They show the occurrence of sul-1, ant(3″)-Ia, aph(30)-Ia, strA, strB, dfrA1, qnrA, and blaCTX-M-9 genes in Pseudomonas spp., Providencia spp., Klebsiella spp., Proteus spp., and Shewanella spp. They found that the occurrence of MGE may be associated with the seafood type and the environmental, farming, and harvest conditions. Their results corroborate the hypothesis that the incidence of antimicrobial-resistant bacteria (ARB) and ARG decrease with increasing distance from potential sources of fecal contamination. By high throughput real-time PCR system and array designed for antimicrobial resistance markers, they confirmed the presence of some ARGs like blaCMX-M-9 and aph(30)-Ia in Klebsiella spp., qnrA in Shewanella spp., and sul1 and ant(3″)-Ia in Pseudomonas spp. In 2019, Fresia et al. (2019) analyzed microbial communities harboring ARG and their characteristics. They collected samples from 20 localities around Montevideo (Uruguay). They found that ARGs covering resistance to sulfonamides, beta-lactams, aminoglycosides, phenicols, macrolides, and streptogramins were more prevalent in plasmids than in bacterial chromosomes. At the same time, ARGs covering resistance to tetracyclines, lincosamides, fluoroquinolones, and elfamycins were more frequently encoded in chromosomes. In 61% of identified integrons, Fresia et al. (2019) found cassette ARGs with conserved attC sites. These cassette genes primarily coded for multi-drug efflux pumps, but authors also found genes coding for carbapenemases (OXA family), GES extended-spectrum beta-lactamases (ESBLs), and aadA1 aminoglycoside nucleotidyltransferases, chloramphenicol acetyltransferases, and aac6-Ib amikacin resistance. This fact may support a hypothesis that ARGs carried by bacteria mostly present in sewages are potentially one of the most significant anthropogenic problems supporting the spreading of microbial resistance into marine bacterial species. Paschoal et al. (2017) indirectly confirmed it by finding carbapenemase genes in Aeromonas, Pseudomonas, Enterococcus, Klebsiella, and other genera isolated from recreational coastal waters, gene variants such as blaGES-16, blaIMP-16, blaOXA-370, and blaOXA-143 which were so far reported only (or predominantly) in clinical isolates from Brazil.

In the Pacific Ocean and the Antarctic, similar research done by Jang et al. (2022) displayed the presence of ARGs in transects including the West Sea of Korea, the Philippine Sea, the Western Equatorial Pacific Ocean, the Tasman Sea, the New Zealand sector of the Southern Ocean, and the Ross Sea. They found tetracycline resistance genes (tetA, tetB, tetBP, tetD, and tetZ), sulfonamide-resistance gene (sul1), one macrolide resistance gene (ermB), one β-lactam resistance gene (blaTEM), one quinolone-resistance gene (qnrD), and one multi-antibiotic resistance gene (oqxA). Overall, ARG abundance in the Southern Ocean was lower than in the Western Pacific Ocean but increased toward Antarctica. This pattern may be affected by human activities in the research stations (e.g., residence for research purposes or tourism) and incomplete wastewater treatment in the Antarctic environment.

Probably the part of bacteria carrying the ARGs may be finally deposited in all filtering organisms living in local seawaters, but even most disturbing is the knowledge that the geographical distribution of these genes seems to be continuous and unlimited. This fact especially concerns human and animal pathogens and emerging species with the potential to outbreak in human populations. It must be noted that the occurrence of antimicrobial-resistant bacterial species is not always a signal of pollution. Many species exhibit natural antibiotic-resistance, which is also expected in the natural marine environment. Miranda et al. (2013, 2015) presented the role of scallops hatcheries as a reservoir of antibiotic-resistant bacterial species. According to the presented data, the resistance of bacteria occurred even when no antibiotics were used.

