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Prevalence, virulence factors, and antibiotic resistance of Staphylococcus aureus in seafood products
BMC Infectious Diseases volume 25, Article number: 554 (2025)
Abstract
Introduction
Seafood contamination by bacteria is a pervasive issue, contributing to foodborne illnesses. This study investigates the prevalence, virulence factors, and antibiotic resistance in Staphylococcus aureus (S. aureus) isolated from various seafood products.
Methods
A total of 460 samples, including fresh, smoked, salted, and dried fish, as well as oysters, crab, lobster, and shrimp, were collected in Shahrekord, Iran. S. aureus isolation followed ISO standards, with confirmation via PCR for 16S rRNA and nuc genes. Antibiotic susceptibility was determined via Kirby-Bauer disc diffusion, while PCR detected enterotoxin and antibiotic resistance genes.
Findings
S. aureus was prevalent in all seafood types, with 27.83% positivity. Methicillin-resistant S. aureus (MRSA) was found in most samples, except oysters and crabs. Virulence genes were common, with Sea, Seb, Sed, Sec, and See being the most prevalent. High resistance to penicillin G and ampicillin (70%- 100%) was observed. Resistance varied for other antibiotics, with linezolid showing 100% susceptibility. The mecA gene was present in over 50% of isolates, with blaZ being the most detected resistance gene.
Conclusion
The study underscores the need for Good Hygiene Practices (GHP) in seafood processing to mitigate S. aureus transmission. While specific comparisons between sample types were limited, the findings emphasize the prevalence of virulence factors and antibiotic resistance in seafood-associated S. aureus, highlighting the importance of vigilant food safety measures.
Introduction
Seafood plays a vital role in global food security, serving as a primary source of protein and essential nutrients for millions of people worldwide [1,2,3,4]. Iran, with its extensive coastline, has a diverse seafood industry, producing a variety of fish and shellfish, including shrimp, trout, caviar, sturgeon, tuna, and sardines [5].
Despite its nutritional benefits, seafood is highly perishable and susceptible to bacterial contamination at multiple points in the supply chain, including harvesting, processing, transportation, and storage [1,2,3,4]. Among foodborne pathogens, Staphylococcus aureus (S. aureus) is a major concern due to its ability to cause food poisoning and severe infections, particularly when antibiotic-resistant strains are involved [6].
S. aureus is a Gram-positive, facultatively anaerobic bacterium capable of producing numerous virulence factors, including enterotoxins, toxic shock syndrome toxin (TSST), hemolysins, and proteases [7,8,9].
These virulence determinants contribute to its pathogenicity, making it a leading cause of foodborne illnesses worldwide. Staphylococcal food poisoning results from the ingestion of enterotoxins, which are heat-stable and resistant to food processing methods. Clinical symptoms include nausea, vomiting, abdominal cramps, and diarrhea, often occurring within hours of consumption [9,10,11,12,13,14].
A particularly concerning aspect of S. aureus is its ability to develop resistance to multiple antibiotics. The emergence of methicillin-resistant S. aureus (MRSA) has significantly complicated treatment options, as MRSA strains exhibit resistance not only to methicillin but also to various beta-lactam antibiotics. The mecA gene, which encodes an altered penicillin-binding protein (PBP2a), confers methicillin resistance and is widely used as a molecular marker for MRSA detection [7, 11, 12]. Additionally, the nuc gene, encoding a thermonuclease enzyme, serves as a highly specific marker for S. aureus identification.
Previous studies in Iran have documented the presence of enterotoxigenic S. aureus in fresh shrimp and fish, yet comprehensive data on its virulence factors and antibiotic resistance in a broader range of seafood products remain scarce [15,16,17]. However, seafood is consumed in a variety of ways, including grilled, fried, and stewed [10]. Unlike previous research, which often focused on limited sample types or specific aspects of S. aureus contamination, this study provides a systematic analysis of the prevalence, virulence profiles, and antibiotic resistance patterns of S. aureus across multiple seafood varieties. By integrating molecular and phenotypic approaches, this research contributes to a more thorough understanding of the pathogen’s risks and informs strategies for mitigating contamination and antimicrobial resistance in the seafood industry.
