Genomic insights into multidrug and extensively drug-resistant Klebsiella pneumoniae from bloodstream infections at three Zambian tertiary hospitals.

BACKGROUND

Klebsiella pneumoniae is a leading cause of hospital-associated infections and a major contributor to antimicrobial resistance (AMR) worldwide. Despite its importance and prioritisation in Zambia's National Action Plan on AMR, genomic surveillance information in sub-Saharan Africa remains limited. This study investigated the population structure, determinants of AMR, and plasmid diversity of K. pneumoniae isolates from three tertiary hospitals in Zambia.

METHODS

Thirty archived K. pneumoniae blood isolates collected between December 2023 and May 2025 from University Teaching Hospitals (UTH), Ndola University Teaching Hospital (NUTH), and Livingstone University Teaching Hospital (LUTH) and subjected to antimicrobial susceptibility testing (AST) and whole-genome sequencing (Illumina NextSeq 2000). Sequence types (STs), plasmid replicons, and antimicrobial resistance genes (ARGs) were identified using MLST, PlasmidFinder, and the Comprehensive Antibiotic Resistance Database, respectively.

RESULTS

Twenty-eight isolates (93%) were multidrug-resistant, of which seven (25%) were extensively drug-resistant (XDR), exhibiting resistance across eight antibiotic classes, including carbapenems. Whole-genome sequencing identified 18 sequence types (STs), including two novel STs, and globally disseminated high-risk clones such as ST11, ST15, ST101, ST307, ST377, and ST607, which are circulating across hospitals. UTH exhibited the highest diversity of STs. The seven XDR K. pneumoniae isolates, six (85%) were from UTH, while the remaining isolate was from NUTH. Among the XDR isolates, five belonged to clinically dominant clones, comprising ST377 (two isolates) and single representatives of ST101, ST307, and ST607. The other two were ST13 and ST831, which have not been reported to have an XDR profile. All isolates carried multiple ARGs, dominated by those encoding β-lactamases (bla CTX-M-15: 93%, bla TEM: 70%), aminoglycoside-modifying enzymes (aac(6')-Ib-cr5: 77%, aac(3)-IIe: 64%), and efflux pump genes (emrD: 100%). The carbapenemase-encoding gene, bla NDM-5, was present in 13% of the isolates.

CONCLUSIONS

This first genomic survey of K. pneumoniae in Zambia reveals extensive clonal diversity dominated by global high-risk lineages carrying plasmid-mediated ESBL and carbapenemase genes. The detection of XDR strains, particularly at UTH, underscores the urgent need to strengthen laboratory surveillance across all tertiary hospitals in Zambia and improve infection prevention programmes.