Members of the genus Pseudomonas, which belongs to the γ-Proteobacteria, can colonize diverse habitats. The main fraction of Pseudomonas species described so far was assigned to terrestrial habitats (Manwar et al., 2004; Romanenko et al., 2005, 2008, 2015); however, there are also reports of species isolated from marine environments, e.g., P. glareae (Romanenko et al., 2015) or P. marincola (Romanenko et al., 2008), P. pachastrellae (Romanenko et al., 2005), and P. aeruginosa (Manwar et al., 2004). The species belonging to Pseudomonas, widespread in scallop hatcheries (Miranda et al., 2013, 2015), constitutes a significant group of antimicrobial-resistant species. Ramírez et al. (2022) published similar results for Mytilus species reared in different years and distances from salmon farms. Authors showed that Mytilus spp. microbiota differs depending on the time and proximity to salmon farms. They also showed that Pseudomonas spp. represent the majority of florfenicol-resistant isolates (89% in 2018 and 78% in 2019). The number of resistant isolates compared with several other species that acquired the resistance for florfenicol may suggest that Pseudomonas spp. are quick at obtaining the resistance to florfenicol and/or colonizing new hosts as members of the first wave of colonizing bacterial species. This hypothesis is supported by data in described publication showing the relative abundance of Pseudomonas spp. per location was <1% but represented the most resistant isolates. In the mentioned publication, along with Pseudomonas spp., only two more genera (Microbacterium spp. and Psychrobacter spp.) were represented by florfenicol-resistant isolates. Following the year, the number of florfenicol-resistant genera increased to four (Acinetobacter spp., Alcaligenes spp., Psychrobacter spp., and Serratia spp.).

Pseudomonas aeruginosa is the third most pathogenic Gram-negative bacteria capable of causing severe diseases (Nolan and Behrends, 2021). This species may be a serious issue in patients with ventilator-associated pneumonia, urinary/peritoneal dialysis catheter infections, bacterial keratitis, cystic fibrosis, and burn wounds (Nolan and Behrends, 2021). P. aeruginosa causes around 13–19% of hospital-acquired infections (HAIs) in the USA (Raman et al., 2018). This species is primarily a waterborne pathogen, thriving in moist habitats and water resources like outlets of sewage treatment plants, from where it can be further spread to the marine environment (Luczkiewicz et al., 2015). In 1975, Denis (1975) observed P. aeruginosa in over 70% of mussels from the Marennes–Oleron Basin (France). Maravić et al. (2018) analyzed Pseudomonas spp. by combining PCR detection of acquired genes and resistance-nodulation-cell division (RND) efflux, studying multifactorial resistant traits of 108 P. aeruginosa isolates recovered from wild-growing Mediterranean mussels (Mytilus galloprovincialis) in Croatia. The multi-drug resistance to at least three pharmaceuticals from three different classes was detected in 17 isolates (15.7%). The most common (8.3% of isolates) profile included resistance to piperacillin (PIP), piperacillin-tazobactam (TZP), ceftazidime (CAZ), cefotaxime (CTX), and aztreonam (ATM). These substances represented penicillins, β-lactam/β-lactamase inhibitor combinations, cephems, and monobactams. Generally, 23.14% of isolates were resistant to at least one pharmaceutical. Also, Udoekong et al. (2021) examined 117 clams, 88 oysters, and 136 periwinkles. The authors found P. aeruginosa strain JB2 in 7.4% of tested molluscs, P. aeruginosa strain N15-01092 in 2.2%. Other species of Pseudomonas found in examined samples were P. xiamenensis (3.7%) and P. anguillisceptica 4,029 (2.2%). Generally, 44 isolates of Pseudomonas species (100%) were resistant to ceftriaxone, cefpodoxime, ceftazidime, cefepime, imipenem, and chloramphenicol. Unfortunately, the authors did not check ARGs’ presence, but the appropriate genes like cmlA and integrons were undoubtedly present. The literature review did not provide enough data to compare the antibiotic-resistance of environmental isolates of P. aeruginosa and other species with terrestrial isolates, although the Pseudomonas clade probably has a water environment origin. Generally, Laborda et al. (2021) considered P. aeruginosa as the species that succeeded in colonizing multiple hosts by relying on its large genome, and the species’ virulence and resistance determinants evolved in natural ecosystems.