Method
Sampling
This cross-sectional study was conducted in Shahrekord, Iran. The sample size (460 samples) was determined using an epidemiological sample size calculator, based on an expected prevalence of S. aureus from prior studies, a 95% confidence level, and a precision of 5%. The samples were collected from seafood sales points and local markets in Shahrekord under aseptic conditions between 2013 to 2014. Fresh seafood was inspected for visual indicators of freshness, such as bright eyes, firm texture, and clean odor. Processed samples (salted, smoked, dried) were evaluated for proper packaging and absence of spoilage signs. Vendors reported that fresh fish and seafood were supplied within 24–48 h of collection or processing. Salted, smoked, and dried fish samples were stored by vendors for up to one week. Sampling included the following categories: Fresh fish (70), Smoked fish (70), Salted fish (70), Dried fish (50), Oysters (31), Crab (29), Lobster (58), and Shrimp (82). All samples were handled aseptically and transported to the microbiology laboratory in insulated containers filled with ice. Transportation time ranged from 2 to 4 h to maintain sample integrity.
Isolation and identification of S. aureus and confirmation of S. aureus by PCR
Isolation of S. aureus was performed following ISO 6888–1 and ISO 6888–2:2003 standards using Baird-Parker Agar [18]. Suspected colonies were identified by morphological characteristics and subjected to coagulase and DNase tests. Strains testing positive for both coagulase and DNase were further characterized.
Confirmation of S. aureus by PCR
DNA was extracted using the PrepMan® Ultra Reagent (Applied Biosystems, UK) as per the manufacturer’s instructions. DNA purity was assessed using the ratio of absorption at 260 nm and 280 nm. An optical density (OD) ratio of 1.8–2.0 indicated high DNA purity. Confirmation of the Staphylococcus genus was conducted by amplifying the 16S rRNA gene (597 bp), and species confirmation of S. aureus was achieved by detecting the nuc gene (320 bp) [19]. The PCR was performed using an Agilent SureCycler 8000 under the following conditions: initial denaturation at 94 °C for 3 min; 34 cycles of denaturation at 94 °C for 30 s, annealing at 60 °C for 30 s, and extension at 72 °C for 30 s; followed by a final extension at 72 °C for 5 min. PCR products were resolved on a 1.5% agarose gel, stained with ethidium bromide, and visualized under UV light using a Gel Doc system (BioRad, USA).
Antimicrobial susceptibility testing
The Kirby-Bauer disc diffusion method was used to assess the antibiotic susceptibility of S. aureus isolates. Antibiotic-impregnated discs were placed on Mueller–Hinton agar inoculated with the isolates. Zones of inhibition were measured and interpreted following Clinical and Laboratory Standards Institute (CLSI) guidelines [20]. The antibiotics tested included ampicillin (10 µg), penicillin G (10 µg), amoxycillin-clavulanic acid (30 µg), cefoxitin (30 µg), ceftazidime (30 µg), cefepime (30 µg), kanamycin (30 µg), streptomycin (10 µg), amikacin (30 µg), gentamicin (10 µg), norfloxacin (10 µg), ciprofloxacin (5 µg), quinupristin (15 µg), erythromycin (15 µg), telithromycin (15 µg), tetracycline (30 µg), clindamycin (2 µg), chloramphenicol (30 µg), trimethroprim-sulfamethoxazole (25 µg), linezolid (30 µg), rifampicin (5 µg), vancomycin, fusidic acid (10 µg) and fosfomycin (200 µg). Results were recorded after overnight incubation at 37 °C.
The antimicrobial agents in the study are grouped based on their mechanisms of action. β-Lactams target bacterial cell walls, Aminoglycosides inhibit protein synthesis, Quinolones and Fluoroquinolones block DNA replication, Macrolides and Lincosamides inhibit protein synthesis by binding ribosomes, Tetracyclines disrupt protein synthesis, Phenicols also inhibit protein synthesis, Sulfonamides block folic acid synthesis, Oxazolidinones inhibit protein synthesis, and Glycopeptides prevent cell wall formation. Fusidic acid, Fosfomycin, and Rifampicin have distinct mechanisms, targeting protein synthesis, cell wall synthesis, and RNA synthesis, respectively. This categorization helps in understanding drug actions and resistance patterns [21].
