Disease in Shrimp Aquaculture: Diagnosis and Strategies for Sustainable Management

Bacterial illnesses may cause a range of problems, including growth retardation, sporadic fatalities, and mass mortality. The most significant pathogenic bacteria that cause disease in shrimps are Vibrio spp. Vibrio spp. are commonly found throughout freshwater, estuaries, and marine environments. Over 20 species have been identified; some of these are human pathogens (e.g., V. cholerae, V. parahaemolyticus and V. vulnificus), while some species are pathogens of aquatic animals, including shrimp (e.g., V. harveyi, V. spendidus, V. penaecida, V. anguillarum, V. parahaemolyticus, V. vulnificus) (Kumar et al., 2018, 2019 a, 2020 b). Vibrio spp. is frequently found in sediments, grow-out ponds, and shrimp hatcheries. Early mortality syndrome (EMS), originally known as acute hepatopancreatic necrosis disease (AHPND), is a bacterial prawn disease caused by the activity of the PirABvp toxin released by V. parahaemolyticus. Since 2009, the aquaculture sector has suffered significant financial losses due to the AHPND pandemic (Lai et al., 2015). Certain strains of vibrios, including V. alginolyticus, V. wensii, V. campbellii, V. harveyi, and V. punensis, can also cause AHPND as they carry the pVA1-type plasmid, which contains the toxin’s genes (Dong et al., 2019). Shrimp are susceptible to the opportunistic pathogen V. alginolyticus, which can be fatal in unfavorable environmental circumstances (Liu and Chen, 2004). While the majority of Vibrio species are thought to be opportunistic infections, some, such as V. harveyi, may be the primary pathogens. V. harveyi are luminous bacteria that are present in both marine and coastal waterways, as well as in the sediment and shrimp pond water. They are also found in the surface and gut of marine and estuarine species (Ruby and Nealson, 1978; Yetinson and Shilo, 1979; Orndorff and Colwell, 1980). However, they can result in significant mass mortalities in shrimp hatcheries in Asia (Sunaryanto and Mariam, 1986; Lavilla-Pitogo et al., 1990; Karunasagar et al., 1994). Penaeid shrimp larvae may become infected with filamentous bacteria such as Leucothrix mucor, Thiothrix sp., Flexibacter sp., Flavobacterium, and Cytophaga sp. Common symptoms of the illness include lethargy, reduced growth and eating, increased mortality, and discoloration of the gills. The illness has been associated with poor-quality water. Gill tissue necrosis may result from a higher infection level. A microscopic inspection of the gills can be used to diagnose the illness (Table 1). Traditional treatments, including antibiotics, have demonstrated limited effectiveness and contribute to the development of antibiotic resistance (Kumar et al., 2021).

Flegel and Sritunyalucksana (2011) documented the onset of viral pandemics in shrimp aquaculture beginning in 1987, which significantly altered the landscape of shrimp farming. Over 20 viruses have been identified affecting shrimp, with new strains evolving due to intensified aquaculture practices (Lee et al., 2022; Chellapandian et al., 2023). These include members of Baculoviruses, Parvoviruses, Picornaviruses, Togalike viruses and some of the newly identified virus families. Karunasagar and Ababouch (2012) discussed newly emerged viral diseases and their implications for international trade and import risk assessments. Walker and Winton (2010) highlighted that emerging viral diseases pose substantial threats to both fish and shrimp populations, emphasizing the need for ongoing surveillance and research. The authors identified several major viral pathogens, including WSSV, monodon baculovirus (MBV), and others, which have been linked to significant mortality rates and economic losses in aquaculture (Table 1).

One of the most significant illnesses that the global prawn industry faces is caused by WSSV (Takahashi et al., 1994; Chou et al., 1995). The prawn industry has suffered significant harm because of WSSV-related mortality (Inouye et al., 1994; Chou et al., 1995). WSSV is considered as the most harmful virus for the penaeid shrimp farming sector due to its high mortality rate, broad host range, widespread geographic dispersion, virulence, and catastrophic economic losses. WSSV is known to affect most commercially important species of penaeid shrimp including P. monodon, P. japonicus, P. indicus, P. chinensis, P. merguiensis, P. aztecus, P. stylirostris, P. vannamei, P. duorarum, and P. setiferus (Lightner, 1996). Most tissues derived from both ectoderm and mesoderm are infected by WSSV. These include gills, lymphoid organs, antennal gland, hematopoietic tissues, connective tissue, ovary, and ventral nerve cord (Wongteerasupaya et al., 1995; Wang et al., 1999). The primary clinical signs of the syndrome are the presence of white spots, with a diameter of 0.5 to 2.0 mm, on the infected shrimp’s exoskeleton and epidermis (Takahashi et al., 1994; Chou et al., 1995; Wang et al., 1995; Lo et al., 1996). Additional symptoms of the disease include anorexia, a sudden decrease in food intake, fatigue, loose cuticles, and frequently a widespread reddish to pink discoloration (Nakano et al., 1994; Durand et al., 1997; Karunasagar et al., 1997; Otta et al., 1999). WSSV is a tailed, rod-shaped, double-stranded DNA virus (Wongteerasupaya et al., 1995; Durand et al., 1996) with a very large genome in the order of 300 kb (Van Hulten et al., 2001). According to the sequence analysis data of WSSV genomic DNA, WSSV is distinct and does not exhibit any homology with any known viruses (Lo et al., 1997). Currently available techniques for diagnosing WSSV include rapid molecular techniques like gene probes as well as more traditional techniques like histology and microscopy (Durand et al., 1996; Lo et al., 1996; Wongteerasupaya et al., 1996; Nunan et al., 1998) and polymerase chain reaction (Takahashi et al., 1996; Lo et al., 1996). In Asia, PCR is frequently used to screen P. monodon larvae before stocking them in ponds. It has been noted that there is a significant risk of crop loss when larvae tested positive for WSSV by non-nested PCR are stocked (Umesha et al., 2003). There have been reports of WSSV coexisting with other viruses like hepatopancreatic parvovirus (HPV) and monodon baculovirus (MBV) from Asia (Otta et al., 2003; Umesha et al., 2003). The impact of WSSV is profound, as noted by Vatsos and Rebours (2015), who identified it as the most deleterious pathogen affecting shrimp species. Verbruggen et al. (2016) provided insights into the molecular mechanisms underlying WSSV infections, detailing how the virus manipulates host cellular processes to facilitate its replication. Their findings suggest that understanding these mechanisms is crucial for developing effective treatment strategies. Furthermore, Lee et al. (2022) reinforced the notion that WSSV and Vibrio parahaemolyticus, a bacterium associated with acute hepatopancreatic necrosis, are prevalent diseases listed by the OIE (World Organisation for Animal Health), underscoring the need for global disease management efforts. Roy et al. (2020) further elaborated on WSSV’s role, exploring concepts such as trained immunity or immune priming, which could offer new avenues for enhancing shrimp resistance to viral infections. This innovative perspective may lead to improved management practices in aquaculture.

