Genomic Characterization of Klebsiella pneumoniae Causing Invasive Disease in South African Infants: Observational Studies Between 2018 and 2023

TL;DR

This study analyzed the genetic makeup of Klebsiella pneumoniae causing severe infections in South African infants, revealing common strains and resistance patterns.

Contribution

The study provides the first detailed genomic characterization of invasive K. pneumoniae in South African infants over a five-year period.

Findings

ST17 was the most common sequence type, followed by ST39.

Over 80% of cases were linked to 11 K loci, suggesting potential vaccine targets.

85% of isolates were multidrug resistant, with significant carbapenem resistance.

Abstract

Klebsiella pneumoniae (KPn) is a leading cause of invasive bacterial disease in African children, albeit with a scarcity of genotypic characterization.

We sequenced invasive KPn isolates from infants ≤90 days, collected through observational hospital surveillance (n = 226) between March 4, 2019 and February 27, 2021, and between May 13, 2022 and October 31, 2023, and postmortem sampling (n = 111) between February 15, 2018 and April 18, 2023. Postmortem Kpn isolates were attributed in the causal pathway to death by the determination of the cause of death panel, which consists of local experts.

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%) predominated, followed by ST39 (12.7%). The dominant K-locus (KL) were KL25 (24.0%), KL2 (14.5%), and KL149 (13/4%), while the dominant O-antigens included O1αβ,2α(48.4%), and O5 (19.9%). Eighty-five percent (287/337) of the KPn isolates harbored multidrug resistant genes, including 32.9% to carbapenems. Notably, blaOXA-181, blaNDM-5, and blaNDM-1 were detected in 26.4%, 2.1% (7/337), and 0.3% (1/337) of isolates, respectively.

Although a wide diversity of strains were associated with Kpn invasive disease, over 80% of the cases were attributed to 11 K loci. These data provide critical insights into KPn epidemiology and highlight potential antigen targets for vaccine development in young African children.

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