Detection of antibiotic resistance genes, virulence genes and SCC mec typing by PCR
Resistance genes (blaZ, mecA, ermA, ermB, ermC, aacA-aphD, tetK, tetM, msrA, vatA, vatB, vatC, linA) and toxin genes (sea, seb, sec, sed, see, pvl, Hla, hlb, fnbA, tsst) were detected among S. aureus isolates by PCR. The mecA gene (279 bp), a gold standard for MRSA confirmation, was detected [22]. To identify the five primary known types of SCCmec, a multiplex PCR was conducted using four sets of primers [23].
The PCR was performed in a 25-µl reaction mixture containing 12.5 µl of 2X master mix (0.04 U/µl Taq DNA polymerase, reaction buffer, 3 mM MgCl2 0.4 mM of each dNTP), 0.4 µM of each primer, and 2 µl of template DNA. For the negative control, sterile water was added instead of nucleic acids. PCR was run as described by the authors. Oligonucleotide primers of the toxin genes, and antibiotic resistance genes and the product size are indicated in Table 1.
Statistical analysis
Data were analyzed using SPSS version 22.0 (IBM Corp., USA). Prevalence rates were calculated as percentages.
Findings
Prevalence of S. aureus in seafood samples
The prevalence of S. aureus in the analyzed seafood samples is summarized in Table 2. The findings indicate that S. aureus was detected in all types of seafood, with an overall prevalence of 27.83%. The highest contamination rates were observed in smoked fish (64.29%) and salted fish (55.71%), while the lowest prevalence was recorded in oysters (3.23%).
Methicillin-resistant S. aureus (MRSA) was detected in all seafood categories except oysters and crabs, with an overall prevalence of 5.21% among the S. aureus isolates. No significant seasonal variations in S. aureus prevalence were observed across sample matrices (p > 0.05).
Distribution of virulence genes
Table 3 presents the distribution of virulence genes among S. aureus isolates. All analyzed genes were detected except hlβ and fnbB, which were absent in all isolates. The most frequently detected genes were sea (71.87%), seb (60.15%), sed (50.78%), and sec (47.65%), whereas pvl and hlα were each found in only one isolate (0.78%).
Antimicrobial resistance patterns
The antimicrobial resistance profile of S. aureus isolates is detailed in Table 4. High resistance rates were observed against β-lactams, particularly penicillin G (89.74–100%) and ampicillin (62.5–100%). Resistance to tetracycline was also notable, ranging from 50 to 100% across different seafood types. Resistance to aminoglycosides varied, with the highest rates observed for kanamycin (50–73.33%) and gentamicin (30–73.33%). Ciprofloxacin resistance was prevalent, particularly in salted fish (94.87%) and dried fish (85.71%).
Prevalence and detection of nuc and mecA of S. aureus isolates
Table 5 presents the detection rate of nuc and mecA among S. aureus isolated from samples.
The results indicated more than 50% (57.36%) of S. aureus isolated from this study carry MecA gene and almost 50% (49.61%) carry nuc gene.
Resistance genes among S. aureus isolates
Table 6 presents the resistance genes detected among S. aureus isolates. All the genes detected were found. The results indicate that blaZ (93,8%) was the resistance gene the most detected followed by tetM (59,69%) and ermA (43,41%).
Distribution of antibiotic resistance genes in S. aureus strains
Table 7 presents the distribution of antibiotic resistance genes in S. aureus strains isolated from samples. All the genes were detected in isolates from smoked and salted fish. The results indicate that resistance genes were less found among isolates from oyster and crab.
