Carbapenem-resistant Klebsiella pneumoniae among hospitalized patients in Cape Town, South Africa: molecular epidemiology and characterization

Gert Marais; Clinton Moodley; Shantelle Claassen-Weitz; Fadheela Patel; Elizabeth Prentice; Hafsah Tootla; Nyasha Nyakutira; Katie Lennard; Kessendri Reddy; Colleen Bamford; Abraham Niehaus; Andrew Whitelaw; Adrian Brink; Cape Town Antimicrobial Stewardship Study Alliance

doi:10.1093/jacamr/dlae050

Carbapenem-resistant Klebsiella pneumoniae among hospitalized patients in Cape Town, South Africa: molecular epidemiology and characterization

JAC Antimicrob Resist. 2024 Mar 25;6(2):dlae050. doi: 10.1093/jacamr/dlae050. eCollection 2024 Apr.

Authors

Gert Marais^{1

2}, Clinton Moodley^{1

2}, Shantelle Claassen-Weitz¹, Fadheela Patel¹, Elizabeth Prentice^{1

2}, Hafsah Tootla^{1

3}, Nyasha Nyakutira¹, Katie Lennard⁴, Kessendri Reddy^{5

6}, Colleen Bamford^{1

7}, Abraham Niehaus⁸, Andrew Whitelaw^{5

6}, Adrian Brink^{1

2

9}; Cape Town Antimicrobial Stewardship Study Alliance

Collaborators

Affiliations

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

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 bla_OXA-48-like, detected in 71% of isolates, with bla_NDM detected in 5%. Notably, co-detection of two carbapenemase genes (bla_OXA-48-like and bla_NDM) 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 bla_OXA-181 and bla_OXA-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 bla_OXA-48-like, in keeping with CRKP epidemiology in South Africa in general. Emerging clones harbouring both bla_OXA-48-like and bla_NDM, such as ST17, ST2497 and the novel ST6787, are a concern due to the limited availability of appropriate antimicrobial agents in South Africa.

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