MBV is the first reported virus of P. monodon and the second virus of penaeid shrimp (Lightner and Redman, 1981). It is a nuclear polyhedrosis virus (NPV) of the family Baculoviridae containing a double-stranded circular DNA genome of 80–100 × 10⁶ Da within a rod-shaped, enveloped particle that is frequently observed occluded within proteinaceous bodies (Rohrmann, 1986). MBV has been identified and reported in P. monodon, P. merguiensis, P. semisulcatus, P. kerathurus, P. vannamei, P. esculentus, P. penicillatus, P. indicus, Metapenaeus ensis (Johnson and Lightner, 1988; Lightner, 1988; Chen et al., 1989; Ramasamy et al., 1995; Vijayan et al., 1995; Karunasagar et al., 1998). For the first time, reports of MBV with WSSV and HPV in P. monodon post-larvae raised in hatcheries were made in India by Manivannan et al. (2002). MBV is a common and widely distributed pathogen that is not a highly virulent pathogen of P. monodon (Nash et al., 1988). On rare occasions, however, significant mortality rates in the juvenile (70%) and post-larval (over 90%) phases may be seen. MBV-infected shrimp exhibit severe growth retardation, and instead of their typical greyish-green color, the hepatopancreas of the affected shrimp turns pale yellow to brownish, a condition known as “white turbid liver” (Lightner et al., 1983 a; Chang and Chen, 1994). MBV is generally found in mixed infection with other pathogens, including viruses (IHHNV, HPV, WSSV), bacteria (Vibrio spp., Pseudomonas spp.), parasites (Zoothamnium spp., Epistylis spp. (Anderson et al., 1987; Lightner et al., 1987; Chen et al., 1989; Manohar et al., 1996; Karunasagar et al., 1998; Umesha et al., 2003). MBV targets the hepatopancreas and anterior midgut (Lightner et al., 1983 a). The primary feature used to diagnose MBV infection is the existence of hypertrophied nuclei with one or more spherical occlusion bodies (Lightner et al., 1983 b; Fegan et al., 1991). Other diagnostic features of MBV include conventional histopathology (Lightner and Redman, 1991), PCR (Vickers et al., 1992; Chang et al., 1993; Lu et al., 1993), ELISA (Hsu et al., 2000) and nested PCR (Belcher and Young, 1998; Otta et al., 2003). MBV can only spread horizontally through the oral fecal route. MBV infects eggs and larvae in hatcheries through the fecal matter of broodstock (Chen et al., 1992; Natividad and Lightner, 1992).

The HPV was first reported by Lightner and Redman (1985) in post-larvae of Penaeus chinensis. In India, P. monodon post-larvae harboring HPV infection was reported by Manivannan et al. (2002) and Umesha et al. (2003). HPV-affected prawns typically exhibit non-specific gross symptoms, such as hepatopancreas atrophy, anorexia, sluggish growth, less preening activities, and hence an increased tendency for surface and gill fouling by epi-commensal organisms (Lightner and Redman, 1985; Chen et al., 1992; Sukhumsirichart et al., 1999). High incidence of HPV infection has been documented, particularly in early juvenile stages (Flegel, 1995; Lightner, 1996) and the transmission of HPV is believed to be both vertical and horizontal (Lightner at al., 1992). HPV can be diagnosed histologically (Lightner and Redman, 1985; Lightner et al., 1992) through rapid field tests using Giemsa-stained smears of hepatopancreas (Lightner, 1996), gene probes (Bonami et al., 1995, Mari et al., 1995) and sensitive PCR assay (Sukhumsirichart et al., 1999; Pantoja and Lightner, 2000).

IHHNV was first detected in juvenile Penaeus sytlirostris from Hawaii in 1981 (Lightner et al., 1983). IHHNV is a small, icosahedral, non-enveloped virus with a genome comprising roughly 4.1 kb of single-stranded linear DNA (Bonami et al., 1990; Mari et al., 1993). This virus causes an illness known as runt-deformity syndrome (RDS) in P. vannamei and P. monodon (Bell and Lightner, 1984; Kalagayan et al., 1991; Primavera and Quinitio 2000), which results in substantial economic losses (Wyban et al., 1992). The diseased prawns exhibit decreased appetite, cannibalism, sluggishness, and elevated mortality rates. The affected animals have many localized melanized regions and opaque abdominal muscles.