Distribution of pvl gene in S. aureus strains isolated
Table 8 presents the Distribution of PVL gene in S. aureus strains isolated from samples. The results showed that pvl gene was absent from isolates from all type of samples excepted isolates from smoked and salted fish. Among the isolates, three were positive for the pvl gene. This finding underscores the sporadic presence of this toxin-associated gene in the study population.
Distribution of SCCmec types in S. aureus strains isolated
Table 9 presents distribution of SCCmec types in S. aureus strains isolated from samples. All SCCmec types were detected among S. aureus strains excepted IVd type.
Frequency of toxin genes among different MRSA sources
Table 10 presents the frequency of toxin genes among different MRSA sources. All the toxin genes detected were found among MRSA isolates recovered from smoked fish and salted fish.
Frequency of toxin genes among different SCCmec types in MRSA isolates
Table 11 presents the frequency of toxin genes among different SCCmec types in MRSA isolates. From this table, sea, seb, sec and sed were the most found genes across the SCCmec types.
Discussion
S. aureus, including methicillin-resistant S. aureus (MRSA), is a significant contributor to zoonotic diseases transmitted from seafood to humans. Transmission can occur through close contact, handling, or consumption of seafood contaminated with this bacterium [14]. Environmental factors during harvesting, processing, storage, and cross-contamination during handling and transportation all contribute to the presence of S. aureus and other pathogenic bacteria in seafood [16, 22, 28].
The results about the prevalence of S. aureus and MRSA in seafood products showed that S. aureus was isolated from all different types of seafood. A total of 27.83% of the samples were positive. Lower rate has been reported 19.8% for the raw fish in Korea [28]. In India, a recent study observed that 15% of the total samples were screened positive for S. aureus [22]. These prevalence were lower than the prevalence (34%) indicated by Arfatahery et al., (2016) [16] among seafood samples (shrimps, fish) in Iran. Similarly, 47.27% of fresh fish samples were found to be contaminated in a study in Jordan [29]. High prevalence rates in fish were reported in Japan (87%) and Northwest Spain (43.5%) [30, 31]. The varying and elevated incidence rates of S. aureus discovered in this study and others may be explained by discrepancies in the care and sanitation procedures implemented by fish handlers who are symptomatic or asymptomatic [32]. While fresh seafood may be more susceptible to contamination during handling and transportation, smoked or salted fish may harbor unique bacterial communities due to the preservation methods employed.
Compared to other food products, fish and fishery items are largely handled manually in Iran [15]. The contamination could also have potentially stemmed from either contaminated freezing systems or improper transfer of aqua products during transportation from their source to their destination. Factors that can contribute to increased contamination levels in such products include delays in transport, failure of workers to adhere to food hygiene standards, inadequate storage conditions such as inappropriate temperature levels, and buildup of seafood [16].
Fish and shellfish do not normally harbor MRSA in their microbiota. The presence of MRSA in these products is likely due to contamination from the environment, either from the harvest area or from mishandling by fish handlers, processors, or consumers before consumption [22]. The prevalence of MRSA in fish and fishery products has been steadily increasing in various parts of the world [32, 33]. Compared to the clinical sector, the prevalence of methicillin-resistant S. aureus (MRSA) in the food sector is relatively low. However, their presence in seafood is a significant public health concern. In the present study, Methicillin resistant S. aureus (MRSA) was found in all different types of seafood excepted oysters and crabs samples. Among collected samples, 5.21% of the isolates were found to be methicillin resistant. Similarly, Sivaraman et al. (2022) [22] observed that 3.0% of the total samples were screened positive for MRSA. During a global comparison, the prevalence of MRSA in seafood products showed considerable variability, ranging from very low to high percentages. In Salvador, Bahia, Brazil, higher incidences of MRSA, amounting to 30.0% and 22.2%, were detected in raw fish and prepared fishery foods in public hospitals, respectively [33]. In Assam, India, a study reported higher level of MRSA (50%) in 173 market fish samples, while in Kerala, India, approximately 60% of shrimp aquaculture setting samples were positive for MRSA [34, 35]. However, in contrast, Vázquez-Sánchez et al. (2012) [31] did not detect any MRSA in fish and fishery products. Various investigations on MRSA have revealed that food handlers'hygiene standards are usually suboptimal, particularly regarding their health conditions, personal hygiene practices, and working habits. These factors can lead to increased cross-contamination in processed foods [30, 36, 37]. Despite ongoing research into the prevalence of MRSA seafood products, the presence of MRSA in such products does not necessarily indicate a higher public health risk than the presence of drug-susceptible S. aureus. Food intoxication caused by S. aureus results from the production of staphylococcal enterotoxins, which occurs when the bacterial concentration exceeds 105 cells per gram in food, leading to sufficient toxin levels to induce illness [38].
