Chilean Salmon Aquaculture Research Articles

Outer membrane vesicles from Piscirickettsia salmonis induce the expression of inflammatory genes and production of IgM in Atlantic salmon Salmo salar.

Piscirickettsiosis outbreaks due to Piscirickettsia salmonis occur globally in the Chilean salmon aquaculture generating significant monetary losses in the industry. P. salmonis secretes outer membrane vesicles (OMVs) which are naturally non-replicating and highly immunogenic spherical nanoparticles. P. salmonis OMVs has been shown to induce immune response in zebrafish; however, the immune response induced by these vesicles in salmonids has not been evaluated. In this study, we inoculated Atlantic salmon with 10 and 30 μg doses of P. salmonis OMVs and took samples for 12 days. qPCR analysis indicated an inflammatory response. Thus, the inflammatory genes evaluated were up- or down-regulated at several times in liver, head kidney and spleen. In addition, the liver was the organ most immune-induced, mainly in the 30 μg-dose. Interestingly, co-expression of pro- and anti-inflammatory cytokines was evidenced by the prominent expression of il-10 at day 1 in spleen and also in head kidney on days 3, 6 and 12, while il-10 and tgf-β were up-regulated on days 3, 6 and 12 in liver. Importantly, we detected the production of IgM against proteins of P. salmonis in the serum collected from immunized fish after 14 days. Thus, 40 and 400 μg OMVs induced the production of highest IgM levels; however, no statistical difference in the immunoglobulin levels produced by these OMVs doses were detected. The current study provides evidence that OMVs released by P. salmonis induced a pro-inflammatory responses and IgM production in S. salar, while regulatory genes were induced in order to regulate their effects and achieve the balance of the inflammatory response.

Piscine Orthoreovirus-1 (PRV-1) Has Been Present in Chilean Salmon Aquaculture since at Least 1994

Heart and skeletal muscle inflammation (HSMI) caused by Piscine orthoreovirus (PRV) was first described in farmed Atlantic salmon in Chile in 2011. However, as PRV induces long-lasting infections, it is not known when Chilean farmed salmon may have started to show PRV positivity. This study aimed to evaluate the presence/absence of PRV-1 in formalin-fixed, paraffin-embedded Atlantic salmon heart tissues (FFPE) cultured in Chile during 1992 and 1999. The most frequent histopathological findings in the 42 FFPE blocks were mild focal cardiomyocyte degeneration (57.1%) and a mild focal mononuclear inflammatory infiltrate (21.4%) in the ventricular stratum spongiosum of the heart. One of the 42 heart samples analyzed by RT-qPCR was positive for PRV-1 (2.4%). All samples were negative for other viral and bacterial pathogens that can induce similar histological changes in the heart. Taken together, our results show that PRV-1 has been present in Chile—as a low-virulence genogroup—since at least 1994, 17 years before the first HSMI outbreak in 2011. Finally, archaeovirology can be a valid alternative to contribute to the understanding of the epidemiology of diseases in aquaculture.

Misunderstandings and misinterpretations: Antimicrobial use and resistance in salmon aquaculture.

The exponential growth of aquaculture over the past 30 years has been accompanied by a parallel increase in the use of antimicrobials. This widespread use has had negative effects on animal, human and environmental health and affected the biodiversity of the environments where aquaculture takes place. Results showing these harmful effects have been resisted and made light of by the aquaculture industry and their scientific supporters through introduction of misunderstandings and misinterpretations of concepts developed in the evolution, genetics, and molecular epidemiology of antimicrobial resistance. We focus on a few of the most obvious scientific shortcomings and biases of two recent attempts to minimise the negative impacts of excessive antimicrobial use in Chilean salmon aquaculture on human and piscine health and on the environment. Such open debate is critical to timely implementation of effective regulation of antimicrobial usage in salmon aquaculture in Chile, if the negative local and worldwide impacts of this usage are to be avoided.

