Comparative genomic analysis of two Chilean Renibacterium salmoninarum isolates and the type strain ATCC 33209T

Abstract

Indexación: Scopus.Two previously characterized Chilean isolates (H-2 and DJ2R), obtained from cage-cultured Atlantic salmon with clinical signs of bacterial kidney disease in southern Chile, were used (Bethke et al. 2016, 2017). The bacteria were routinely cultured in KDM-2 agar for 15–20 days at 15°C. For sequencing, genomic DNA of the two isolates was extracted using the InstaGene Purification Matrix (Bio-Rad) according to manufacturer instructions. The DJ2R genome was sequenced using an Illumina MiSeq platform with 2 ⨯ 250 paired-end reads by the AUSTRAL-omics Institute, hosted by the Universidad Austral de Chile (Valdivia, Chile). Using the same technology and parameters, H-2 genomic DNA was sequenced by the Central Support Service for Experimental Research (SCSIE, Spanish acronym) at the University of Valencia (Valencia, Spain).This work was supported by funding of the Comisión Nacional de Investigación Científica y Tecnológica (CONICYT, Chile) [Grant Numbers FONDAP No. 15110027 and FONDECYT No. 1150695]. J.B. also acknowledges support received by CONICYT [Doctoral Scholarship No. 21140421].Renibacterium salmoninarum, a slow-growing facultative intracellular pathogen belonging to the high C+G content Actinobacteria phylum, is the causative agent of bacterial kidney disease, a progressive granulomatous infection affecting salmonids worldwide. This Gram-positive bacterium has existed in the Chilean salmonid industry for >30 years, but little or no information is available regarding the virulence mechanisms and genomic characteristics of Chilean isolates. In this study, the genomes of two Chilean isolates (H-2 and DJ2R)were sequenced, and a search was conducted for genes and proteins involved in virulence and pathogenicity, andwecompare with the type strain ATCC 33209T genome. The genome sizes of H-2 and DJ2R are 3,155,332 bp and 3,155,228 bp, respectively. They genomes presented six ribosomal RNA, 46 transcription RNA, and 25 noncodingRNA, and both had the same 56.27% G+C content described for the type strain ATCC 33209 T. A total of 3,522 and 3,527 coding sequences were found for H-2 and DJ2R, respectively. Meanwhile, the ATCC 33209T type strain had 3,519 coding sequences. The in silico genome analysis revealed a genes related to tricarboxylic acid cycle, glycolysis, iron transport and others metabolic pathway. Also, the data indicated that R salmoninarum may have a variety of possible virulence-factor and antibiotic-resistance strategies. Interestingly, many of genes had high identities with Mycobacterium species, a known pathogenic Actin obacteria bacterium. In summary, this study provides the first insights into and initial steps towards understanding the molecular basis of antibiotic resistance, virulence mechanisms and host/environment adaptation in twoChilean R. salmoninarum isolates that contain proteins of which were similar to those of Mycobacterium. Furthermore, important information is presented that could facilitate the development of preventive and treatment measures against R. salmoninarum in Chile and worldwide. © The Author(s) 2018.https://academic.oup.com/gbe/article/10/7/1816/504777