J Fish Dis. 2019;00:1–11. wileyonlinelibrary.com/journal/jfd | 1 © 2019 John Wiley & Sons Ltd 1 | INTRODUCTION Chile is the second largest producer of farmed salmon and trout in the world after Norway (FAO, 2011). The national and interna‐ tional salmon farming industry is mainly threatened by extensive losses caused by infectious and contagious diseases occurring during the production cycle. Salmonid rickettsial septicaemia (SRS) or Piscirickettsiosis is one of the leading diseases affecting salmon reared in net pens in Chile, whose bacterial causative agent is Piscirickettsia salmonis, a Gram‐negative, obligate, intracellular, non‐motile and non‐encapsulated pathogen characterized by a variable diameter ranging between 0.5 and 1.5 µm. Piscirickettsia salmonis isolate LF‐89, described by Fryer, Lannan, Giovannoni, and Wood (1992), is classified as a reference strain (Cvitanich, Garate n., & Smith, 1991; Fryer, Lannan, Garcés, Larenas, & Smith, 1990). Piscirickettsiosis affects different varieties of salmon species, mainly Atlantic salmon (Salmon salar L.), rainbow trout (Oncorhynchus mykiss W.) and Coho salmon (Oncorhynchus kisutch W.). Antibiotics have been used for many years as the first tool in the prevention and treatment of this infectious and contagious disease, being florfenicol and oxytetracycline by far the two most commonly used antimicrobials in Chile (Grave, Lingaas, Bangen, Received: 3 June 2019 | Revised: 2 August 2019 | Accepted: 5 August 2019 DOI: 10.1111/jfd.13089 ORIGINAL ARTICLE Analysis of single nucleotide polymorphisms (SNPs) associated with antibiotic resistance genes in Chilean Piscirickettsia salmonis strains Jaime Figueroa 1,2 | Diana Castro 2 | Fernando Lagos 2 | Carlos Cartes 2 | Adolfo Isla 2 | Alejandro J. Yáñez 1,2 | Rubén Avendaño‐Herrera 2,3 | Denise Haussmann 4 1 Faculty of Sciences, Institute of Biochemistry and Microbiology, Universidad Austral de Chile, Valdivia, Chile 2 FONDAP Centre, Interdisciplinary Centre for Aquaculture Research (INCAR), Concepción, Chile 3 Laboratory of Pathology of Aquatic Organisms and Aquaculture Biotechnology, Faculty of Life Sciences, Universidad Andrés Bello, Viña del Mar, Chile 4 Department of Basic Sciences, Faculty of Sciences, Universidad Santo Tomás, Valdivia, Chile Correspondence Jaime Figueroa, Faculty of Sciences, Institute of Biochemistry and Microbiology, Universidad Austral de Chile, Valdivia, Chile. Email: jefigueroa@uach.cl Funding information Interdisciplinary Centre for Aquaculture Research (INCAR) at Universidad Austral de Chile, Grant/Award Number: 122929 and 15110027 Abstract The aetiological agent of Piscirickettsiosis is Piscirickettsia salmonis, a Gram‐negative intracellular pathogen, and high doses of antibiotics have regularly been employed to treat this infection. Seven florfenicol and/or oxytetracycline resistance genes (tet pump, tetE, Tclor/flor , Tbcr , TfloR, ompF and mdtN) were identified in strains by in silico genome analyses. Later, the number of single nucleotide polymorphisms (SNPs) and its relationship with the resistance to these antibiotics were identified and analysed, using the original LF‐89 strain as reference. Trials to determine and compare the minimum inhibitory concentration (MIC) of oxytetracycline and florfenicol in each strain, as well as to quantify the gPCR transcripts levels in the selected genes, were performed. Therefore, variations in the resistance to both antibiotics were observed, where the strain with fewer SNPs showed the highest susceptibility. Consistently, the in silico 3D analyses of proteins encoded by the selected genes revealed struc‐ tural changes, evident in the sequences with the highest number of SNPs. These re‐ sults showed that the bacterial resistance to oxytetracycline was mainly linked to the presence of SNPs in relevant sites, antibiotic resistance genes and an OmpF porin, leading to important changes in the protein structure. KEYWORDS florfenicol, oxytetracycline, Piscirickettsiosis, resistance genes, SNPs