Bacteria belonging to the genus Aeromonas are ubiquitous in marine environments, and Aeromonas spp. has held the title “emerging foodborne pathogen” (Janda and Abbott, 2010; Chuang et al., 2011; Abdel-Latif and Khafaga, 2020; Fernández-Bravo and Figueras, 2020; de Silva et al., 2021). Aeromonas spp. is a Gram-negative, non-spore-forming rod-shaped, facultatively anaerobic bacteria easily found in aquatic environments. Members of the genus Aeromonas are potential pathogens to many hosts, such as fish, amphibians, reptiles, mammals, and humans (Janda and Abbott, 2010; Fernández-Bravo and Figueras, 2020). Aeromonas spp. may cause various human infections, such as gastroenteritis, soft tissue infection, septicemia, hepatobiliary tract infections and occasionally pleuropulmonary infections, indwelling device-related infections, meningitis, peritonitis, and haemolytic uremic syndrome (Chuang et al., 2011). Among Aeromonas species that cause fish diseases, A. hydrophila has been identified as one of the most dangerous pathogens causing mortality outbreaks in diverse cultured fish species (Abdel-Latif and Khafaga, 2020). Among pathogens associated with human diseases, A. caviae, A. veronii, and A. hydrophila biovar sobria were isolated from mussels, scallops, and oysters (de Silva et al., 2021). These species Aeromonas spp. can grow relatively uninhibited in food during refrigeration under a broad range of pH and NaCl concentrations and in various packaging atmospheres. Given its high prevalence in seafood included in many RTE (Ready-To-Eat) seafood meals, the significance of Aeromonas spp. as a potential foodborne pathogen and a food spoilage organism increases. Strains of several Aeromonas species have shown spoilage potential by producing spoilage-associated metabolites in various seafood products (Hoel et al., 2019). Another point is the presence of genes encoding exotoxins, such as haemolysin (hlyA), aerolysin (aerA), cytotoxic heat-labile enterotoxin (act), cytotonic heat-labile enterotoxin (alt), cytotonic heat-stable enterotoxin (ast), and Shiga-like toxins (stx). Mentioned exotoxins are well-known virulence factors related to clinical symptoms during Aeromonas infection. A problem is deepened by the simultaneous harboring of AR genes. Maravić et al. (2013) found isolates of Aeromonas spp. co-producing blaCTX-M-15, blaSHV-12, blaPER-1, and blaFOX-2 in Mediterranean mussels (Mytilus galloprovincialis) from Croatia (Table 2). Generally, A. caviae, and A. hydrophila displayed full phenotypic resistance to ampicillin; 86% were resistant to cefotaxime, 68% to ticarcillin, and 63% to aztreonam. Hossain and Heo (2022) found in Mytilus coruscus from South Korea, 33 Aeromonas species are carrying blaTEM (27.3%), blaSHV (24.2%), blaCTX-M (24.2%), tetB (18.2%), tetE (15.2%), and intI1 genes (27.3%). Their results suggest that mussels can serve as a reservoir of multi-drug resistant Aeromonas spp. Manila clams (R. philippinarum) purchased on the market in South Korea also contained A. hydrophila, A. media, A. veronii, A. allosaccharophila, and A. caviae resistant to various antibiotics (Sanz-Lazaro and Sanchez-Jerez, 2020). Isolates of Aeromonas spp. harbored seven resistance genes (blaTEM, blaSHV, blaCTX-M, tetB, tetE, qnrS, and StrA-strB) and class 1 integron [intl1, aac(6’)-Ib] in various combinations. The most universal was the β-lactamase-resistance complex of genes (bla) (Table 2) (Dahanayake et al., 2019).

