Carbapenem-resistant Klebsiella pneumoniae among hospitalized patients in Cape Town, South Africa: molecular epidemiology and characterization
Author:
Marais Gert12ORCID, Moodley Clinton12ORCID, Claassen-Weitz Shantelle1, Patel Fadheela1, Prentice Elizabeth12, Tootla Hafsah13, Nyakutira Nyasha1, Lennard Katie4, Reddy Kessendri56, Bamford Colleen17, Niehaus Abraham8ORCID, Whitelaw Andrew56, Brink Adrian129ORCID, , Page Claudine, Schoeman Elizabeth, de Klerk Elizma, Lategan Karin, Pienaar Karlien, Henning Liezl, Du Plessis Mandy, Maseko Nomfundo, Nel Salome, Narainsamy Melenie, Vermeulen Michelle, du Toit Narissa, van Heerden Teresa, Sitharam Liza, Barendse Asa, Nagel Dane, Prince Jacqueline, Vass Letitia, Strauss Rileen, Fakier Rushana, Samuel Catherine, van Zyl Marelieze, Isaacs Leigh-Ann, Hendricks Shareefa, Dodd Amy, Daniels Reecka, Zemanay Widaad, Van Heerden Judi, Hapeela Nchimunya, Brown Parveen, Daniels Zubayr, Vasuthevan Sharon, Scott Enid, Ricks Esmeralda, Curle Patricia, Wojno Justyna
Affiliation:
1. Division of Medical Microbiology, University of Cape Town , Cape Town, Western Cape , South Africa 2. National Health Laboratory Service Laboratory , Groote Schuur Hospital, Cape Town, Western Cape , South Africa 3. Medical Microbiology, National Health Laboratory Service, Red Cross War Memorial Children’s Hospital , Cape Town , South Africa 4. Division of Computational Biology, University of Cape Town , Cape Town, Western Cape , South Africa 5. Division of Medical Microbiology, Stellenbosch University , Cape Town, Western Cape , South Africa 6. National Health Laboratory Service, Tygerberg Hospital , Cape Town, Western Cape , South Africa 7. Division of Medical Microbiology, Pathcare , Cape Town , South Africa 8. Division of Medical Microbiology, Ampath , Cape Town , South Africa 9. Institute of Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, Western Cape , South Africa
Abstract
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.
Funder
Pfizer National Research Foundation Thuthuka
Publisher
Oxford University Press (OUP)
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