We report the first isolation, identification and characterization of a group of Chilean strains of atypical Aeromonas salmonicida isolated from freshwater farmed Atlantic salmon, Salmo salar. Affected fish showed superficial ulcers and pale liver with or without petechial haemorrhages. Outbreaks of the disease occurred in two farms in the south of Chile about 2200 km apart. Five strains were isolated in pure culture and identified by serological assays and immunofluorescence tests as belonging to Aeromonas salmonicida. Although the bacterial isolates were phenotypically homogeneous, minor differences with the reference strain A. salmonicida subsp. salmonicida ATCC 33658 were noted. Three specific primer sets and partial 16S rRNA gene sequencing allowed the identification of the Chilean isolates as atypical A. salmonicida, with A. salmonicida subsp. achromogenes and A. salmonicida subsp. masoucida as their closest relatives (100% sequence similarity). Molecular typing indicated that the atypical isolates belong to two genetic groups that were associated with the geographical origin.

The objective of this study was to evaluate the application of a TaqMan ® real-time reverse transcriptase PCR (RT-PCR) assay for the detection of infectious salmon anaemia virus (ISAV) in formalin-fixed paraffin-embedded (FFPE) fish tissues from Atlantic salmon Salmo salar with and without clinical signs of infection, and to compare it with histological and immunohistochemical (IHC) techniques. Sixteen fish samples obtained in 2007 and 2008 from 4 different farms in Chile were examined. The real-time RT-PCR allowed the detection of ISAV in FFPE samples from 9 of 16 fish, regardless of the organs analyzed, whereas 4 of the real-time RT-PCR negative fish were positive as indicated by histological examination and 3 of the real-time RT-PCR positive fish were negative as indicated by immunohistochemistry evaluation. The presence of ISAV in RT-PCR positive samples was confirmed by amplicon sequencing. This work constitutes the first report on the use of real-time RT-PCR for the detection of ISAV in FFPE sections. The assay is very useful for the examination of archival wax-embedded tissues, and allows for both prospective and retrospective evaluation of tissue samples for the presence of ISAV. However, the method only confirms the presence of the pathogen and should be used in combination with histopathology, which is a more precise tool. The combination of both techniques would be invaluable for confirmatory diagnosis of infectious salmon anaemia (ISA), which is essential for solving salmon farm problems.

Caligus rogercresseyi is the dominant sea louse parasite affecting the salmon and trout industry in southern Chile. This parasite has a wide range of native and endemic fish hosts. The Patagonian blenny Eleginops maclovinus, which is parasitized mostly by the caligid species Lepeophtheirus spp. and C. rogercresseyi, is presumably responsible for the transmission of C. rogercresseyi to salmonids. The aim of this study was to characterize the transmission of parasites between different fish species and parasite cohort development under laboratory conditions. Parasite abundances and intensities were quantified. Transmission of parasites from Patagonian blenny to Atlantic salmon Salmo salar was lower (~9%, mainly corresponding to C. rogercresseyi) than from salmon to Patagonian blenny (14.7-26.9%, where only C. rogercresseyi were observed). This suggests that the transmission of C. rogercresseyi from salmon individuals is higher than the transmission from a native fish. Parasite cohorts developed successfully on both fish species, but apparently under different developmental rates. Water temperature, oxygen, and juvenile abundances were the variables that better explained cohort development success and variation in C. rogercresseyi adult abundances over time.

A major challenge for Chilean salmon farming is infestation by the ectoparasite Caligus rogercresseyi. In addition, there is evidence that a loss of chemotherapeutic treatment efficacy against important fish pathogens is occurring in salmon farming, including antiparasitic efficacy. Currently, there are known techniques that allow the determination of the susceptibility profile of parasites to antiparasitic treatment. However, there is scarce information about both threshold values and categorization of antiparasitic susceptibility for C. rogercresseyi. Bioassay technique allowed the determination of both mean values and the natural variation of EC50%, which were contrasted with available susceptibility thresholds. Results allowed to determine that parasites from the native fish host, Eleginops maclovinus, are susceptible to azamethiphos, deltamethrin and cypermethrin treatments, showing a high susceptibility profile to antiparasitics.