Besides the prevalent pathogens from anthropogenic and animal pollution, marine bivalves can be colonized by Vibrio spp. This group of bacteria consists of species living in seawater and being pathogens both to bivalves and humans. In marine environments, metazoans constitute habitats for bacteria of the Vibrionaceae family (vibrios). These γ-proteobacteria are ubiquitous in marine and brackish environments representing one of the most abundant culturable fractions of the marine microbial community (Ceccarelli et al., 2019). The most known species are V. cholerae, V. vulnificus, V. parahaemolyticus, and V. alginolyticus, but other species are also recognized as associated with food consumption. V. vulnificus and V. parahaemolyticus are seasonally present in molluscs (Lorenzoni et al., 2021) V. fluvialis, V. mimicus, V. metschnikovii, V. metoecus, and V. furnissii are related to foodborne diseases (Ceccarelli et al., 2019). Among these vibrios, V. fluvialis is an emerging human pathogen (Ramamurthy et al., 2014) related to diarrhoeal outbreaks. Other pathogenic species are V. cincinnatensis and V. carchariae, whose significance as human pathogens remains determined as agents causing several types of vibriosis. About 13 species of Vibrionaceae have been reported to cause several human diseases (Hou et al., 2011; Ramamurthy et al., 2014; Cheng et al., 2015). At the same time, Vibrio spp. frequently coexists with Pseudomonas spp. and Aeromonas spp. species, which are another group of potential human pathogens. In Benin City (Nigeria), Igbinosa (2016) found isolates of V. fluvialis, V. vulnificus, V. parahaemolyticus and unidentified Vibrio spp. in four water ponds by collecting fish and water samples. These isolates were resistant to β-lactams, macrolides, quinolones, norfloxacin, sulphonamides, nitrofurantoin, aminoglycoside, tetracyclines, and phenicol derivatives. Isolates represented a broad spectrum of resistance, from 0% of isolates resistant to ciprofloxacin to 100% resistant to tetracycline. There is no reason to exclude the possibility that vibrios cannot infect the edible bivalves in the water. Many species of cultured or wild molluscs accompany fish aquacultures serving as potential filtration systems or just as free-living animals, settling the environment rich in food particles. According to Vu et al. (2018), the distribution of Vibrio spp. in different species (blue mussels, venus clams, razor shells, cockles, and white leg shrimps) from retail food found in Berlin included 40.8% of blue mussels, 100% of cockles, and 93.3% of venus clams and 27.3% of razor shells. Similar results were published by Roque et al. (2009) in the case of four species of cultured molluscs on the Spanish coast (Mytilus galloprovincialis, Crassostrea gigas, Ruditapes decussatus, and Ruditapes philippinarum). In 4.08% of samples, Obaidat et al. (2017) found V. parahaemolyticus isolates resistant to chloramphenicol and cefotaxime in seafood from Yemen, India and Egypt. Besides this, 100% of isolates were resistant to colistin sulfate, kanamycin, and neomycin. In hard-shelled mussel (Mytilus coruscus) and tiger shrimp (Penaeus monodon) purchased in South Korea, Ashrafudoulla et al. (2019) found isolates of V. parahaemolyticus resistant to erythromycin, vancomycin, kanamycin, ciprofloxacin, clindamycin, and other antibiotics. In Poland (Lopatek et al., 2015) found that 17.5% of 400 tested samples of mussels, clams, oysters, and scallops were positive for the presence of V. parahaemolyticus. Among positive isolates, the authors found resistance to β-lactams (56%), ciprofloxacin (1.6%), streptomycin (45%), and gentamicin (7%). The food represented by bivalves is not present in the Baltic Sea, and all specimens were imported from the Netherlands, Italy, Norway and France. Dubert et al. (2016) noted that chloramphenicol had been banned in food animals, including aquaculture, because it has been associated with aplastic anemia. However, the authors noticed that experimental hatchery aquacultures still use this antibiotic due to its broad antimicrobial spectra. They analyzed samples from The Centro de Investigacións Mariñas (Spain), where seven species of clams were produced, and found that among 121 isolates of Vibrio spp. representing V. hemicentroti, V. splendidus, V. kanaloae, V. neocaledonicus, and V. jasicida, of non-human-pathogenic bacteria, 19 were resistant to chloramphenicol (CHL), tetracycline (TET) and amoxicillin (AMX), and nine were resistant to chloramphenicol (CHL) and streptomycin (STR). In 28 isolates of AGR genes, they confirmed the presence of the gene responsible for the resistance to chloramphenicol. Moreover, they demonstrated that antibiotic-resistance genes could be transferred to E. coli and other marine bacteria from Vibrio spp. In light of information about the possibility of transferring the ARGs among bacterial clades (Ellabaan et al., 2021), it can be highly possible that marine vibrios can serve as a potential reservoir for antibiotic-resistance genes (Table 2) for many emerging bacterial species. Besides being the reservoir of AR, a secondary problem generated by this genus is the number of exotoxins secreted by vibrios. Even bacteria from this purely marine genus can produce exotoxins (ciliostatic factors and hemolysins), which cause deciliation and injure tissues. According to West (West, 1989), the increase of Vibrio spp. number (up to an infective dose) can occur as water temperatures rise seasonally, which facilitates the growth and rising concentration of bacteria on/in higher animals, such as chitinous plankton, or accumulation of the bacteria by shellfish and other seafood. Pathogenic Vibrio species must elaborate a series of virulence factors to elicit human disease. Activities predisposing to diarrhoeal and extraintestinal infections include ingesting seafood and occupational or recreational exposure to natural aquatic environments, especially warm ones with temperatures rising above 20°C. Iwamoto et al. (2010), analyzing V. parahaemolyticus and V. vulnificus outbreaks, noticed that cases of Vibrio spp. infections have a marked seasonal distribution. Most occur during summer and early fall, corresponding to the period of warmer temperatures. In Japan, V. parahaemolyticus is one of the leading causes of foodborne gastroenteritis; annually, 500–800 outbreaks affecting more than 10,000 people are reported (Food and Agriculture Organization [FAO], and World Health Organization [WHO], 2020b). According to FDA data, between 1973 and 1991, all occasional cholera cases related to raw or undercooked shellfish consumption were associated with a non-O1 biotype of V. cholerae (Kaysner et al., 2012).

