Genomic Characterization of Klebsiella pneumoniae Causing Invasive Disease in South African Infants: Observational Studies Between 2018 and 2023 - Report - MDSpire
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Genomic Characterization of Klebsiella pneumoniae Causing Invasive Disease in South African Infants: Observational Studies Between 2018 and 2023
Genomic Analysis of Klebsiella pneumoniae in South African Infants with Invasive Infections
Overview
This study analyzed 337 Klebsiella pneumoniae isolates from infants ≤90 days in South Africa collected between 2018 and 2023. The genomic characterization revealed high genetic diversity with predominance of ST17 and multidrug resistance in 85% of isolates, including carbapenem resistance in nearly one-third, highlighting critical targets for vaccine development.
Background
Sepsis is a leading cause of death in young infants in low-middle-income countries, with Klebsiella pneumoniae a major pathogen implicated in invasive infections and neonatal mortality. In sub-Saharan Africa, neonatal sepsis incidence and case-fatality rates are substantially higher than in high-income countries. Despite its clinical importance, genomic data on KPn in African infants remain scarce, hindering vaccine development efforts. This study addresses this gap by providing detailed genomic surveillance of KPn isolates from hospitalized and postmortem cases in South African infants.
A total of 337 KPn isolates from infants ≤90 days were genomically analyzed, including 111 from fatal cases.
High genetic diversity was observed with 85 distinct clonotypes; ST17 was the predominant sequence type (22%).
Multidrug resistance genes were present in 85% of isolates, with carbapenem resistance in nearly one-third (32.9%).
Key carbapenemase genes identified included blaOXA-181 (26.4%), blaNDM-5 (2.1%), and blaNDM-1 (0.3%).
Over 80% of invasive disease cases were linked to 11 K-loci, suggesting potential antigen targets for vaccine development.
Dominant K-loci and O-antigens were KL25, KL2, KL149 and O1αβ,2α, O5 respectively, indicating geographic strain patterns.
Clinical Implications
The high prevalence of multidrug-resistant and carbapenem-resistant KPn strains in young infants underscores the urgent need for enhanced antimicrobial stewardship and infection control in South African hospitals. Identification of predominant K-loci and O-antigens provides critical targets for vaccine development, which could significantly reduce invasive KPn disease burden in this vulnerable population. Continued genomic surveillance is essential to monitor evolving resistance and inform therapeutic and preventive strategies.
Conclusion
This comprehensive genomic analysis reveals extensive diversity and high multidrug resistance among KPn isolates causing invasive infections in South African infants, highlighting key antigenic targets for vaccine development and the critical need for improved management of antimicrobial resistance in neonatal care.
References
Authors/Source/2024 -- Genomic Analysis of Klebsiella pneumoniae Linked to Invasive Infections in Infants in South Africa
by Courtney P Olwagen, Alane Izu, Shama Khan, Stephanie Jones, Carmen Briner, Gaurav Kwatra, Lara Van der Merwe, Nicholas J Dean, Vicky L Baillie, Sana Mahtab, Kimberleigh Storath, Imaan Dunn, Lubomira Andrew, Urvi Rajyaguru, Firdose L Nakwa, Sithembiso C Velaphi, Jeannette Wadula, Renate Strehlau, Anika M van Niekerk, Niree Naidoo, Yogandree Ramsamy, Mohamed Said, Robert G K Donald, Raphael Simon, Ziyaad Dangor, Shabir A Madhi
