ORIGINAL ARTICLE Comparison of gene expression in post-smolt Atlantic salmon challenged by LF-89-like and EM-90-like Piscirickettsia salmonis isolates reveals differences in the immune response associated with pathogenicity M Rozas-Serri 1,2 | A Pe ~ na 1 | G Arriagada 3 | R Enr  ıquez 4 | L Maldonado 1 1 Pathovet Laboratory Ltd., Puerto Montt, Chile 2 Faculty of Veterinary Sciences, Graduate School, Austral University of Chile, Valdivia, Chile 3 EPI-data Research & Consulting, Santiago, Chile 4 Laboratory of Aquatic Pathology and Biotechnology, Faculty of Veterinary Sciences, Animal Pathology Institute, Universidad Austral de Chile, Valdivia, Chile Correspondence M Rozas-Serri, Pathovet Laboratory Ltd., Puerto Montt, Chile. Email: marco.rozas@pathovet.cl Funding information This work was supported by a Doctorate Scholarship (21120228) from the Program for the Formation of Advanced Human Capital Program, National Commission for Scientific and Technological Research, CONICYT, Chile, by a Grant to Operating Expenses (2014–2015), provided by CONICYT, Chile, by the Strategic Investment Fund (FIE-2015-V014) of the Health Management Program for Aquaculture, National Fisheries and Aquaculture Service, Sernapesca, Chile, by the Chilean Economic Abstract Piscirickettsiosis is the main bacterial disease affecting the Chilean salmon farming industry and is responsible for high economic losses. The aim of this study was to describe and comparatively quantify the immune response of post-smolt Atlantic salmon infected by cohabitation with fish bearing LF-89-like and EM-90-like Piscir- ickettsia salmonis. The expression of 17 genes related to the immune response was studied in head kidney from cohabitant fish by RT-qPCR. Our results at the transcriptomic level suggest that P. salmonis is able to manipulate the kinetics of cytokine production in a way that might constitute a virulence mechanism that pro- motes intracellular bacterial replication in cells of Atlantic salmon. This strategy involves the creation of an ideal environment for the microorganism based on induction of the inflammatory and IFN-mediated response, modulation of Th1 polar- ization, reduced antigen processing and presentation, modulation of the evasion of the immune response mediated by CD8 + T cells and promotion of the CD4 + T-cell response during the late stage of infection as a mechanism to escape host defences. This response was significantly exacerbated in fish infected by PS-EM-90 compared with fish infected by PS-LF-89, a finding that is probably associated with the higher pathogenicity of PS-EM-90. KEYWORDS immune response, Piscirickettsia salmonis, RT-qPCR Development Agency (CORFO) and by the Pathovet Laboratory Ltd. (15ITE2-47464). 1 | INTRODUCTION Piscirickettsiosis (SRS) is the main bacterial disease of fish in the Chi- lean salmon farming industry and is responsible for annual economic losses of approximately US $500 million (Rozas & Enriquez, 2014). The aetiologic agent of SRS is Piscirickettsia salmonis (Fryer, Lannan, Giovannoni, & Wood, 1992), which is classified within the recently denominated Piscirickettsiaceae family of the Thiotrichales order (Mauel, Giovannoni, & Fryer, 1999). Piscirickettsia salmonis isolates show high levels of similarity, although the EM-90 isolate is situated separately (Mauel et al., 1999). The LF-89-like and EM-90-like field isolates exhibit genomic differences that appear to determine differ- ent degrees of virulence (Bohle et al., 2014) and different SRS pathogenesis in post-smolt Atlantic salmon infected via cohabitation (Rozas-Serri et al., 2017). In Chile, the strategy for controlling SRS focuses primarily on antimicrobial therapy and vaccination (Jakob et al., 2014; Rozas & Enriquez, 2014). However, to control SRS, it is necessary to use large amounts of antibiotics in fish farming, and Received: 18 August 2017 | Revised: 14 October 2017 | Accepted: 17 October 2017 DOI: 10.1111/jfd.12756 J Fish Dis. 2017;1–14. wileyonlinelibrary.com/journal/jfd © 2017 John Wiley & Sons Ltd | 1