AUTHOR=Villacís José E. , Castelán-Sánchez Hugo G. , Rojas-Vargas Jorge , Rodríguez-Cruz Ulises E. , Albán Viviana , Reyes Jorge A. , Meza-Rodríguez Pablo M. , Dávila-Ramos Sonia , Villavicencio Fernando , Galarza Margarita , Gestal Monica C. 

TITLE=Emergence of Raoultella ornithinolytica in human infections from different hospitals in Ecuador with OXA-48-producing resistance

JOURNAL=Frontiers in Microbiology

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1216008

DOI=10.3389/fmicb.2023.1216008

ISSN=1664-302X

ABSTRACT=<sec><title>Purpose</title><p>The purpose of this study was to highlight the clinical and molecular features of 13 <italic>Raoultella ornithinolytica</italic> strains isolated from clinical environments in Ecuador, and to perform comparative genomics with previously published genomes of <italic>Raoultella</italic> spp. As <italic>Raoultella</italic> is primarily found in environmental, clinical settings, we focused our work on identifying mechanisms of resistance that can provide this bacterium an advantage to establish and persist in hospital environments.</p></sec><sec><title>Methods</title><p>We analyzed 13 strains of <italic>Raoultella ornithinolytica</italic> isolated from patients with healthcare associated infections (HAI) in three hospitals in Quito and one in Santo Domingo de Los Tsáchilas, Ecuador, between November 2017 and April 2018. These isolates were subjected to phenotypic antimicrobial susceptibility testing, end-point polymerase chain reaction (PCR) to detect the presence of carbapenemases and whole-genome sequencing.</p></sec><sec><title>Results</title><p>Polymerase chain reaction revealed that seven isolates were positive isolates for <italic>bla</italic><sub>OXA–48</sub> and one for <italic>bla</italic><sub>KPC–2</sub> gene. Of the seven strains that presented the <italic>bla</italic><sub>OXA–48</sub> gene, six harbored it on an IncFII plasmid, one was inserted into the bacterial chromosome. The <italic>bla</italic><sub>KPC</sub> gene was detected in an IncM2/IncR plasmid. From the bioinformatics analysis, nine genomes had the gene <italic>bla</italic><sub>OXA–48</sub>, originating from Ecuador. Moreover, all <italic>R. ornithinolytica</italic> strains contained the ORN-1 gene, which confers resistance for β-lactams, such as penicillins and cephalosporins. Comparative genome analysis of the strains showed that the pangenome of <italic>R. ornithinolytica</italic> is considered an open pangenome, with 27.77% of core genes, which could be explained by the fact that the antibiotic resistance genes in the ancestral reconstruction are relatively new, suggesting that this genome is constantly incorporating new genes.</p></sec><sec><title>Conclusion</title><p>These results reveal the genome plasticity of <italic>R. ornithinolytica</italic>, particularly in acquiring antibiotic-resistance genes. The genomic surveillance and infectious control of these uncommon species are important since they may contribute to the burden of antimicrobial resistance and human health.</p></sec>