In 1990, YHV was first identified in black tiger prawns (Penaeus monodon) raised in ponds in central Thailand. It is a positive-sense, single-stranded RNA virus in a new family Roniviridae (Cowley et al., 2000; Mayo 2002). The common symptoms of yellowhead disease include a pale or bleached appearance of the affected prawn as well as a light-yellow coloring of the dorsal cephalothorax area. The yellow color seen in the cephalothorax region of moribund prawns is due to the underlying yellow hepatopancreas that is visible through the thin shell (Chantanachookin et al., 1993). YHV is widely present in P. monodon cultivated stocks in Thailand. Affected prawns perish within a few hours after turning color. The entire crop may be lost in three to five days following the first signs of the YHV infection (Flegel, 1995). YHV has also been shown to infect and cause disease in P. vannamei and P. stylirostris (Lu et al., 1994). Mastophilic cytoplasmic inclusions and extensive systemic necrosis in the tissues of ectodermal and mesodermal origin are histological indicators of YHV infection in affected prawns (Boonyaratpalin et al., 1993; Chantahachookin et al., 1993). For the detection of YHV, a number of rapid diagnostic procedures like simple staining (Flegel and Sriurairatana, 1994) dot blot nitrocellulose enzyme immunoassay (Lu et al., 1996; Nadala and Loh, 2000), western blot technique (Nadala et al., 1997), reverse transcriptase PCR (Wongteerasupaya et al., 1997) and gene probe (Tang and Lightner, 1999) have been developed.

The first evidence of the gill-associated virus (GAV) was found in Queensland, Australia, where it has caused significant mortalities in juvenile, adult cultured and wild spawners of P. monodon since 1996 (Spann and Lester, 1997). It is a rod-shaped, enveloped (+) RNA nidovirus (Cowley et al., 1999; Cowley and Walker, 2002). The body and appendages of a P. monodon infected with GAV turn pink to red, while the gills turn pink to yellow in color. Additional symptoms of the illness include tail rot, secondary fouling, indifference, and lethargic behavior (Spann et al., 1997).

It is a type C baculovirus of penaeid shrimp. When BMNV disease appears in larval stages, it is characterized by a rapid onset and a high mortality rate. The disease is typically characterized by a white, turbid midgut gland with notable cell necrosis and no inclusion body in the affected area. Under an electron microscope, rod-shaped particles that resemble baculovirus are discovered in the damaged nucleus (Takahashi et al., 1998). Histological evidence of the typical BMNV pathology might be used to confirm the diagnosis. The significantly hypertrophied nuclei of hepatopancreatic tubercle epithelial cells undergoing necrosis are characterized by marginated chromatin, decreased nuclear chromatin, nuclear dissociation, and the lack of occlusion bodies (Sano et al., 1981, 1984; Sano, 1985; Momoyama, 1993; Sano and Fukuda, 1987).

Significant fatalities have been associated with BP in P. aztecus, P. stylirostris, P. vannamei, and P. penicillatus larval, post-larval, and early juvenile stages. BP solely affects the hepatopancreas and midgut epithelial cells and it is transmitted from shrimp to shrimp (Lightner and Redman, 1998). Shrimp larvae are usually infected by cannibalism of diseased larvae, fecal oral contamination through feces from infected larvae, or fecal contamination of produced eggs from BP-infected adult spawners (Johnson and Lightner, 1988; Lightner, 1996; Overstreet et al., 1988). Tetrahedral occlusion bodies are detected by light microscopy examination of fresh squash preparation of the hepatopancreas or feces in order to diagnose BP (Overstreet et al., 1988; Lightner et al., 1992). To identify this virus, advanced techniques such as gene probes and immunodiagnostics like ELISA have been developed (Lewis 1986; Bruce et al., 1994).

Shrimps affected with LOPV exhibit the production of multinucleated giant cells in their hypertrophied lymphoid organs (Ownes et al., 1991). The affected prawns exhibited modest nuclear hypertrophy and marginated chromatin in their ‘giant cells’. Additionally, the cells included discrete, frequently fibrocyte-encapsulated spherical aggregates that were identical to the lymphoid organ spheroids reported in P. monodon from Taiwan. Acridine orange staining and fluorescence microscopy were used to determine the presence of DNA in basophilic intranuclear inclusion bodies, which are frequently observed in giant cells (Ownes et al., 1991).

According to Fraser and Owens (1996), the first documented case of SMV in P. monodon was in 1993 at a research center located in Townsville, northern Queensland, Australia. SMV has been associated with grow-out pond mud-crop mortality syndrome and fatalities in P. monodon broodstock. The affected animals exhibited signs of fatigue, inability to eat, redness of the pleopods and carapace, and a higher death rate. A 100% death rate has resulted from experimental infection. This condition is characterized by the excretion of red feces. Transmission electron microscopy revealed the small (20 nm) icosahedral virions in gut cells, and preliminary characterization revealed it was a non-enveloped DNA virus, identical to parvovirus (Fraser and Owens, 1996). According to Owens et al. (1998), the gastrointestinal tract is the first tissue to get infected with SMV. SMV targets the hepatopancreas, midgut ceca, midgut, and, to a lesser degree, the hindgut ceca. In a severe infection, the virus would penetrate the gut’s lamina propria, spread throughout the body, and settle in the heart, gonads, and lymph nodes. As a result, the stomach, which is cleared of feces, would be the most likely site of SMV (Owens et al., 2003).