Seafood contaminated with preformed staphylococcal enterotoxins is a frequent cause of foodborne illness outbreaks globally. Among these toxins, staphylococcal enterotoxin A and D are the most associated with such outbreaks, although the other classical type toxins, as well as SEH, have also been reported [39]. In this study, all the virulence genes detected were found among the S. aureus strains excepted Hlβ (0%), fnbB (0%). Sea, Seb, Sed, Sec and See genes were the most detected with respectively 72.44%, 60.63%, 51.18%, 48.03%, 14,96% detection rate. The detected virulence genes (sea, seb, sed, sec, and see) encode staphylococcal enterotoxins that are key contributors to foodborne illnesses by promoting toxin production, which causes gastrointestinal distress upon ingestion. The findings are consistent with the research conducted by Arfatahery et al. (2016) [16]. Simon and Sanjeev (2007) [40] identified only SEA (43%) and SEC (57%) as toxin types out of 21 strains isolated from fishery products. In Galicia, most isolates (88%) from fishery products marketed were found to be sea positive [31]. Poor personal hygiene, inadequate refrigeration, delays in processing, and post-processing contamination have all been identified as contributing factors to the growth of Staphylococcus bacteria and the production of enterotoxins in food [39].
The occurrence of multidrug-resistant pathogens is acknowledged as an environmental peril to both the food supply and human health [41]. This is because it creates a challenge for eradication and leads to an increase in incidence. While S. aureus has developed multidrug resistance globally, there are significant regional variations in its incidence [42]. The antimicrobial susceptibility pattern was carried out for all S. aureus isolates in the present study. The results indicated a high rate of resistant strains toward penicllin G and ampicillin (70%− 100%). Various resistance pattern has been observed for ciprofloxacin, tetracycline, kanamycin, gentamycin, norfloxacin, streptomycin, chloramphenicol, vancomycin, rifampicin and fosfomycin depending on the sources. All isolates were susceptible toward linezolid (100%). Similarly, Arfatahery et al. (2016) [16] reported high resistance to antibiotics including penicillin (79%) and ampicillin (78.6%). In line with previous findings from Portugal, China, and France, Obaidat et al. (2015) [28] observed a notable resistance to penicillin among S. aureus strains in the three countries [42,43,44,45,46]. It has been established that there is a growing resistance among S. aureus strains to beta-lactam antibiotics such as penicillin derivatives, cephalosporins, monobactams, and carbapenems. These antibiotics are commonly used to treat staphylococcal infections [13]. Variations in antibiotic resistance are also the result of other different factors.
The mecA gene, which is responsible for methicillin resistance, was initially identified in hospitals, but it is now becoming more prevalent in the community and food sources [13]. The results indicated more than 50% (57.36%) of S. aureus isolated from this study carry mecA gene and almost 50% (49.61%) carry nuc gene. Several countries have reported the occurrence of S. aureus strains carrying the mecA gene in fish, with rates of 1.1% in retail ready-to-eat raw fish in Japan [30] and 11.1% in fish in the Czech Republic [47]. However, Vázquez-Sánchez et al. (2012) [31] did not found isolates from fishery products carrying the mecA gene. Basic measures in this respect include promoting hygiene and preventing the uncontrolled use of antibiotics [48].