Co-Infection by LF-89-Like and EM-90-Like Genogroups of Piscirickettsia Salmonis in Farmed Atlantic Salmon in Chile: Implications for Surveillance and Control of Piscirickettsiosis

Piscirickettsiosis (SRS), caused by Piscirickettsia salmonis, is the main infectious disease that affects farmed Atlantic salmon in Chile. Currently, the official surveillance and control plan for SRS in Chile is based only on the detection of P. salmonis, but neither of its genogroups (LF-89-like and EM-90-like) are included. Surveillance at the genogroup level is essential not only for defining and evaluating the vaccination strategy against SRS, but it is also of utmost importance for early diagnosis, clinical prognosis in the field, treatment, and control of the disease. The objectives of this study were to characterize the spatio-temporal distribution of P. salmonis genogroups using genogroup-specific real-time probe-based polymerase chain reaction (qPCR) to discriminate between LF-89-like and EM-90-like within and between seawater farms, individual fish, and tissues/organs during early infection in Atlantic salmon under field conditions. The spatio-temporal distribution of LF-89-like and EM-90-like was shown to be highly variable within and between seawater farms. P. salmonis infection was also proven to be caused by both genogroups at farm, fish, and tissue levels. Our study demonstrated for the first time a complex co-infection by P. salmonis LF-89-like and EM-90-like in Atlantic salmon. Liver nodules (moderate and severe) were strongly associated with EM-90-like infection, but this phenotype was not detected by infection with LF-89-like or co-infection of both genogroups. The detection rate of P. salmonis LF-89-like increased significantly between 2017 and 2021 and was the most prevalent genogroup in Chilean salmon aquaculture during this period. Lastly, a novel strategy to identify P. salmonis genogroups based on novel genogroup-specific qPCR for LF-89-like and EM-90-like genogroups is suggested.

Neostructural innovation and directionality in Chilean salmon aquaculture

The recent work of Mariana Mazzucato on the role of public funding in economic development seeks to rebalance debates on innovation to highlight the role of the State, as opposed to the dominant narrative of unregulated private initiative. This is particularly relevant for the case of the Chilean salmon industry where, besides the diffusion of technology and management practices by a combination of international agencies and private initiatives, its boom has been supported by considerable national public funding since the 1970s and especially after the transition to democracy in 1990. In this regard, the main argument of this paper is that the innovation system of the Chilean salmon industry should be understood within a neostructural model of economic development. However, although the State has had an essential role in financing and promoting innovation, we found that it has not served as a guiding entity (directionality) for how innovation should be undertaken. This is important to recognise since it helps to explain why the Chilean salmon industry has been able to direct innovation towards its own economic interests without attending to broader social issues related to its operations, despite this public expenditure. The main conclusion is that, due to the type of knowledge developed and how innovations are valued within the sector’s innovation system, the goal is to increase volume, reduce costs, and marginally mitigate negative socio-ecological externalities.

Nanopore sequencing evidenced the presence of fish bacterial pathogens in the sea louse (Caligus rogercresseyi) microbiota collected from distant salmon farms in Chile

The recognized negative impacts of the ectoparasite Caligus rogercresseyi in the Chilean salmon aquaculture are primarily related to environmental and economic issues. However, recent evidence suggests a large and diverse microbial community associated with sea lice, where fish bacteria pathogens emerge as a sanitary concern. This study aimed to characterize the bacterial community associated with C. rogercresseyi, focusing on those microorganisms with potential impacts in salmon welfare. The sea lice-associated microbiota was identified using the microbial full-length16S rRNA gene sequencing by Oxford Nanopore Technology. Sea lice specimens were collected from three salmon farming zones in Los Lagos, Aysén, and Magallanes, Southern Chile. The bioinformatic analyses revealed DNA from potential pathogens inhabiting the C. rogercresseyi microbiota, representing 7.86% of the annotated sequences. Among the sampled sites, the most significant number of pathogenic bacteria DNA was found in Los Lagos (up to 23,6%), followed by Aysen (1,8%) and Magallanes (0.3%). Herein, genetic evidence from a total of 30 potential fish bacterial pathogens species were identified. Notably, fourteen Vibrio spp. were predominantly found in the Los Lagos region, while six Tenacibaculum spp. were more equally distributed among the sites. A core of five fish pathogens was observed in all farming zones, including Aliivibrio wodanis, Tenacibaculum dicentrarchi, Tenacibaculum ovolyticum, Tenacibaculum soleae, and Vibrio splendidus. Based on the reported findings, sea lice emerge as a potential reservoir for fish diseases in the aquatic environment.