Fungi are found in aquatic environments, and around 500 distinct fungal species have been identified from the marine and estuary environments. Shrimp are opportunistic hosts to certain aquatic fungi. The majority of the affected states are larval, and Lagenidium callinectes and Serolpidium spp. are the predominant causative agents. Clinical symptoms, including fatigue and death, are typically present in the protozoea and mysis phases. Affected tissue, especially the gills and appendages, has fungal spores and mycelia visible. In many hatcheries in India, larval mycosis is an issue. Infection with Sirolpidium parasitica and Lagenidium marina in P. monodon was documented by Gopalan et al. in 1980. P. monodon larvae mortality at the nauplii, zoea, and mysis stages were documented by Ramasamy et al. in 1996. All stages of penaeid prawn development may be impacted by fusariosis and black gill disease, which are brought on by Fusarium spp. Fusarium species, such as F. solani and F. moniliforme, are opportunistic diseases that have a 90% mortality rate. Ponds with inadequate water quality management have disease problems. Light microscopy can be used to identify fungal hyphae in animal tissue that has been impacted. Recent research indicates that immunostimulants may play a role in enhancing the shrimp’s immune response through mechanisms such as “immune priming” or “trained immunity” and highlighted that the modulation of the immune system can potentially improve resistance against fungal infections, suggesting that the application of immunostimulants could be a viable strategy for disease control in aquaculture (Table 1).

The emergence of antifungal-resistant fungal pathogens poses a significant challenge to managing fungal infections in shrimp. Sanglard (2016) discusses the rising threats posed by these resistant strains, emphasizing the need for novel therapeutic approaches and the importance of understanding the resistance mechanisms at play. Nnadi and Carter (2021) explored the relationship between climate change and the emergence of fungal pathogens, noting that changing environmental conditions can exacerbate the prevalence and severity of fungal infections in aquatic systems. This highlights the necessity for ongoing research into how climate-related factors influence pathogen dynamics and shrimp health. However, there is limited research on the specific molecular pathways involved in shrimp immune responses to fungal infections. Additionally, the ecological impact of fungal diseases on shrimp populations in natural environments is not well understood.

Shrimp are susceptible to many parasites at different stages of their development, especially protozoa. Adhesions of epi- and endocommensal protozoa have been observed on internal organs, periopods, cephalothorax, gills, and other appendices. Anorexia, decreased growth, impaired mobility, and an increased vulnerability to infection by opportunistic pathogens are all consequences of severe infection caused by these protozoa, which can also cause brown gill blockage. The external parasites Ephelota, Lagenophrys, Anophrys, Epistylis, and Zoothamnium are examples of protozoa. Ciliates that induce mortality in larvae and juveniles include Paranophrys spp. and Parauronema sp. Invasion of hemolymph and gills by ciliates is possible through lesions in the shrimp body. Mass fatalities could result from this, especially when combined with other parasitic flagellates, such as Leptomonas sp. Diagnosis can be achieved through examination of hemolymph, which appears turbid, does not clot, and shows reduced hemocyte count and numerous ciliates (Kumar et al., 2024).

Shrimp are infected with gregarians, which are endoparasitic protozoa. Typically, these parasites have two hosts: crustaceans and molluscs or annelid worms. Gregarians found in shrimp include Nematopsis spp., N. litopenaeus, Paraphioidina scolecoide, Cephalobolus litopenaeus, C. petiti and Cephaloidophoridae stenai. Trophozoites and gametocytes can exist in the lumen or adhere to the gut wall. Although intestinal obstruction and decreased food absorption from the stomach are possible side effects of parasites, aquaculture appears to be relatively unaffected by these illnesses. Agmasoma sp. and Microsporidium sp. are examples of microsporidia that can infect the heart, gonads, gills, liver, and pancreas. The common microsporidian disease is cotton shrimp disease. Shrimp may look crooked as a result of the illness, which causes the damaged tissue to become opaque (Table 1).

Shrimp lacking the adaptive immune system, rely on their cellular and humoral components of innate immune responses to combat the invading pathogens, due to which the development of therapeutic agents that enhance the adaptive immune response, e.g., vaccines against infectious disease in shrimp aquaculture had very limited success (Hong et al., 2016; Santos et al., 2020; Kumar and Martin, 2025; Roy et al., 2025). Therefore, methods that can boost the host’s innate immune response and enhance disease resistance against diseases have gathered much interest in recent years. The disease caused by bacterial pathogens in shrimp farming systems are generally controlled by using appropriate management strategies, including supplementation of immunostimulants, prebiotics, probiotics or phages, maintaining optimum water quality, stocking density, post-larvae quality, aeration and feed quality and quantity (Defoirdt, 2014; Hostins et al., 2019). However, since the outbreak of AHPND in China back in 2009, most of the research has mainly focused on epidemiological studies, including the characterization of AHPND etiological agents and associated pathological changes from various geographical locations. Hence, there is an urgent need to develop promising new methods that can become a potential tool to protect the shrimp against AHPND-causing V. parahaemolyticus. Some studies have reported management strategies to control the disease and possibly prevent disease outbreaks in shrimp aquaculture.

