Carbapenem-resistant (CR) Ochrobactrum anthropi pseudo-outbreak: phenotypic and genotypic characterization of the strains involved

BARENBOIM, M; CARULLA, M; ALMUZARA M; MONTAÑA S; RAMIREZ MS; FERNANDEZ J S; HERNANDEZ M

Congreso; ASM Microbe 2018; 2018

American society for microbiology

Background: In the last years the use of technologies in the microbiology diagnostic laboratory have contributed to the increase in identification of uncommon pathogens. Ochrobactrum anthropi is an emerging pathogen that was recently recognized as an opportunistic nosocomial pathogen. In 2016, an outbreak caused by O. anthropi occurred in a hospital. Surprisingly the six isolates involved in the outbreak were CR. More cases have been reported in the past few months leading to the authorities of the institution to lead a search for the source of the outbreak.Objective: The aim of this project was to characterize the strains involved in the outbreak and identify the resistant determinants that can explain the multidrug-resistance (MDR) phenotype observed. Methods: Six isolates were recovered from the blood sample of four patients. The isolates were identified as O. anthropi by 16s rDNA sequencing. Susceptibility tests were performed and PCR reactions for various carbapenemases were carried. OD-PCR was used to determine their genetic relationship. In addition, the draft genome sequence of one of the strains (OA 5) was obtained with Illumina MiSeq-I and Nextera XT DNA library. De novo assembly was performed with SPADES and RAST was used to predict the open reading frames (ORF). Further genomic analysis was carried out using ARG-ANNOT, ISFinder, and PHAST. Results: All isolates were MDR and EDTA synergies exhibited positive results, suggesting the presence of a MBL in each isolate. However, PCR reactions for blaIMP, blaVIM, blaKPC and blaNDM were negative. The same pattern of bands was obtained by OD-PCR suggesting an epidemiological relationship. The whole genome sequencing of OA 5 was performed and its draft genome consists of 4,792,719-bp sequences. By RAST server, 4554 protein-coding genes were predicted. Sequence analysis of the genome identified the presence of multiple resistance genes including various class C β-lactamases, and most importantly, a metal-dependant hydrolase, phnP. Moreover, genes coding for efflux pumps and two intact phages were also found.Conclusion: To our knowledge, this is the first description of a pseudo-outbreak caused by carbapenem-resistant O. anthropi. We have identified different β-lactamases genes in the genome of O. anthropi as well as various efflux pumps. The presence of these determinants could explain the observed resistance phenotype. We also highlight the importance of the isolation of uncommon MDR pathogens from clinical specimens since they can serve as reservoir of resistance determinants.