Oral Presentation Australian Society for Microbiology Annual Scientific Meeting 2024

Vancomycin heteroresistant Staphylococcus epidermidis from a refractory peritonitis case (104047)

Malgorzata Kopczyk 1 2 , Joshua Ramsay 3 , Kieran Mulroney 1 2 , Emily Salisbury 1 2 , Teagan Paton 1 2 , Elena Colombi 3 , Christine Carson 2 , Shakeel Mowlaboccus 4 5 , Geoffrey Coombs 4 5 , Aron Chakera 1 6
  1. The Harry Perkins Institute of Medical Research, Perth, WA
  2. UWA Centre for Medical Research, Perth, WA
  3. Curtin Health Innovation Research Institute and Curtin Medical School, Curtin University, Perth, WA
  4. School of Medical, Molecular, and Forensic Sciences, Murdoch University, Perth, WA
  5. Department of Microbiology, PathWest Laboratory Medicine WA, Perth, WA
  6. Department of Renal Medicine, Sir Charles Gairdner Hospital, Perth, WA

Background: Peritoneal dialysis (PD) is an effective treatment option for end-stage kidney disease, a condition affecting between 4.9 to 9.7 million people globally1. A serious complication of PD is peritonitis; an infection in the peritoneal cavity that is associated with significant morbidity and mortality. The rapid administration of appropriate antimicrobial therapy is critical to improving patient outcomes. Antimicrobial susceptibility testing (AST) methods such as the broth-microdilution (BMD) are used to guide clinicians in antibiotic administration. The BMD has remained the “gold standard” for AST, however lacks sensitivity to detect heteroresistance – a phenomenon implicated in treatment failure. We investigated a patient with multiple presentations of cloudy PD effluent after 5 days of vancomycin treatment (refractory peritonitis). Cultures were positive for Staphylococcus epidermidis and using  phenotypic and genotypic methods, we aimed to elucidate the cause for treatment failure.

Methods: Three S. epidermidis isolates (C099, C100 and C101) were cultured longitudinally from the patient. The VITEK®2 and BMD were used for AST. DNA was extracted using the Monarch® Genomic DNA kit and whole genome sequencing (WGS) performed on the Illumina NextSeq and MinION. Sequences were assembled using Flye and polished using Racon and Pilon. Resfinder, ABRicate and CARD were used to predict the resistome of the isolates. Population analysis profiling, area under the curve (PAP-AUC) was performed as described by Satola et al2. The AUC was calculated using GraphPad Prism (V10.0.2) and isolates classified as heteroresistant if the AUC of the test isolate divided by the control strain, ATCC 700698 was ≥ 0.902.

Results: The BMD and VITEK®2 classified isolates as susceptible to vancomycin. We did not find the presence of van genes or SNPs in regions associated with vancomycin heteroresistance in other species (e.g rpoB in S. aureus). The PAP-AUC method confirmed heteroresistance to vancomycin with AUC values of 1.072, 1.070 and 1.071 recorded for C099, C100 and C101.  

Conclusions: Both conventional AST and WGS failed to detect vancomycin heteroresistance in the S. epidermidis isolates, the likely cause for treatment failure. There is an urgent need for rapid and reliable assays that could be utilised in clinical laboratories to detect heteroresistance.

  1. 1. Liyanage T, Ninomiya T, Jha V, Neal B, Patrice HM, Okpechi I, et al. Worldwide access to treatment for end-stage kidney disease: a systematic review. The Lancet. 2015;385(9981):1975-82.
  2. 2. Satola SW, Farley MM, Anderson KF, Patel JB. Comparison of detection methods for heteroresistant vancomycin-intermediate Staphylococcus aureus, with the population analysis profile method as the reference method. J Clin Microbiol. 2011;49(1):177-83.