Clinical and molecular epidemiology of carbapenemase-producing Enterobacterales in hospitalized patients

Project title
Clinical and molecular epidemiology of carbapenemase-producing Enterobacterales in hospitalized patients in the Cape Town Metropole, South Africa

People involved
Principal investigator : Dr Clinton Moodley & Dr. Shantelle Claassen-Weitz
Bioinformatics support team: Katie Lennard

Short description of project
Integrating clinical and molecular epidemiology and determining transmission patterns of CREs among in-patients in both private and public sectors in the Cape Town Metropole, South Africa. This to enable a better understanding of the risk factors, clinical outcomes, and transmission patterns of CREs among in-patients in the Cape Town Metropole. The objective is to inform evidence-based regional patient management, antimicrobial stewardship (AMS) and infection prevention and control (IPC) strategies and interventions.

Objectives
All phenotypically confirmed carbapenem non-susceptible bacterial isolates collected during the study period were submitted for confirmatory PCR, to identify the presence of a carbapenemase (CPE) or otherwise non-carbapenemase-producing carbapenem-resistant Enterobacterales (NCPE). Phenotypically confirmed carbapenem non-susceptible bacterial isolates submitted for whole genome sequencing (WGS) were stored at -80ᵒC until cultivated overnight at 35ᵒC. Two pooled libraries, representing 11 and 12 isolates respectively, were sequenced using the MiSeq Reagent Kit v2 (300 cycles). Define AMR profiles, VFs, MLSTs, plasmids, mobile genetic elements (MGE), capsular typing (using Kaptive) and Klebsiellar profiling (using Kleborate)

Department: Medical Microbiology