Re-framing salmon aquaculture in the aftermath of the ISAV crisis in Chile

Globally, aquaculture is expanding rapidly, with salmon becoming one of the most dynamic and fast-growing production systems in the world. Despite its commercial success, Chilean salmon production has navigated through severe economic and sanitary crises; followed by consecutive policy changes. Between 2007 and 2009, the rapid spread and the multiple effects of the Infectious Salmon Anemia virus (ISAV) marked a tipping point in the trajectory of the salmon aquaculture in southern Chile. This paper examines the discursive mechanisms through which the Chilean salmon aquaculture industry is currently being re-framed in the aftermath of the ISAV crisis, with a focus on searching for the emergence of ecosystem-related elements post crisis. The analysis shows that Chilean salmon aquaculture is being re-framed by the reproduction of three main discourses: biosecurity, sustainable protein and The Promise of Patagonia. The paper concludes that despite the staggering effects of the ISAV crisis on the national salmon production and on coastal communities more than a decade ago, new discourses are focused on the legitimization to growth, in the absence of integrated marine ecosystem-related elements, indicating a crucial gap toward environmental sustainability in salmon aquaculture.

Identification and characterization of outer membrane vesicles from the fish pathogen Vibrio ordalii.

Vibriosis outbreaks due to Vibrio ordalii occur globally, but Chilean salmon aquaculture, in particular, has suffered significant monetary losses in the last 15years. Little is known about the virulence mechanisms employed by V.ordalii. However, most Vibrio pathogens (e.g., Vibrio anguillarum, a very close taxonomic species) present outer membrane vesicles (OMVs) that are released extracellularly and implicated in the delivery of virulence factors to host cells. This study provides the first reported evidence of the fish pathogen V.ordalii producing and releasing OMVs under normal growth conditions. Analyses were conducted with the V.ordalii strain Vo-LM-18 and the type strain ATCC 33509T . For comparative purposes, the reference strain V.anguillarum ATCC 43307 was employed. The average size for the three Vibrio strains was 0.215±0.6µm (via scanning electron microscopy) or between 0.19 and 1.8µm (via dynamic light scattering), with each bacterium presenting a wide range. SDS-PAGE revealed similarities in OMV patterns, but neither total nor external proteins were identical. Comparing V.ordalii ATCC 33509T and Vo-LM-18, bands were most evident in the total proteins, and the greatest degree of similarity in OMV profiles was between 37 and 50kDa. The purified OMVs demonstrated haemolytic enzyme activity, which could play a role during V.ordalii infection. These data represent an initial step towards gaining new insights into this virulence factor, of which a lot is known in other pathogenic microorganisms.

Current Status of the Use of Antibiotics and the Antimicrobial Resistance in the Chilean Salmon Farms.

