Genomic characterization of Klebsiella pneumoniae isolates from sepsis patients in Ethiopian tertiary hospitals: a multicenter cross-sectional study

Abstract

Background Treating sepsis caused by high-priority K. pneumoniae remains challenging, particularly in low- and middle-income countries. Methods A multicenter study was conducted from October 2019 to September 2020 at four hospitals across Ethiopia's central, southern, and northern regions. Blood cultures from 1,416 patients suspected of sepsis were processed, and isolates were identified using MALDI-TOF. Whole-genome sequencing (WGS) was performed on an Illumina HiSeq 2500, and various bioinformatics tools were used for genome analysis and visualization. Results A total of 97 K. pneumonia e isolates were identified from Tikur Anbessa ( n = 37), Yekatit ( n = 30), Hawassa ( n = 20), and Dessie ( n = 10) hospitals. Phylogenetically diverse K. pneumoniae variants (35 sequence types) were identified, with ST39 ( n = 15), ST14 ( n = 11), ST391 ( n = 10), and ST397 ( n = 9) being the most common. Almost all isolates ( n = 94) carried ESBL genes, mainly bla CTX − M−15 , while bla TEM − 1 ( n = 75), bla SHV − 11 ( n = 43), and bla OXA − 1 ( n = 41) were frequently detected, along with other β-lactamases. Carbapenemase genes included bla NDM − 1 ( n = 13), bla NDM − 5 ( n = 4), and bla OXA − 181 ( n = 4). Several additional genes were identified that confer resistance to aminoglycosides ( n = 70), sulphonamides ( n = 70), tetracyclines ( n = 64), trimethoprim ( n = 54), phenicol ( n = 40), quinolones ( n = 37), and macrolides ( n = 15). Frequent plasmid replicons were Col(pHAD28), Col440I, IncFII(K), IncFIB(K), IncFIB(K)(pCAV1099-114), IncR, and repFIB. Plasmid-borne antimicrobial resistance genes were frequently detected, with IncC exhibiting the broadest spectrum across multiple antibiotic classes. Yersiniabactin subtypes ybt4, ybt8, ybt9, ybt10, ybt13, ybt14, ybt15 , and ybt16 were identified as virulence genes and were present in 44 of 97 K. pneumoniae strains. Conclusion K. pneumoniae from sepsis patients in Ethiopia showed significant genomic diversity, with widespread ESBL and other plasmid-mediated antimicrobial resistance genes. These findings highlight the urgent need to enhance infection prevention and antimicrobial stewardship nationwide.