Genomic characterization of Klebsiella pneumoniae causing invasive disease in South African infants: observational studies between 2018 to 2023
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Background
Klebsiella pneumoniae (KPn) is a leading cause of invasive bacterial disease in African children, albeit with a scarcity of genotypic characterization.
Methods
Invasive KPn isolates collected from young infants ≤90 days of age through observational surveillance across six hospitals in South Africa between March 4 th , 2019 to February 27 th , 2021, and between May 13 th , 2022 to October 31 st , 2023 were sequenced. Postmortem Kpn isolates attributed in the causal pathway to death, collected from decedents ≤90 days of age and stillbirths between February 15 th , 2018 to April 18 th , 2023, were also sequenced.
Results
Three hundred and thirty-seven isolates (226 identified during hospital surveillance and 111 from postmortem sampling) were included in the final analysis. Genomic analysis identified 85 distinct clonotypes. Sequence type (ST) 17 (22.0%,74/337) predominated, followed by ST39 (12.7%,43/337). The dominant K-locus (KL) identified were KL25 (24.0%,81/337), KL2 (14.5%,49/337), KL149 (13/4%,45/337), and KL102 (9.5%,32/337), and the dominant O-antigens detected were O1ab (48.4%,149/310), O5 (19.9%,67/337), and O4 (7.7%,26/337). Eighty-five percent (287/337) of the KPn isolates harboured multi-drug resistant (MDR) genes, including 32.9% (111/337) to carbapenems. The oxacillinase-type β-lactamase-48 (bla OXA-181 ) gene was detected in 26.4% (89/337) of the isolates, while the New Delhi metallo β-lactamase-five (bla NDM-5 ) and -one (bla NDM-1 ) detected in 2.1% (7/337) and 0.3% (1/337) of isolates, respectively.
Conclusions
Although a wide diversity of strains were associated with Kpn invasive disease in South African children, over 80% of the cases were attributed to eleven K loci. The findings from this study could be useful in selecting KPn antigen targets for potential vaccine candidates.