The Chilean salmon industry has undergone a rapid development making the country the world’s second largest producer of farmed salmon, but this growth has been accompanied by an intensive use of antibiotics. This overuse has become so significant that Chilean salmon aquaculture currently has one of the highest rates of antibiotic consumption per ton of harvested fish in the world. This review has focused on discussing use of antibiotics and current status of scientific knowledge regarding to incidence of antimicrobial resistance and associated genes in the Chilean salmonid farms. Over recent years there has been a consistent increase in the amount of antimicrobials used by Chilean salmonid farms, from 143.2 tons in 2010 to 382.5 tons in 2016. During 2016, Chilean companies utilized approximately 0.53 kg of antibiotics per ton of harvested salmon, 363.4 tons (95%) were used in marine farms, and 19.1 tons (5%) in freshwater farms dedicated to smolt production. Florfenicol and oxytetracycline were by far the most frequently used antibiotics during 2016 (82.5 and 16.8%, respectively), mainly being used to treat Piscirickettsia salmonis, currently considered the main bacterial threat to this industry. However, the increasing development of this industry in Chile, as well as the intensive use of antimicrobials, has not been accompanied by the necessary scientific research needed to understand the impact of the intensive use of antibiotics in this industry. Over the last two decades several studies assessing antimicrobial resistance and the resistome in the freshwater and marine environment impacted by salmon farming have been conducted, but information on the ecological and environmental consequences of antibiotic use in fish farming is still scarce. In addition, studies reporting the antimicrobial susceptibility of bacterial pathogens, mainly P. salmonis, have been developed, but a high number of these studies were aimed at setting their epidemiological cut-off values. In conclusion, further studies are urgently required, mainly focused on understanding the evolution and epidemiology of resistance genes in Chilean salmonid farming, and to investigate the feasibility of a link between these genes among bacteria from salmonid farms and human and fish pathogens.

Intestinal incomplete process on the osmoregulation system during Salmo salar smoltification in a productive conditions

Smoltification under intensive aquaculture conditions involves important physiological changes to intestinal structures that facilitate acclimation to hyperosmotic environments. This study evaluated if genic expression of primary contributors during the smoltification process in the intestine are in synchrony with gill Na+/K+-ATPase activity. Discordance was found between gill Na+/K+-ATPase activity levels and intestinal genic expressions. In particular, the intestine showed increased mRNA expression for prolactin, a hormone that participates in hypoosmotic environments, and in mRNA expression of the growth hormone, which mediates the hydromineral balance in hyperosmotic environments. These findings indicate a lack of sufficient intestinal maturation in the fish at the moment when they were transferred to seawater environments in the normal aquaculture practices. This intestinal immaturity is a possible explanation for the high rates of desadapted individuals in the seawater phase in Chilean salmon aquaculture.

Insights into the diversity and metabolic function of bacterial communities in sediments from Chilean salmon aquaculture sites

Aquaculture is an extremely valuable and rapidly expanding sector worldwide, but concerns exist related to environmental sustainability. The sediment below aquaculture farms receives inputs of antimicrobials, metal-containing products, and organic matter from uneaten food and fecal material. These inputs impact the surrounding marine microbial communities in complex ways; however, functional diversity shifts related to taxonomic composition remain poorly understood. Here, we investigated the effect of pollution from marine fish farms on sediment bacterial communities. We compared the bacterial communities and functional bacterial diversity in surface sediments at salmon aquaculture and reference sites in Chiloe, southern Chile, using Roche 454 pyrosequencing of the 16S ribosomal RNA (rRNA) gene and the predictive metagenomics approach (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States, PICRUSt). Bacterial diversity, measured as the inverse Simpson index, was significantly lower at aquaculture than at reference sites, while species richness, based on Chao’s estimator, was not significantly different. Nevertheless, community composition differed significantly between reference and aquaculture sites. We found that Gammaproteobacteria and several taxa involved in remediating metal contamination and known to have antimicrobial resistances were enriched at aquaculture sites. However, PICRUSt predicted functions indicated a degree of functional redundancy between sites, whereas taxonomic-functional relationships indicated differences in the functional traits of specific taxa at aquaculture sites. This study provides a first step in understanding the bacterial community structure and functional changes due to Chilean salmon aquaculture and has direct implications for using bacterial shifts as indicators of aquaculture perturbations.

