Multilocus sequence typing detects new Piscirickettsia salmonis hybrid genogroup in Chilean fish farms: Evidence for genetic diversity and population structure

Abstract

Piscirickettsia salmonis is the causative bacterial pathogen of piscirickettsiosis, a salmonid disease that causes notable mortalities in the worldwide aquaculture industry. Published research describes the phenotypic traits, virulence factors, pathogenicity and antibiotic‐resistance potential for various P. salmonis strains. However, evolutionary and genetic information is scarce for P. salmonis . The present study used multilocus sequence typing (MLST) to gain insight into the population structure and evolution of P. salmonis . Forty‐two Chilean P. salmonis isolates, as well as the type strain LF‐89 T , were recovered from diseased Salmo salar, Oncorhynchus kisutch and Oncorhynchus mykiss from two Chilean Regions. MLST assessed the loci sequences of dnaK , efp , fumC , gly A, murG , rpoD and trpB . Bioinformatics analyses established the genetic diversity among P. salmonis isolates (H = 0.5810). A total of 23 sequence types (ST) were identified, 53.48% of which were represented by ST1, ST5 and ST2. Population structure analysis through polymorphism patterns showed few polymorphic sites (218 nucleotides from 4,010 bp), while dN/dS ratio analysis indicated purifying selection for dnaK , epf , fumC , murG , and rpo D but neutral selection for the trpB loci. The standardized index of association indicated strong linkage disequilibrium, suggesting clonal population structure. However, recombination events were detected in a group of seven isolates. Findings included genogroups homologous to the LF‐89 T and EM‐90 strains, as well as a seven‐isolate hybrid genogroup recovered from both assessed regions (three O. mykiss and four S. salar isolates). The presented MLST scheme has comparative potential, with promising applications in studying distinct P. salmonis isolates (e.g., from different hosts, farms, geographical areas) and in understanding the epidemiology of this pathogen.

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