Shewanella is the sole genus belonging to the family of marine bacteria Shewanellaceae. As far as four species of this genus are considered dangerous for humans: S. algae, S. putrefaciens, S. haliotis, and S. xiamenensis (Vignier et al., 2013; Cimmino et al., 2015; Tena et al., 2016; Huang et al., 2018). These species may cause bacteremia, Fournier’s gangrene, empyema, pneumonia, and intracranial infections (Yousfi et al., 2017). This family is represented by widespread species and extremophiles living in habitats with a broad range of temperatures and high pressures (Abboud et al., 2005; Lemaire et al., 2020). For example, S. loihica from thermal vents can grow at 4–42°C. The taxon includes species isolated from around all oceans, including Antarctic subglacial and arctic marine waters, tropical coastlines, deep oceanic trenches, and various fish and shellfish. Their survival in various ecological niches is due to their impressive physiological and respiratory versatility (Lemaire et al., 2020). Some strains have been isolated in particular geographic areas, suggesting a putative specificity, while other isolates were found in many distant zones. One of the most spread species, often related to seafood, is S. putrefaciens, the species responsible for food spoilage and disease outbreaks (Liu et al., 2006; To et al., 2010; Janda and Abbott, 2014). Many consumable products have yielded Shewanella species upon laboratory analysis. Among others, the analysis of oyster samples from Delaware Bay showed that concentrations of Shewanella (presumptive) in oyster meats ranged from non-detectable levels to ≥400 CFU/g per sample (Richards et al., 2008).

Members of this genus are generally susceptible to third- and fourth-generation cephalosporins, carbapenems, β-lactamase inhibitor combinations, aminoglycosides, chloramphenicol, erythromycin, aztreonam, and quinolones (Table 2) (Kang et al., 2013; Cimmino et al., 2015; Zago et al., 2020).