In the shadow: The emerging role of long non-coding RNAs in the immune response of Atlantic salmon

The genomic era has increased the research effort to uncover how the genome of an organism, and specifically the transcriptome, is modulated after interplaying with pathogenic microorganisms and ectoparasites. However, the ever-increasing accessibility of sequencing technology has also evidenced regulatory roles of long non-coding RNAs (lncRNAs) related to several biological processes including immune response. This study reports a high-confidence annotation and a comparative transcriptome analysis of lncRNAs from several tissues of Salmo salar infected with the most prevalent pathogens in the Chilean salmon aquaculture such as the infectious salmon anemia (ISA) virus, the intracellular bacterium Piscirickettsia salmonis and the ectoparasite copepod Caligus rogercresseyi. Our analyses showed that lncRNAs are widely modulated during infection. However, this modulation is pathogen-specific and highly correlated with immuno-related genes associated with innate immune response. These findings represent the first discovery for the widespread differential expression of lncRNAs in response to infections with different types of pathogens in Atlantic salmon, suggesting that lncRNAs are pivotal player during the fish immune response.

Novel insights into the response of Atlantic salmon (Salmo salar) to Piscirickettsia salmonis: Interplay of coding genes and lncRNAs during bacterial infection

Despite the high prevalence and impact to Chilean salmon aquaculture of the intracellular bacterium Piscirickettsia salmonis, the molecular underpinnings of host-pathogen interactions remain unclear. Herein, the interplay of coding and non-coding transcripts has been proposed as a key mechanism involved in immune response. Therefore, the aim of this study was to evidence how coding and non-coding transcripts are modulated during the infection process of Atlantic salmon with P. salmonis. For this, RNA-seq was conducted in brain, spleen, and head kidney samples, revealing different transcriptional profiles according to bacterial load. Additionally, while most of the regulated genes annotated for diverse biological processes during infection, a common response associated with clathrin-mediated endocytosis and iron homeostasis was present in all tissues. Interestingly, while endocytosis-promoting factors and clathrin inductions were upregulated, endocytic receptors were mainly downregulated. Furthermore, the regulation of genes related to iron homeostasis suggested an intracellular accumulation of iron, a process in which heme biosynthesis/degradation pathways might play an important role. Regarding the non-coding response, 918 putative long non-coding RNAs were identified, where 425 were newly characterized for S. salar. Finally, co-localization and co-expression analyses revealed a strong correlation between the modulations of long non-coding RNAs and genes associated with endocytosis and iron homeostasis. These results represent the first comprehensive study of putative interplaying mechanisms of coding and non-coding RNAs during bacterial infection in salmonids.

Antimicrobial resistance genes in marine bacteria and human uropathogenic Escherichia coli from a region of intensive aquaculture.

Antimicrobials are heavily used in Chilean salmon aquaculture. We previously found significant differences in antimicrobial-resistant bacteria between sediments from an aquaculture and a non-aquaculture site. We now show that levels of antimicrobial resistance genes (ARG) are significantly higher in antimicrobial-selected marine bacteria than in unselected bacteria from these sites. While ARG in tetracycline- and florfenicol-selected bacteria from aquaculture and non-aquaculture sites were equally frequent, there were significantly more plasmid-mediated quinolone resistance genes per bacterium and significantly higher numbers of qnrB genes in quinolone-selected bacteria from the aquaculture site. Quinolone-resistant urinary Escherichia coli from patients in the Chilean aquacultural region were significantly enriched for qnrB (including a novel qnrB gene), qnrS, qnrA and aac(6')-1b, compared with isolates from New York City. Sequences of qnrA1, qnrB1 and qnrS1 in quinolone-resistant Chilean E. coli and Chilean marine bacteria were identical, suggesting horizontal gene transfer between antimicrobial-resistant marine bacteria and human pathogens.

Transcriptome immunomodulation of in-feed additives in Atlantic salmon Salmo salar infested with sea lice Caligus rogercresseyi.

