Exploration of an Acinetobacter johnsonii clinical strain genome revealed the presence of extensive horizontal gene transfer (HGT)

SABRINA MONTAÑA; GERMAN MATÍAS TRAGLIA; CLAUDIA BARBERIS; CECILIA QUIROGA; KEVIN CHIEM; GISELA PARMECIANO DI NOTO; MARCELO TOLMASKY; ANDRÉS IRIARTE; SAREDA T.J. SCHRAMM; MARISA ALMUZARA; CARLOS VAY; MARÍA SOLEDAD RAMÍREZ

Boston

Congreso; ASM Microbe 2016; 2016

ASM

Background: In recent years, Acinetobacter spp. such as A. johnsonii has been considered an emergent pathogen that can cause human infections like catheter-related bloodstream infections and peritonitis. While most A. johnsonii isolates are susceptible, strains harboring a variety of β-lactamases have recently been described. Here, we decided to study the genome of an Aj2199 clinical strain that was co-producing PER-2 and OXA-58. Methods: A draft sequence for A. johnsonii Aj2199 was obtained using Illumina MiSeq. SPAdes assembler version 3.1.0 was used for denovo assembly and RAST server to predict open reading frames. RAST predictions were confirmed by BLAST (version 2.0). Average nucleotide identity (ANI) was performed. Identification of homologous genes was carried out using the OrthoMCL method by the use of the get homologous software. ARG-ANNOT, ISfinder, PHAST, PlasmidFinder, Rfam database and the software Infernal, etc., were used to explore the genome. PCR reactions and conjugation assays were also carried out.Results: Assembled contigs totaled 3.803.969 base pairs with an N50 contig size of 70.198 (max length 286.583) and has a G+C content of 41.4 %. A total of 3737 possible open reading frames were predicted using the RAST server. Genomic comparison identified 1204 gene families in A. johnsonii strains, while 240 were exclusively found in Aj2199. The 240 gene families were comprised of 254 genes, of which, more than 164 of these were annotated as hypothetical proteins and 24 were mobile elements. Moreover, 46 complete insertion sequences (IS) and truncated IS and the presence of three intact prophages were found. The analysis of blaPER-2 genetic context revealed the presence of the typical context previously described in the Enterobacteriacea family suggesting genetic exchange.Conclusions: Genomic analysis showed evidence of extensive HGT events indicated by the presence of a wide variety of different mobile elements and resistance determinants in Aj2199. The data obtained from our genomic analysis strongly suggested the potentiality and promiscuity of A. johnsonii to easily acquire exogenous DNA from other bacterial species. The detection of resistance determinants and sequences related to HGT will not only expose the potential of A. johnsonii to acquire and store resistance determinants but it will also explain the spread of these genes into other species.