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Genomic insights of optrA carrying linezolid resistant Enterococcus faecium using hybrid assembly: First report from India: optrA harbouring linezolid resistant VRE.

Y. Bakthavatchalam,K. Vasudevan,Priyanka Babu,A. Neeravi,Vignesh Narasiman,B. Veeraraghavan

Published 2021 in Journal of Global Antimicrobial Resistance

ABSTRACT

OBJECTIVES Linezolid resistance in Enterococcus faecium is emerging across the world. In this study, we aimed to characterise two linezolid resistant E. faecium isolates using whole genome sequencing. METHODS Antimicrobial susceptibility testing was performed using broth micro-dilution method. Hybrid assembly approach of IonTorrent and MinION sequencing reads was used to generate the complete genome of linezolid resistant E. faecium isolates (VB3025, VB3240). RESULTS VB3025 and VB3240 isolates had linezolid MICs of 1024 and 512 µg/ml respectively. In addition, VB3025 was found to be resistant to both vancomycin and teicoplanin, while VB3240 was susceptible to these antibiotics. Hybrid assembly approach was used to generate the complete genome of VB3025 and VB3240 isolates harbouring optrA gene. Notably, VB3025 carried two copies of optrA gene (chromosome and plasmid), while in VB3240 isolate, optrA was identified on the chromosome. Interestingly, the plasmid pVB3025_2 co-carries the resistance gene cluster aph(3)-IIIa -sat4- ant (6)-Ia-ermB, vanHAX operon and a copy of optrA gene. Moreover, the gene optrA was inserted into the transposon Tn554 carrying ermA gene was identified in both the isolates of VB3025 and VB3240. Further, mutation analysis revealed the presence of G2592T mutation in the 23S rRNA of both VB3025 and VB3240 isolates. CONCLUSION This is the first study in reporting optrA positive linezolid resistant E. faecium from India. A novel plasmid co-carrying vancomycin and linezolid resistant determinants highlights the threat for potential dissemination.

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