The significant presence of resistance genes must be acknowledged as a potential health hazard for both humans and seafood [48]. All the genes detected were found in this study. The results indicate that blaZ (93.8%) was the resistance gene the most detected followed by tetM (59,69%) and ermA (43,41%). Similarly, resistance genes such as tetM, tetA, ermB, blaZ, and femA were detected in two or more resistant strains isolated from healthy edible marine Fish [49]. The rising usage of identical or similar antibiotics in aquaculture, animal farming, and human disease management has resulted in an increasing number of antibiotic-resistant bacterial strains. Furthermore, the extensive aquaculture settings have contributed to the emergence of antibiotic resistance in bacteria that could potentially cause diseases in both humans and fish [50].
The PVL toxin has emerged as a significant virulence factor in S. aureus strains, drawing considerable attention in studies [51, 52]. As a result, it has been utilized as an epidemiological method to identify the characteristics of MRSA. In this study, the identification of epidemiological groups was carried out through a multiplex PCR assay that relied on SCCmec carriage type, followed by the identification of genes encoding staphylococcal enterotoxins sea-sed and the Panton-Valentine leucocidin gene (pvl). The results showed that pvl gene was absent from isolates from all type of samples excepted isolates from smoked and salted fish. Low percentage of pvl gene was also reported in previous studies [30, 33, 53]. The existence of PVL results in the toxicity of various types of leukocytes, macrophages, and other cells [22]. SCCmec typing is a reliable approach for identifying strains linked to hospital-acquired infections. On the other hand, spa typing offers valuable insights into the transmission patterns of MRSA strains and aids in the discovery of novel genotypes [54]. The results about the distribution of SCCmec types in S. aureus strains isolated from samples showed that all SCCmec types were detected among S. aureus strains excepted IVd type and sea, seb, sec and sed were the most found genes across the SCCmec types. SCCmec types I, II, III, and IV were identified, but the frequency of types I and II was relatively lower compared to types III (n = 17) and IV (n = 10) [49]. This finding contrasts with the results of a study conducted in Pakistan on MRSA isolates from processed food, where SCCmec type IV was the most common, followed by types II and III [55]. This suggests that fish may serve as a possible source of hospital acquired and community acquired-MRSA transmission to humans [49].
Conclusion
S. aureus can cause serious diseases, including septicemia, endocarditis, pneumonia, and toxic shock syndrome, which are exacerbated by its production of virulence factors and its ability to rapidly develop resistance to antimicrobial agents. S. aureus and MRSA were isolated from almost all different types of seafood. In this study, all the virulence genes detected were found among the S. aureus strains excepted Hlβ and fnbB. The results also indicated a high rate of resistant strains toward penicllin G and ampicillin and high number of S. aureus isolates carry antibiotic resistance genes including mecA, blaZ, tetM, and ermA. All SCCmec types were detected among S. aureus strains excepted IVd type and sea, seb, sec and sed were the most found genes across the SCCmec types. This study has raised additional food safety concerns regarding S. aureus beyond its role as an agent that causes seafood poisoning. To prevent seafood contamination by S. aureus, it is important to practice good food safety habits such as washing hands before handling food, storing seafood at proper temperatures, and cooking seafood thoroughly. It is also recommended to purchase seafood from reputable sources and to avoid consuming raw or undercooked seafood.
Data availability
The datasets used and analyzed during the current study are available from the corresponding author upon reasonable request.
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ER, and RS carried out the molecular genetic studies, participated in the primers sequence alignment and drafted the manuscript. RS and ER carried out the sampling and culture method. ER and AS, FK participated in the design of the study, performed the statistical analysis and writing the manuscript. All authors read and approved the final manuscript.
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The research was ethically approved by the Council of Research of the Faculty of Veterinary Medicine, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran. Verification of this research project and the licenses related to sampling process were approved by the Prof. Ebrahim Rahimi (Approval Ref Number MIC19929).
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Derke, R.E., Rahimi, E., Shakerian, A. et al. Prevalence, virulence factors, and antibiotic resistance of Staphylococcus aureus in seafood products. BMC Infect Dis 25, 554 (2025). https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s12879-025-10870-1
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DOI: https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s12879-025-10870-1