The prophylaxis measures to control disease mainly focus on pond renovation and disinfections before shrimp post-larvae stocking (De Schryver et al., 2014). However, these approaches are not capable of stopping the epidemiological situation once the disease has emerged in a pond or its neighborhood, and hence more effective therapeutic measures are urgently needed to control shrimps. The conventional approach so far applied in the mitigation or cure of disease, such as the application of antibiotics and disinfectants, has had limited success (Hong et al., 2016). Additionally, their usage in the food-producing sector is under severe scientific and public scrutiny due to the development of multiple resistance (Smith, 2008). For example, the AHPND-causing V. parahaemolyticus strain from Mexico (13-511/A1 and 13-306D/4) was reported to carry tetB gene coding for tetracycline resistance gene (Han et al., 2015), and V. campbellii from China was found to carry multiple antibiotic-resistance genes (Dong et al., 2017), hence the application of traditional methods like antibiotics may be ineffective in controlling the diseases in the shrimp farming system.

Effective shrimp health management requires consideration of the fact that there is a delicate balance between the host, pathogen, and environment. Typically, infections coexist with their surroundings, although shrimps seem healthy and exhibit typical growth. Shrimp diseases pose a major challenge to the sustainability of aquaculture operations. Disease outbreaks often result in massive financial losses, increased use of antibiotics and chemicals, and the collapse of shrimp farms. These practices can have broader environmental consequences, including the overuse of antibiotics and chemicals affecting aquatic ecosystems and biodiversity, and can lead to antibiotic-resistant bacteria, posing risks to both shrimp and human health. Disease outbreaks can devastate shrimp farming communities, leading to the abandonment of farms, loss of livelihoods, and increased poverty in coastal regions. Effective biosecurity practices include quarantining new stocks and disinfecting pond water to prevent pathogen introduction (Delphino et al., 2022). In Indonesia, farms were categorized based on biosecurity intensity, revealing that larger farms implemented more rigorous practices compared to smaller ones (Delphino et al., 2022). Alternatives to antibiotics, such as probiotics, phytobiotics, and biofilm-based vaccines, are being explored to enhance shrimp health and reduce disease incidence (Seethalakshmi et al., 2021). Developing shrimp populations with enhanced resistance to endemic diseases is crucial for sustainable aquaculture (Cock et al., 2017 b). Traditional methods like the use of antibiotics and immunostimulants are still prevalent, though they come with risks of resistance and environmental impact (Sivakamavalli et al., 2021). Limited regulatory monitoring and enforcement can lead to inadequate disease control measures. Early detection data can be used to identify high-risk areas and implement preventive strategies like improved water quality management or vaccination programs. A robust surveillance system with early detection capabilities can enhance confidence in the quality and safety of Asian shrimp products, improving market access. The four gold standard ideals are high sensitivity, specificity, rapid diagnosis, and cost-effectiveness (MacAuley et al., 2022). The implementation of better management practices (BMPs) involves sustainable farming techniques and the formation of Self-Help Groups, which can enhance crop outcomes and mitigate the impact of diseases. The adoption of sustainability practices, such as the Code of Conduct for Responsible Fisheries, is essential to address the environmental degradation caused by intensified aquaculture. Research advancements, particularly in disease management, have been crucial for sustaining production levels and addressing challenges (Dastidar et al., 2013). Innovations in farming techniques, such as the use of probiotics and ecological practices, are being explored to enhance sustainability. Lundin (1995) emphasized the need for drastic changes in management practices to ensure the sustainability of shrimp farming in India, highlighting that without such changes, the aquaculture sector may continue to suffer from disease outbreaks and economic instability. While these strategies show promise, integrating sustainability practices with effective disease management is vital for the future of shrimp farming in Asia. Some of the important strategies for health management have been outlined below.

Growing shrimp in a biofloc system can be a promising alternative strategy to improve the environmental conditions and health status of cultured animals. The basic principle of the biofloc system is to recycle waste nutrients, in particular, inorganic nitrogen resulting from uneaten feed and feces into microbial biomass, which can be used in situ by the cultured animals or be harvested and processed into feed ingredients (Avnimelech, 1999; Crab et al., 2012). In fact, the metabolic processes and biochemical transformations take place directly in the water column, which promotes the overall balance of the system and the health of the farmed shrimp (Bossier and Ekasari, 2017). The heterotrophic microbiota is stimulated by steering the C/N ratio of the water through the modification of carbohydrate content in feed or by the addition of a carbon source in the water so that bacteria can assimilate the waste ammonium for new biomass production (Avnimelech, 1999). Hence, ammonium/ammonia can be maintained at a low and non-toxic concentration so that water replacement is no longer required (Figure 6). For instance, Avnimelech (2007) noted that the use of biofloc in intensive tilapia culture significantly improves nitrogen recovery from 23% to 43%.

Figure 6.

Schematic role of biofloc system in host, pathogen, and environment in a shrimp aquaculture facility (Kumar et al., 2021 b)

The biofloc is rich in free amino acids such as alanine, glutamate, arginine, and glycine, which are reported to serve as diet attractants for shrimp (Ju et al., 2008). Hence, it is noted that shrimp in the biofloc system consume up to 29% of the flocculating particles of their daily feed intake (Burford et al., 2003). Apart from serving as protein and lipid sources, these aggregate flocs can contain microbially bioactive components such as carotenoids, vitamins, glutathione, antioxidants, and minerals, which nutritionally modulate the shrimp’s health and immune response and result in better growth performance and resistance against pathogenic microbial infections (Figure 6) (Cardona et al., 2015; Ju et al., 2008). For instance, in situ utilization of microbial flocs in biofloc systems by aquaculture organisms, as well as the utilization of processed biofloc as a feed ingredient, has been reported to improve the growth performance and health of shrimp (Shyne Anand et al., 2017; Azim and Little, 2008).

