Genome Analysis of Klebsiella pneumoniae Reveals International High-Risk Pandemic MDR Clones Emerging in Tertiary Healthcare Settings in Uganda

Abstract

Klebsiella pneumoniae is a threat to public health due to its continued evolution. In this study, we investigated the evolution, convergence, and transmission of hypervirulent and multi-drug resistant (MDR) clones of K. pneumoniae within healthcare facilities in Uganda. There was high resistance to piperacillin (90.91%), cefuroxime (86.96%), ceftazidime (84.62%), cefotaxime (84.00%), amoxicillin/clavulanate (75%), nalidixic acid (73.68%), and nitrofurantoin (71.43%) antibiotics among K. pneumoniae isolates. The isolates were genetically diverse, consisting of 20 different sequence types (STs) and 34 K-serotype groups. Chromosomal fosA (for fosfomycin) and oqxAB efflux pump genes were detected in all isolates. Two carbapenem resistance genes, blaNDM-5 and blaOXA-181 plus extended-spectrum beta-lactamase (bla_CTX-M-15) gene (68.12%), quinolone-resistant genes qnrS1 (28.99%), qnrB1 (13.04%), and qnrB6 (13.04%) and others were found. All, except three of the isolates, harbored plasmids. While the isolates carried a repertoire of virulence genes, only two isolates carried hypervirulent genes demonstrating a low prevalence (2.90%) of hypervirulent strains. Our study demonstrated genetically diverse populations of K. pneumoniae, low levels of carbapenem resistance among the isolates, and no convergence of MDR and hypervirulence. Emerging high-risk international pandemic clones (ST11, ST14, ST147, ST 86 and ST307) were detected in these healthcare settings which are difficult to treat.

Keywords: hypervirulence; multidrug resistant; resistance genes; virulence.

Figure 1

SNP-based phylogenetic tree from core genes of 69 Klebsiella pneumoniae isolates analyzed in this study characterized by clonal group, MLST, serotype, sample type, healthcare care facility and antimicrobial resistance genes (absent, open circle; present, filled colored circle according to the class of AMR genes).

Figure 2

Comparison of the number of resistance gene classes (A), number of resistance genes (B), and relative abundance of resistance gene classes (C) of Klebsiella pneumoniae isolated from the different hospitals. Bwera: Bwera General Hospital, Bombo: General Military Hospital Bombo, Gulu: Gulu Regional Referral Hospital, and Kiruddu: Kiruddu National Referral Hospital.

Figure 3

Partial annotation of the plasmid from isolates MUWRP7816 (A) and MUWRP8507 (B) carrying carbapenemase-resistant gene blaNDM-5 and blaOXA-181, respectively, with other acquired antimicrobial-resistant genes (aadA1, sul1, QacE, and dfrA12) and quinolone-resistant (qnrS1).

Figure 4

SNP-based phylogenetic tree from core genes of Klebsiella pneumoniae isolates analyzed comparing isolates for their virulence score, virulence genes, sequence type, serotypes, and sample isolation source (absent, open circle; present, filled colored circle according to the class of AMR genes).

Figure 5

Comparison of number of resistant classes with virulence score (A) and number of resistant gene with virulence score (B).

Figure 6

Phylogenetic relationship of Klebsiella pneumoniae isolated from Uganda in a global context demonstrating the diversity of isolates. The Reference sequence Alignment-based Phylogeny builder was used to map the sequences against the reference via bowtie2. Multiple alignments of core genes were generated from which a phylogenetic tree was inferred via PhyML.