Emergence of pstS-Null Vancomycin-Resistant Enterococcus faecium Clone ST1478, Canada, 2013–2018

Rates of vancomycin-resistant enterococci bloodstream infections have remained relatively low in Canada. We recently observed an increase of 113% in these infections rates, which coincided with emergence of Enterococcus faecium pstS-null sequence type 1478. The proportion of this sequence type increased from 2.7% to 38.7% for all tested isolates from 2013–2018.


Rates of vancomycin-resistant enterococci bloodstream
infections have remained relatively low in Canada. We recently observed an increase of 113% in these infections rates, which coincided with emergence of Enterococcus faecium pstS-null sequence type 1478. The proportion of this sequence type increased from 2.7% to 38.7% for all tested isolates from 2013-2018.
All isolates that failed to give a sequence type by conventional MLST (10) were subjected to wholegenome sequencing on the MiSeq Platform (Illumina, https://www.illumina.com). Assembled reads (contigs) were analyzed by using an in-house MLST tool based on 1 from the Center for Genomic Epidemiology website (https://cge.cbs.dtu.dk/services).
During 2013-2018, a total of 797 VRE BSI cases were reported among 62 participating acute care hospitals across 10 provinces for which 608 VRE BSI isolates were submitted. During this surveillance period, the rate of VRE BSI significantly increased from 0.16 cases/10,000 patient-days to 0.34 cases/10,000 patient-days (p<0.001) (Figure). These rates are much higher than those reported during 1999-2009 (0.005 cases/1,000 admissions during 1999 to 0.068 cases/1,000 admissions during 2009) (5). Of the 608 VRE BSI collected, different MLST types were identified, which included 4 of the newly reported pstS-null sequence types ST1478 (n = 115), ST1421 (n = 7), ST1424 (n = 2), and ST1612 (n = 1). The increase of ST1478 isolates from 2.7% in 2013 to 38.7% in 2018 coincides with the increase in VRE BSI rates ( Figure). After emergence of ST1478, STs that once dominated (ST18, ST117, and ST412) dramatically decreased. This shift in clonal types is similar to what has been reported in other countries after identification of these pstS-null mutants (12).
As The predominant van gene among ST1478 isolates was vanA (99.1%, n = 114); only 1 isolate harbored a vanB gene (0.9%). We determined resistance to antimicrobial drugs by using broth microdilution and GPALL1F Sensititer panels (Trek Diagnostics, http://www.trekds.com). We interpreted MICs by using breakpoints described by the Clinical and Laboratory Standards Institute (14). Antimicrobial drug susceptibility tests showed that ST1478 isolates have increased resistance to chloramphenicol (10.4%), daptomycin (13.0%), HL-gentamicin (80.0%), and tetracycline (91.3%) compared with non-ST1478 isolates (Table 1). We verified daptomycin nonsusceptibility by using Etest (bioMérieux, https://www.biomerieux. com). Clinically, increased daptomycin nonsusceptibility among the ST1478 isolates is of particular concern because daptomycin is 1 of the few remaining treatment options for VRE and resistance to it is an increasing clinical problem (15). CNISP surveillance data show a nonsignificant increase in the use of daptomycin to treat patients with VRE bloodstream infections. During 2015, a total of 53.7% of patients with a VRE BSI were given daptomycin, and during 2018, this proportion increased to 61.1% (p = 0.5).
During 2013-2018, we identified 115 ST1478 VRE BSI isolates among 110 patients. The median age of ST1478 patients was 58 years (interquartile range 52-69 years), and most (63.1%, 69/111) were male. The most commonly identified risk factors at the time of positive culture included use of a central venous catheter (69.5%, 57/82), solid organ transplant recipient (24.7%, 24/97), receiving hemodialysis (21.4%, 15/70), and receiving chemotherapy (15.7%, 11/70). A total of 31% (28/92) of ST1478 patients were already in an intensive care unit at the time of positive culture, and an additional 11 (12.1%) were admitted within 30 days of positive blood culture. The all cause 30-day mortality rate was 32.4%. Bacteremia patients with ST1478 VRE were similar with respect to age, sex, intensive care unit admission, and mortality rate compared with patients who had non-ST1478 VRE. Patients with ST1478 VRE were more likely to have undergone solid organ transplantation (24.7%) than patients with non-ST1478 VRE (12.9%; p = 0.005) ( Table 2). However a VRE outbreak was reported by 1 center in their multiorgan transplant unit, which might explain this finding.

Conclusions
The emergence of the pstS-null mutant ST1478 identified in acute care hospitals in Canada coincides with a major increase in VRE BSI rates. This increase might be attributed to an increased virulence/fitness of this strain type or changes in VRE infection prevention and control practices.
Clinically, the increased proportion of daptomycin nonsusceptibility among this emerging strain type is of concern. Future work, including whole-genome sequencing, and collection of enhanced epidemiologic and infection prevention and control practices data are being undertaken to provide a better understanding of the transmission, clonal relatedness, and evolution of this strain type within and between hospitals across Canada. Clinicians should be aware of these drug-resistant bacteria.

About the Author
Ms. McCracken is a microbiologist at the National Microbiology Laboratory in Winnipeg, Manitoba, Canada. Her primary research interests are vancomycin-resistant enterococci and methicillinresistant Staphylococcus aureus.