One of the most significant threats to the Chilean salmon aquaculture industry is the ectoparasitic sea louse Caligus rogercresseyi. To cope with sea lice infestations, functional diets have become an important component in strengthening the host immune response. The aim of this study was to evaluate molecular mechanisms activated through immunostimulation by in-feed plant-derived additives in Atlantic salmon infected with sea lice. Herein, a transcriptome-wide sequencing analysis was performed from skin and head kidney tissues, evidencing that the immune response genes were the most variable after the challenge, especially in the head kidney, while other genes involved in metabolism were highly expressed individuals fed with the immunostimulants. Interestingly, defensive enzymes such as Cytochrome p450 and serpins were down-regulated in infested individuals, especially in skin tissue. Additionally, MHC-I and MHC-II genes were differentially expressed after the incorporation of the in-feed additives, giving some cues about the protection mechanisms of plant-derived compound as immunostimulants for infested salmons. This is the first published study that evaluates the transcriptomic response of sea lice-infested Atlantic salmon fed with in-feed additives.

Frequent haplotypes of caged Caligus rogercresseyi in the austral south of Chile: The result of a long term serial passage experiment?

Caligus rogercresseyi is an ectoparasite that causes enormous economic losses to the Chilean salmon aquaculture industry. It has been proposed that native fish are a reservoir of this parasite and that pesticide treatments to control it have led to pharmacological resistance to the chemotherapeutic substances that are broadly used in the austral south of Chile. During 2012–2013, 686bp in the 18s rRNA gene of C. rogercresseyi were sequenced, collected from Salmo salar cultured in five areas between 41°30′S and 45°30′S in Chile. The results show a total of 24 haplotypes, two of which were highly frequent and present in all studied areas (A=36.7% and B=16.3%), as well as in larvae raised under laboratory conditions (A=44% and B=25%). A and B haplotypes were also present in stored sequences of this parasite in the GenBank database from 2003. Seven less frequent haplotypes were found dispersed in four of the areas studied, and the remaining fifteen haplotypes were only present in low frequencies and only in one area. Analysis of the population structure of C. rogercresseyi indicated that the samples collected are part of a panmictic population but with low genetic flow inside the study area, as following a bottleneck event. Hypothetically, after over a decade of this population parasitizing a caged host with low genetic diversity (S. salar), and after repeated exposure to neurotoxic pesticides, the most frequent haplotypes A and B could be the result of drug selective pressure acting inside the cages in a kind of long term serial passage experiment. Finally, the characterization of the molecular footprints of these most frequent haplotypes makes them good candidates for use in experiments to test their resistance to drug treatments. Statement of relevanceThe use of haplotypes described in this study, especially A and B, in experiments of drug resistance in this parasite is relevant compared to the use of unknown haplotypes. This could be important for determining the kind of drugs used against this parasite as well as in the study of resistance mechanisms to the chemotherapeutic substances used in Chilean aquaculture.

Transcriptomic insights on the ABC transporter gene family in the salmon louse Caligus rogercresseyi.

BackgroundATP-binding cassette (ABC) protein family encode for membrane proteins involved in the transport of various biomolecules through the cellular membrane. These proteins have been identified in all taxa and present important physiological functions, including the process of insecticide detoxification in arthropods. For that reason the ectoparasite Caligus rogercresseyi represents a model species for understanding the molecular underpinnings involved in insecticide drug resistance.Methodsllumina sequencing was performed using sea lice exposed to 2 and 3 ppb of deltamethrin and azamethiphos. Contigs obtained from de novo assembly were annotated by Blastx. RNA-Seq analysis was performed and validated by qPCR analysis.ResultsFrom the transcriptome database of C. rogercresseyi, 57 putative members of ABC protein sequences were identified and phylogenetically classified into the eight subfamilies described for ABC transporters in arthropods. Transcriptomic profiles for ABC proteins subfamilies were evaluated throughout C. rogercresseyi development. Moreover, RNA-Seq analysis was performed for adult male and female salmon lice exposed to the delousing drugs azamethiphos and deltamethrin. High transcript levels of the ABCB and ABCC subfamilies were evidenced. Furthermore, SNPs mining was carried out for the ABC proteins sequences, revealing pivotal genomic information.ConclusionsThe present study gives a comprehensive transcriptome analysis of ABC proteins from C. rogercresseyi, providing relevant information about transporter roles during ontogeny and in relation to delousing drug responses in salmon lice. This genomic information represents a valuable tool for pest management in the Chilean salmon aquaculture industry.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-015-0801-x) contains supplementary material, which is available to authorized users.