Zago et al. (2020) checked resistance against antibiotics of Shewanella algae. The authors collected water samples along the Veneto coastline of the Adriatic Sea, Lugi di Varano (Foggia) and the open sea. They found isolates of S. algae resistant to β-lactams (blaOXA-55-LIKE, ampC), tetracyclines (tetR, tet34, and tet35), fluoroquinolones (qnrA3, qnrA7, mepAB—multi-drug efflux pump, mfpA—qnr homolog, emrD- multi-drug efflux pump, and mtdN—multi-drug resistance protein), polymyxin (eptA), chloramphenicol (cat). Also, Delannoy et al. (2022) found Shewanella spp. (S. indica, S, haliotis, S. algae, and unidentified Shewanella spp.) isolates from shellfish resistant to quinolone and possessing the qnrA gene on a plasmid. In Asian hard clams (M. lusoria), Lee et al. (2019) found isolates identified as S. algae SYT4 harboring β-lactamase encoding blaOXA-55 responsible for carbapenem resistance. Authors suggested that environmental S. algae could be a potential class D β-lactamase gene source.

Besides blaOXA-55, authors also identified the dfrA3 gene associated with resistance to sulfonamide-trimethoprim and genes responsible for resistance to fluoroquinolone (mfd, qnrA3). Due to the high zoonotic potential and wide distribution, Shewanella spp. are found practically in most seafood and marine environments. The characteristics of their genomes (Nuñez et al., 2022) may suggest that this genus can intensively transfer genetic information, including AR genes. Nuñez et al. (2022) found 52% of analyzed genomes of Shewanella spp. with conservative integrase genes (intI). They showed that Shewanella spp. could acquire and disseminate integrase genes that may lead to the emergence of novel mobile integrons. The substantial diversity of gene cassettes found in the variable regions and their association with MGEs may imply the host’s constant evolution and adaptation. This relation responds to environmental niche changes and the composition of each microbial community. Furthermore, it must be considered that antimicrobial-resistance gene cassettes found in hospital settings can be recruited from environmental chromosomal integrons. The above characteristic may suggest the solid potential ability to adapt to new hosts and new environments, and the plasticity of that genus fully justifies treating this species as an emerging organism most dangerous to humans and animals.

Escherichia coli is one of the most popular and widespread bacteria in seawater, as it is a significant member of the bacterial microbiota community in the gut of many animals and humans (Michalska et al., 2021). There is a possibility of transmission of pathogenic E. coli strains to the seas from land animal feces and human feces, especially during periods of intense rainfall (Lunestad et al., 2016). Consumption of raw or inadequately cooked mussels poses a potential risk for consumers because of E. coli infections (Feng et al., 2020). According to the current EU regulations [Regulation (EU) 2017/625 of the European Parliament and of the Council, 2017], mussel sampling sites must be classified according to their suitability for microbiological and chemical water quality (De Witte et al., 2014). The fecal indicator organism (FIO) E. coli is frequently used as a general indicator of sewage contamination and for evaluating the success of mollusc cleaning (depuration) processes. Depending on the content of E. coli in mussels, all localities should be affiliated based on Most Probable Numbers (MPN) as Class A (<230 MPN E. coli/100 g mussel), B (<4,600 MPN E. coli/100 g mussel), or C (4,600–46,000 MPN E. coli/100 g mussel) areas (Grevskott et al., 2016). Most of the research on the effectiveness of depuration has been conducted using oysters, as these are usually eaten raw. In 2019, Martin et al. (2019) found Shiga-toxin-producing E. coli (STEC) in Norwegian bivalves (1.1%). This percentage in the work of other authors was higher in shellfish, ranging from 3.5% in France (Gourmelon et al., 2006) to 6.1% in Morocco (Bennani et al., 2011). The relatively low isolation rate of STEC strains does not exclude the presence of stx-carrying bacteriophages in the samples, which pose a threat by playing an essential role in the evolution of STEC strains but also can transfer stx genes from non-pathogenic strains E. coli (Krüger and Lucchesi, 2015).