There are a few reports that have illustrated the role of biofloc in stimulating the non-specific immunity and resistance of shrimp against microbial pathogens, including AHPND, V. parahaemolyticus (Hostins et al., 2019). These studies highlighted that the biofloc system decreases the impact of AHPND-causing V. parahaemolyticus and provides protection to L. vannamei against AHPND bacteria. However, the study also indicates that the protective response in shrimp depends on the operational parameters of the biofloc system. Recently, Kumar et al. (2020 b) demonstrated that biofloc-mediated enhanced survival of L. vannamei upon AHPND-causing V. parahaemolyticus challenge is partially mediated by reduced expression of its virulence genes. The study showed that, in the biofloc system, AHPND-causing V. parahaemolyticus possibly switched from a free-living virulent plank-tonic phenotype to a non-virulent biofilm phenotype, as demonstrated by a decreased transcription of flagella-related motility genes (flaA, CheR and fliS), Pir toxin (PirB^VP), and AHPND plasmid genes (ORF14) and increased expression of the phenotype switching marker AlkPhoX gene in both in vitro and in vivo conditions (Kumar et al., 2020 b). Taken together, the ability of the biofloc system to boost the water quality, growth performance, and resistance of L. vannamei against V. parahaemolyticus AHPND strain makes it a potent aquaculture technology that will be valuable to prevent microbial infection, including AHPND, and increase the shrimp production with high-density and minimal or no water exchange culture.

Pond management has shown promising results in controlling the incidence of AHPND in shrimp. However, most of these studies are based on laboratory trials, and further validation of dose, route of delivery, and associated risk factors is still needed to establish the effectiveness in shrimp farm conditions. Recently, Songsangjinda and Polchana (2016) demonstrated that by adopting better farm management practices, shrimp farmers can control AHPND and avoid production losses. The study showed that the pre-stocking and post-stocking measures, including evaluation and screening of healthy post-larvae, feed quality assessment, and disinfection of input materials (e.g., seawater), were helpful in controlling the AHPND in shrimp farms (Songsangjinda and Polchana, 2016).

Apart from management measures, the polyculture system has been identified as a potential strategy to control AHPND in shrimp farms. Tran (2014) studied the effect of polyculture systems, including tilapia and L. vannamei, in controlling AHPND infection and mortality. The results showed that tilapia-induced beneficial algal and bacterial blooms in water promote healthy and balanced biota communities that confer positive effects in controlling AHPND in shrimps (Tran, 2014). In another study, Boonyawiwat et al. (2017) evaluated factors related to farm characteristics, farm management, pond and water preparation, feed management, post-larvae, and stock management in the occurrence of AHPND in shrimp. The results demonstrated that the presence of predator fish, multiple shrimp species, or high stocking density in the culture system contributes to an increased risk of AHPND infections. While the delay in the first day of feeding, polyculture, and water aging (≥7 days long) were likely to promote protection against AHPND in shrimp (Boonyawiwat et al., 2017).

