Genomic characterization of Klebsiella pneumoniae causing invasive disease in South African infants: observational studies between 2018 to 2023

BackgroundKlebsiella pneumoniae (KPn) is a leading cause of invasive bacterial disease in African children, albeit with a scarcity of genotypic characterization. MethodsInvasive KPn isolates collected from young infants [≤]90 days of age through observational surveillance across six hospitals in South Africa between March 4th, 2019 to February 27th, 2021, and between May 13th, 2022 to October 31st, 2023 were sequenced. Postmortem Kpn isolates attributed in the causal pathway to death, collected from decedents [≤]90 days of age and stillbirths between February 15th, 2018 to April 18th, 2023, were also sequenced. ResultsThree 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 {beta}-lactamase-48 (blaOXA-181) gene was detected in 26.4% (89/337) of the isolates, while the New Delhi metallo {beta}-lactamase-five (blaNDM-5) and -one (blaNDM-1) detected in 2.1% (7/337) and 0.3% (1/337) of isolates, respectively. ConclusionsAlthough 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.