The multi-drug resistance of E. coli has become a worrying problem (Table 2). E. coli is internally susceptible to almost all clinically relevant antimicrobials (the ability to accumulate resistance genes mainly through horizontal gene transfer). The most complicated mechanisms in E. coli are the acquisition of genes encoding broad spectrum β-lactamases (broad-spectrum cephalosporin resistance), carbapenemases (carbapenem resistance), resistance to (aminoglycosides), plasmid-mediated quinolone resistance (PMQR), and mcr genes(conferring resistance to polymyxins) (Poirel et al., 2018).

Of all Gram-positive bacteria characteristics for bivalves, one is definitively typical for the marine environment but may be pathogenic to humans. The Nocardia genus is a prevalent member of the molluscs microbiota. This genus can be responsible for a broad spectrum of human diseases. Species like Nocardia nova, N. farcinica, N. cyriacigeorgica, N. brasiliensis, and N. abscessus are responsible for such cases as invasive pulmonary infection, disseminated infection, or brain abscess; 20% present as cellulitis. From the marine environment, the most known species is N. crassostrea, responsible for Pacific oyster nocardiosis observed in North America from the Strait of Georgia, British Columbia, to California and Japan (Matsushima Bay). Carella et al. (2013) observed this disease in Mediterranean bivalves first time. In 2013 (Taj-Aldeen et al., 2013) and 2016 (Igbaseimokumo et al., 2016), two outbreaks of N. crassostrea were observed in immunocompromised patients independently. No comprehensive information about genes responsible for antibiotic-resistance or antibiogram analysis was available. Igbaseimokumo et al. (2016) added information about antibiogram results. N. crassostrea, in this analysis, was sensitive to beta-lactams, including carbapenems but was resistant to lincosamides (clindamycin), vancomycin, and teicoplanin. This observation suggests the constitutive mechanism of defense against mentioned groups of antibiotics if the environmental origin of N. crassostrea is considered. In the cases described by Taj-Aldeen et al. (2013), the authors also checked the antibiotics-resistance of N. crassostrea and found one isolate resistant to linezolid (oxazolidinones group) and moxifloxacin (fluoroquinolones group). Still, they found the tested strain’s sensitivity to beta-lactamases (including cefotaxime and imipenem) and aminoglycosides (amikacin).

Symptoms of botulism include fatigue, dizziness, double vision, progressive difficulties in speaking and swallowing, shortness of breath, and muscle weakness (Aberoumand, 2010). Most seafood-related botulism is associated with inadequate processing, temperatures or maintenance (National Advisory Committee on Microbiological Criteria for Foods [NACMCF], 2008; Hudson and Lake, 2012). The occurrence of another Clostridium sp. in shellfish, C. difficile, raises concern because spores can survive the cooking temperatures given that shellfish is often consumed poorly cooked or raw. For example, C. difficile has been isolated from edible bivalve molluscs in Spain and Italy (Agnoletti et al., 2019; Candel-Pérez et al., 2020). C. difficile collected from 702 molluscs harvested in the North Adriatic Sea (Agnoletti et al., 2019) were detected in 16.9% of all bivalves specimens. Isolates showed microbiological resistance against clindamycin (17%), erythromycin (23%), rifampicin (8.8%), and moxifloxacin (10.6%). All isolates were susceptible to metronidazole, and one showed MIC> ECOFF for vancomycin. C. difficile strains showed a wide variety in PCR-ribotypes, most already detected in other animals or known as highly virulent and epidemic in humans. In Spain, Candel-Pérez et al. (2020) analyzed 129 mollusc samples from different fishmongers and grocery stores in Murcia. C. difficile was isolated from 8.53% (11 specimens per total 129) of the investigated molluscs. Four C. difficile isolates harbored genes for producing toxins A and B. Examining mussels for antibiotic-resistant strains of C. difficile should be another essential aim of seafood monitoring.