Many shrimp farmers lack the knowledge or motivation to report disease outbreaks consistently, leading to incomplete data on disease prevalence and distribution. Access to advanced diagnostic tools like molecular techniques is often limited at the farm level, delaying the accurate identification of pathogens. A well-connected, nationwide network for disease surveillance is missing, hindering rapid information sharing and response. Many farmers may not be adequately trained in recognizing early signs of disease or reporting suspected cases. Limited regulatory monitoring and enforcement can lead to inadequate disease control measures. Creation of a well-coordinated network of government agencies, research institutions, and private sector stakeholders is needed to collect and analyze disease data. There is a need to educate farmers on disease identification, reporting mechanisms, and best practices for disease prevention and to increase the availability of rapid diagnostic tests at the farm level and in regional laboratories (Subasinghe et al., 2023). Development of robust data management platforms is essential to effectively analyze and interpret disease surveillance data, and incentives implemented for farmers to report suspected disease outbreaks promptly. There is regional variation in disease prevalence and impact on small-scale versus large-scale shrimp farms. Although quantitatively estimating the overall impacts of disease on rural livelihoods was difficult due to a lack of adequate socioeconomic information, the consensus among the workshop participants was that aquatic animal health problems are a risk to the livelihoods of people involved in small-scale aquaculture and enhanced fisheries in Asia. From the information derived from specific case studies, it was clear, though, that health problems impact the livelihoods of rural, resource-poor aqua farmers, fishers, and their dependents through loss of production, income, and assets. Government policies play a crucial role in influencing sustainable shrimp farming practices (Nada et al., 2025) and can help reduce pressure and threats to shrimp farming businesses, enabling them to operate more sustainably. The National Shrimp Policy in Bangladesh emphasizes promoting environmentally friendly shrimp mixed cultivation for sustainable development, highlighting the importance of government support in fostering sustainable practices (Akber et al., 2017). Additionally, the successful alignment of incentives by government and industry initiatives has shown that shrimp farming thrives in healthy environments, leading to higher profits and sustainable outcomes (Lebel et al., 2016). Public-private partnerships (PPPs) play a crucial role in enhancing shrimp health management strategies by fostering collaboration between governmental bodies and private entities. These partnerships can address the significant challenges posed by diseases in shrimp aquaculture, which threaten industry sustainability. This includes joint research initiatives to identify and combat pathogens affecting the shrimp population. Knowledge sharing between public and private sectors can lead to the adoption of best practices in shrimp health management, reducing reliance on harmful chemicals and antibiotics (Ceseña et al., 2021). While PPPs offer significant benefits, challenges such as power asymmetry and the need for transparent governance structures must be addressed to ensure equitable collaboration and effective health management in shrimp aquaculture. Studies have shown that genetic diversity within shrimp populations, such as Penaeus vannamei, is vital for breeding programs. Techniques like RFLPs and RAPD have identified polymorphisms that correlate with desirable traits, including disease resistance. Quantitative genetics approaches, such as the cure model, have been employed to assess resistance to diseases like Taura syndrome, revealing distinct genetic traits for susceptibility and endurance. Developing disease-resistant shrimp strains through selective breeding can help reduce the impact of viral and bacterial diseases. Studies on Pacific white shrimp (Penaeus vannamei) have utilized a cure model approach to assess resistance to the Taura syndrome virus, revealing high heritability for susceptibility (0.41) and distinct genetic traits for endurance and susceptibility (Ødegård et al., 2011). While significant advances have been made in understanding shrimp-pathogen interactions and applying genetic and nutritional strategies, further research is needed to bridge existing knowledge gaps. By addressing these gaps, researchers can facilitate the development of robust disease-resistant strains, ultimately leading to more resilient shrimp aquaculture systems. The identification of genetic markers associated with disease resistance can facilitate selective breeding programs, enhancing the resilience of shrimp stocks against prevalent pathogens (Ødegård et al., 2011). Despite these advancements, challenges remain, including the potential for antibiotic resistance and the need for a comprehensive understanding of disease mechanisms, particularly for emerging threats like acute hepatopancreatic necrosis disease (AHPND) (Kumar et al., 2021 b). Continued research is essential to ensure the long-term viability of shrimp aquaculture. Recent studies have focused on understanding the intricate interactions between shrimp and their pathogens. Investigations into the immune responses of shrimp have revealed promising avenues for enhancing disease resistance. Notably, the use of immunostimulants has emerged as a potential strategy for “immune priming” or “trained immunity”, which could bolster the shrimp’s innate defenses against pathogens (Laan, 2013). These findings underscore the importance of exploring biochemical mechanisms that underpin shrimp immunity, which may lead to innovative approaches in breeding and management practices. The application of genetic modification and molecular breeding techniques has been highlighted as a pivotal strategy in developing disease-resistant shrimp strains. Techniques such as CRISPR/Cas9 technology have demonstrated efficacy in enhancing disease resistance in various organisms, suggesting their potential applicability in aquaculture (Borrelli et al., 2018). Recent advances in genetic selection and CRISPR technology show promising potential for combating shrimp diseases. Selective breeding programs have yielded continuous progress in improving production traits and disease resistance in penaeid shrimp (Ren et al., 2025; Castillo-Juárez et al., 2015). Genomic selection has demonstrated increased accuracy and genetic gain compared to traditional methods, particularly for disease-resistance traits (Castillo-Juárez et al., 2015). CRISPR/Cas9 genome editing offers significant potential to accelerate genetic improvements in shrimp, with recent advancements showing promising results in achieving high transfection efficiency in shrimp embryos (Ren et al., 2025). The characterization of CRISPR genetic sequences in microorganisms associated with shrimp infections provides insights into potential phage therapy strategies (Parra et al., 2021). Additionally, the application of genetic technologies, including gene editing and selective breeding, holds promise for combating infectious diseases in aquaculture, although ethical considerations and implementation challenges need to be addressed (Robinson et al., 2023). However, the specific genetic pathways and markers associated with disease resistance in shrimp remain largely unexplored. Marker-assisted selection has been successfully employed in other agricultural species, such as wheat and barley, to improve disease resistance (Miedaner and Korzun, 2012), yet its application in shrimp breeding is still in its infancy. Research has shown that probiotics, particularly strains of Bacillus subtilis, can significantly improve the growth performance and immune responses of white shrimp, Litopenaeus vannamei (Zokaeifar et al., 2012; Kumar et al., 2016). Probiotics enhance shrimp gut health, improve nutrient absorption, and bolster disease resistance, contributing to a balanced microbial community in aquaculture systems (Tamilselvan and Raja, 2024). Successful probiotic integration requires careful strain selection and dosage optimization.

