Fish Pathogens: Infection and Biological Control

Over the last few decades, diseases have emerged as a major bottleneck in fish farming, especially with the emergence of several fish pathogens and increasing resistance to treatments. It is estimated that 15% of total fish production is lost due to fish diseases, with this figure rising to over 40% during occasional outbreaks [1]. Understanding the interactions of pathogens with their host and how the increased antibiotic resistance works is key to developing new control and treatment strategies against these challenges. This Special Issue aims to explore the frontiers of our scientific knowledge, focusing on increasing our understanding of emerging fish pathogens and improving applicable strategies related to the control (biocontrol and immune stimulation), prevention, and immunoprophylaxis of emerging fish pathogens, with four primary foci: pathogen characterization, bioinformatics and comparative genomics, disease prevention, and probiotics as a control measure.

In pathogen characterization, pathogens such as Aeromonas spp. and Edwardsiella spp. have always been treated as secondary agents of diseases, but in recent years their isolation rate in disease outbreaks has been increasing [2]. Aeromonas is a genus of 36 species, with new species and variations being described regularly [3]. Despite this phylogenetic variation, it can be difficult to distinguish between Aeromonas species using traditional laboratory diagnostic methods. In addition, species differences and the inherent ability of Aeromonas to mutate and transfer plasmids between species contribute to low vaccine efficacy, providing only partial protection for a limited time [4,5]. On the other hand, Edwardsiella is a genus with only five known species, four of which have a significant impact in aquaculture. One of the major problems with Edwardsiella spp. is their wide host range, including eels, catfish, tilapia, and turbot, and their ability to cause interspecies infection, an overlooked point [6]. There is also a paucity of studies on pathogenesis and host–pathogen interactions and/or predilection. Similarly to Aeromonas, Edwardsiella also suffers from laboratory misdiagnosis and low vaccine efficacy; however, several researchers are addressing these challenges by developing sensitive molecular differential diagnosis [7,8], and even vaccines with cross-protection between species [9,10]. Not only on these, but other bacteria of importance in aquaculture, such as Streptococcus spp., Francisella orientalis, and Lactococcus spp., are always in need of study to better understand their dynamics and disease characterization in fish species.

One state-of-the-art tool used in aquaculture research is bioinformatics, a field that combines computational biology, mathematics, and statistics to analyze large datasets, and omics sciences: genomics, transcriptomics, proteomics, and metabolomics. Comparative genomics is the omics science responsible for analyzing the genomes of microorganisms, providing a view of the variation and evolution of pathogens to better understand their virulence, pathogenicity, and diversity [11,12]. In aquaculture, comparative genomics enables researchers to identify gene functions, discover new drug targets, develop vaccines and new diagnostic methods, and even apply it to genetic selection to identify fish with the desired allelic genes to make them more resistant to a pathogen or to improve their immune response [13,14,15,16]. With the help of bioinformatics, researchers can find computational solutions to important biological problems in a much shorter time, improving research efficiency and producing more results than ever before.

A key aspect of infectious diseases in fish farming is which preventive approaches should be prioritized to effectively block the emergence of disease outbreaks and the emergence of new pathogens or pathogen genotypes with high virulence (or with no cross-protection of available vaccines). Due to the wide range of infectious agents (different types of bacteria/genotypes, viruses, fungi, and protozoa), there are many knowledge gaps to be filled, such as import barriers between countries or production regions of live fish [16], the standardization of diagnosis methods that can detect fish in chronic stage of infection (or asymptomatic carriers), the monitoring of wild fish as sentinel animals/reservoirs to understand the risk of new emerging pathogens in farmed fish, especially in large water reservoirs located between the borders of countries with different stringency of sanitary programs [17], pathogenesis studies to better understand which tissues show high risk factors in fish imported as food, biosecurity plans within each country and fish farms, including basic protocols for fingerling or juvenile supplier, environmental and feed quality, cleaning and disinfection protocols, and new well-tested immunoprophylaxis products (commercial and/or autogenous vaccines) [18,19,20].

Finally, the control of fish diseases has historically relied on antibiotics, which are often used as food additives, even in the absence of disease. This indiscriminate use has led to selective pressure on the environmental microbiome, with the subsequent transfer of resistance genes to other bacteria. This situation is critical not only for animal safety, but also for human and environmental safety (One Health) [2]. To alleviate this situation, studies have tried to find alternatives to the use of antibiotics, be it genetic selection for fish with better immune parameters/resistance to some diseases [21,22]; the use of alternative molecules, such as new drugs that can be researched using bioinformatics [14,23]; and natural immunostimulants, such as probiotics, prebiotics, symbiotics, and phytogenics [24,25]. These alternatives have been widely used in aquaculture to enhance immune response, compete for binding sites with pathogens, produce antibacterial substances, and improve nutrient absorption [26]. Two factors may be of concern for the research and use of probiotics: first, probiotic effects may vary from species to species, with the need to validate strains for different aquaculture species, which is not currently being undertaken; and second, the use of non-indigenous bacteria may result in changes to the environmental microbiome, for which the use of indigenous bacteria is advisable, a safe alternative for fish and the environment. Research into probiotics for pharmacokinetics, host interactions, nutritional improvement, and pathogen inhibition is needed to develop new immunostimulants and safer products for aquaculture.

In summary, it is necessary to know your enemy (pathogens) in order to develop strategies to control them. In this Special Issue, we have collected important articles within these considerations to highlight the importance of pathogen knowledge and control in the development of better aquaculture.