The Australian Enterococcal Surveillance Outcome Program (AESOP) is one of the three active antimicrobial resistance (AMR) national surveillance programs conducted by the Australian Group on Antimicrobial Resistance (AGAR). Participating laboratories across Australia collect enterococci causing bacteraemia and perform species identification using the MALDI Biotyper. Antimicrobial susceptibility testing is performed on each enterococcal isolate using the Vitek® 2 or BD Phoenix™ automated systems. Whole genome sequencing is performed on isolates identified as Enterococcus faecium.
In 2021, 48 institutions from all Australian states and mainland territories participated in AESOP and a total of 1,297 episodes of enterococcal bacteraemia were reported. Although nine enterococcal species were identified, E. faecalis (n=702) and E. faecium (n=523) predominated. Of the 523 E. faecium, 496 (94.8%) were available for WGS. WGS was performed using short-read sequencing technology on the NextSeq® 500 Illumina platform. Various bioinformatics pipelines were used to confirm the species and identify the multi-locus sequence type (ST) and genes associated with AMR.
Although 73 STs were identified, 77.2% (n=383) of isolates were grouped into seven major STs represented by at least 10 isolates: ST17 (n=124), ST1424 (n=86), ST796 (n=53), ST78 (n=43), ST80 (n=40), ST1421 (n=24), and ST555 (n=13). Overall, 39.3% (n=195) of isolates harboured a vancomycin resistance gene of which 69 harboured vanA and 126 harboured vanB. No isolate harboured both vanA and vanB, and no other van genes were detected. Most of the vanA-positive and vanB-positive isolates belonged to ST1424 and ST796, respectively. All ST796 and ST78 isolates were vanB-positive. AMR genes conferring resistance to aminoglycosides, chloramphenicol, macrolides, oxazolidinones, tetracycline, and trimethoprim were identified. Mutations associated with quinolone resistance were also identified.