Marker-assisted selection (MAS) is emerging as a powerful tool in breeding programs, enabling the identification of genetic factors linked to disease resistance. This approach has been successfully applied in other aquaculture species and holds potential for shrimp (Yáñez and Martínez, 2010). The potential of CRISPR technology in combating viral infections in shrimp remains largely unexplored despite its proven efficacy in other domains. This innovative gene-editing tool could revolutionize shrimp aquaculture by targeting specific viral genes responsible for diseases like white spot syndrome. CRISPR can be designed to target and disrupt viral genes, potentially preventing viral replication and infection in shrimp (Nasko et al., 2019). The flexibility of CRISPR-Cas9 allows for precise modifications, which could be harnessed to enhance shrimp resistance to viral pathogens (Barrangou and May, 2015). Combining CRISPR with RNA interference (RNAi) strategies may provide a dual approach to silencing viral genes and enhancing shrimp immunity. While CRISPR shows promise, challenges such as off-target effects and delivery mechanisms need to be addressed to ensure its safe application in aquaculture. Further research is essential to fully realize its potential in this field. Despite the progress made in shrimp farming, several knowledge gaps remain. There is a need for more research into the long-term effects of feed composition on shrimp health and growth rates, particularly concerning the integration of alternative protein sources such as marine microalgae (Kiron et al., 2012). Additionally, studies focusing on the genetic diversity of shrimp populations could enhance breeding programs and contribute to disease resistance (Li et al., 2018). Future research should also prioritize understanding the ecological implications of shrimp farming practices, especially in relation to biodiversity and coastal ecosystem health (Bush et al., 2010). Climate change poses significant challenges to shrimp farming, necessitating adaptation strategies to mitigate disease outbreaks and maintain productivity. Farmers in Bangladesh and Vietnam have implemented various measures, including increasing pond depth, exchanging tidal water, strengthening dikes, and using settling ponds (Islam et al., 2019). These adaptations have shown positive effects on shrimp farming performance and productivity. Key factors influencing disease occurrence include crop duration, years of operation, and farmers’ adaptation practices. Regular feed conversion ratio calculations, participation in training programs, and adjusting feeding schedules have been found to reduce disease risk (Le et al., 2024). Viruses and bacteria remain significant pathogens in shrimp farming, with traditional chemical and antibiotic treatments becoming less effective due to resistance (Guzmán and Valle, 2003). As the industry continues to evolve, emphasis on sustainable practices like polyculture and improved biosecurity measures is crucial for adapting to climate change and ensuring long-term viability (Islam et al., 2019; Le et al., 2024). Recent research highlights the integration of IoT and AI technologies in smart shrimp farming, offering real-time monitoring and management solutions. These systems typically employ sensors to measure crucial water quality parameters such as temperature, pH, salinity, and dissolved oxygen (Capelo et al., 2021). Data collected from these sensors is transmitted to cloud servers or edge devices for analysis and decision-making. Some systems incorporate automated control mechanisms to maintain optimal conditions, such as activating aerators when necessary (Capelo et al., 2021). Mobile applications have been developed to provide farmers with remote access to farm data and management tools. Advanced systems also utilize AI-based video analysis to monitor shrimp and feed conditions in turbid underwater environments. These smart farming techniques aim to increase productivity, improve shrimp quality, and reduce mortality rates by enabling early disease detection and treatment (Daud et al., 2022). Early warning systems and surveillance frameworks for shrimp diseases in Asia have evolved with technological advancements. Mobile technology offers new opportunities for real-time disease reporting in archipelagic countries like Indonesia (Fadillah et al., 2019). The white spot syndrome virus (WSSV) and yellow head virus (YHV) have caused significant economic losses in Asian shrimp aquaculture (Flegel and Alday-Sanz, 1998). To combat these diseases, improved grow-out systems have been developed, including closed recirculating water systems and inland shrimp culture (Menasveta, 2002). Since 2011, Thailand’s prawn industry has also been affected by acute hepatopancreatic necrosis disease (AHPND) and early mortality syndrome (EMS). Surveillance programs have benefited greatly from the incorporation of technology, such as PCR methods for quick disease detection. By addressing environmental issues and enhancing resource utilization, integrated multi-trophic aquaculture (IMTA) has become a viable substitute for conventional prawn farming methods (Chang et al., 2020). By combining extractive species like seaweeds and invertebrates, which use excess nutrients, with fed species like prawns, IMTA lessens its negative effects on the environment while boosting overall productivity. With different models adapted to local conditions, this strategy has been widely adopted in China (Chang et al., 2020). Eco-friendly techniques, such as biocontrol agents, green water technology, and biofloc technology, have been used to fight diseases like luminous vibriosis. Eco-friendly methods, including biocontrol agents, green water technology, and biofloc technology, have shown promise as alternatives to antibiotics (Dash et al., 2017). However, implementing these practices can be challenging, particularly for smallholder farmers with limited financial resources (Munasinghe et al., 2012). Recognizing the economic value of environmental services provided by extractive species in IMTA systems could create incentives for wider adoption and contribute to the long-term sustainability of the shrimp farming industry. The incorporation of biofloc technology, which utilizes microbial communities to enhance feed quality and shrimp health, has also been linked to improved disease resistance (Ekasari et al., 2014). These findings suggest that nutritional strategies can play a critical role in enhancing disease resistance, yet more research is needed to identify optimal formulations and their mechanisms of action. Despite the promising results from various studies, significant challenges remain in developing disease-resistant shrimp. One critical area is the need to understand the virulence mechanisms of pathogens such as Vibrio spp., which are responsible for acute hepatopancreatic necrosis disease (AHPND) in shrimp (Flegel, 2019). Comprehensive studies on these microorganisms’ pathogenicity and virulence factors are essential for developing effective management strategies to combat disease outbreaks in shrimp aquaculture. Several knowledge gaps persist in the current literature. Firstly, while the application of immunostimulants and genetic modifications shows promise, there is a need for systematic studies that evaluate their long-term effects on shrimp health and productivity in natural aquaculture environments. Furthermore, the genetic basis of disease resistance in shrimp is not fully characterized, necessitating more in-depth genetic studies to identify specific genes and pathways involved in immune responses. Research into shrimp health management is increasingly focusing on genetic resistance to diseases. Genome-wide association studies (GWAS) may be used to explore the genetic architecture of disease resistance, providing valuable insights into breeding programs for resilient shrimp populations. Furthermore, the synergistic effects of probiotics and genetic modifications can enhance shrimp health and immunity. Comprehensive management practices that integrate nutritional strategies, immunostimulants, and genetic selection are also being developed. These approaches aim to bolster disease resistance while minimizing the need for antibiotics, ultimately promoting sustainable shrimp aquaculture and reducing environmental impact.