Genetic co-variation between resistance against both Caligus rogercresseyi and Piscirickettsia salmonis, and body weight in Atlantic salmon (Salmo salar)

Abstract Infectious and parasitic diseases are recognized worldwide as primary causes of economic losses in salmon production. Piscirickettsia salmonis and Caligus rogercresseyi are the main diseases affecting the Chilean salmon aquaculture. In this study, we used data from experimental challenges against P. salmonis and C. rogercresseyi in full- and half-sibs from 118 families belonging to a Salmo salar breeding nucleus. Resistance against P. salmonis (SRS) was defined as the day of death of each fish and C. rogercresseyi resistance (CAL) was measured as the parasite load. We also measured body weight (BW) in full-sibs of the tested fish. We used a multi-trait animal model to estimate (co)variance components and to calculate genetic parameters. For BW we included contemporary group (sex*tank) as factor and age as a covariate. In addition, tank was included as a factor and weight at the end of test as a covariate for SRS and CAL. The estimated heritabilities for BW, SRS and CAL were 0.4 (± 0.05), 0.18 (± 0.03) and 0.1 (± 0.03), respectively. The genetic correlations between BW–SRS, BW–CAL and SRS–CAL were − 0.19 (± 0.12), − 0.32 (± 0.14) and − 0.02 (± 0.17), respectively. The levels of genetic variation and the magnitude of the genetic correlations between resistance to P. salmonis , C. rogercresseyi and body weight found in the present study demonstrate the feasibility for the improvement of these traits simultaneously by means of selective breeding.

Antimicrobial resistance and antimicrobial resistance genes in marine bacteria from salmon aquaculture and non‐aquaculture sites

Antimicrobial resistance (AR) detected by disc diffusion and antimicrobial resistance genes detected by DNA hybridization and polymerase chain reaction with amplicon sequencing were studied in 124 marine bacterial isolates from a Chilean salmon aquaculture site and 76 from a site without aquaculture 8 km distant. Resistance to one or more antimicrobials was present in 81% of the isolates regardless of site. Resistance to tetracycline was most commonly encoded by tetA and tetG; to trimethoprim, by dfrA1, dfrA5 and dfrA12; to sulfamethizole, by sul1 and sul2; to amoxicillin, by blaTEM ; and to streptomycin, by strA-strB. Integron integrase intl1 was detected in 14 sul1-positive isolates, associated with aad9 gene cassettes in two from the aquaculture site. intl2 Integrase was only detected in three dfrA1-positive isolates from the aquaculture site and was not associated with gene cassettes in any. Of nine isolates tested for conjugation, two from the aquaculture site transferred AR determinants to Escherichia coli. High levels of AR in marine sediments from aquaculture and non-aquaculture sites suggest that dispersion of the large amounts of antimicrobials used in Chilean salmon aquaculture has created selective pressure in areas of the marine environment far removed from the initial site of use of these agents.

Transmission of Piscirickettsia salmonis among salt water salmonid farms in Chile

Salmon Rickettsia Syndrome (SRS), also known as Salmon Rickettsia Septicemia, caused by Piscirickettsia salmonis is the most common bacterial disease in the Chilean salmon aquaculture industry. The epidemiology of this pathogen is relatively unknown. Using the Chilean salmon aquaculture industry monthly diagnostic data collected between January 2009 and December 2012, we assessed the spatial and environmental factors associated with the reporting of SRS on Atlantic salmon, coho salmon, and rainbow trout farms. Crops of fish were on average 60% likely to report SRS during our study time period. The probability of a farm reporting SRS was positively associated with temperature, time in salt water, and the number of SRS infected neighbors. The distance effect from infected neighboring farms that best fit the model for predicting SRS on a farm varied by species but ranged between 7.5 and 10 km. Our study suggests reducing disease on farms will not only benefit the producer but also reduce the probability that P. salmonis is transferred to neighboring farms.