Abstract

Background

The molecular epidemiology of carbapenem-resistant Enterobacterales in Cape Town remains largely unknown.

Objectives

This study aimed to describe the molecular epidemiology, resistome, virulome and mobilome of carbapenem-resistant Klebsiella pneumoniae (CRKP) within Cape Town to guide therapy, antimicrobial stewardship and infection prevention and control practices.

Methods

Eighty-five CRKP isolates from hospitalized patients underwent WGS as part of a prospective, multicentre, cross-sectional study, conducted between 1 November 2020 and 30 November 2022, across public-sector and private-sector hospitals in Cape Town, South Africa.

Results

MLST revealed three novel types, ST6785, ST6786 and ST6787, while the most common were ST219, ST307, ST17, ST13 and ST2497. Different predominant clones were noted in each hospital. The most common carbapenemase gene was blaOXA-48-like, detected in 71% of isolates, with blaNDM detected in 5%. Notably, co-detection of two carbapenemase genes (blaOXA-48-like and blaNDM) occurred in 13% of isolates. The yersiniabactin siderophore was detected in 73% of isolates, and was most commonly associated with the ICEKp5 mobile element. All carbapenemases were located on plasmids. The genes blaOXA-181 and blaOXA-232 colocalized with a ColKP3 replicon type on assembled contigs in 83% and 100% of cases, respectively.

Conclusions

CRKP epidemiology in Cape Town reflects institutionally dominant, rather than regional, clones. The most prevalent carbapenemase gene was blaOXA-48-like, in keeping with CRKP epidemiology in South Africa in general. Emerging clones harbouring both blaOXA-48-like and blaNDM, such as ST17, ST2497 and the novel ST6787, are a concern due to the limited availability of appropriate antimicrobial agents in South Africa.

Details

Title
Carbapenem-resistant Klebsiella pneumoniae among hospitalized patients in Cape Town, South Africa: molecular epidemiology and characterization
Author
Marais, Gert 1   VIAFID ORCID Logo  ; Moodley, Clinton 1   VIAFID ORCID Logo  ; Claassen-Weitz, Shantelle 1 ; Patel, Fadheela 1 ; Prentice, Elizabeth 1 ; Tootla, Hafsah 1 ; Nyakutira, Nyasha 1 ; Lennard, Katie 2 ; Reddy, Kessendri 3 ; Bamford, Colleen 1 ; Niehaus, Abraham 4   VIAFID ORCID Logo  ; Whitelaw, Andrew 3 ; Brink, Adrian 1   VIAFID ORCID Logo  ; Page, Claudine; Schoeman, Elizabeth; Elizma de Klerk; Lategan, Karin; Pienaar, Karlien; Henning, Liezl; Mandy Du Plessis; Maseko, Nomfundo; Nel, Salome; Narainsamy, Melenie; Vermeulen, Michelle; Narissa du Toit; Teresa van Heerden; Sitharam, Liza; Barendse, Asa; Nagel, Dane; Prince, Jacqueline; Vass, Letitia; Strauss, Rileen; Fakier, Rushana; Samuel, Catherine; Marelieze van Zyl; Isaacs, Leigh-Ann; Hendricks, Shareefa; Dodd, Amy; Daniels, Reecka; Zemanay, Widaad; Judi Van Heerden; Hapeela, Nchimunya; Brown, Parveen; Daniels, Zubayr; Vasuthevan, Sharon; Scott, Enid; Ricks, Esmeralda; Curle, Patricia; Wojno, Justyna

1  Division of Medical Microbiology, University of Cape Town , Cape Town, Western Cape , South Africa 
2  Division of Computational Biology, University of Cape Town , Cape Town, Western Cape , South Africa 
3  Division of Medical Microbiology, Stellenbosch University , Cape Town, Western Cape , South Africa 
4  Division of Medical Microbiology, Ampath , Cape Town , South Africa 
Publication year
2024
Publication date
Apr 2024
Publisher
Oxford University Press
e-ISSN
26321823
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1093/jacamr/dlae050
ProQuest document ID
3170568150
Copyright
© The Author(s) 2024. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy. This work is published under https://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.