Molecular epidemiology of Klebsiella pneumoniae isolates causing invasive disease from a private laboratory in South Africa

Abstract

Klebsiella pneumoniae (K. pneumoniae) is the most clinically significant species within the Klebsiella genus. The main burden of K. pneumoniae infections are healthcare-associated infections (HAIs), generally caused by the classical multidrug resistant (MDR) strains that can resist the activity of multiple antibiotics. The most clinically significant antibiotic resistance in K. pneumoniae is toward the beta-lactam antibiotics mediated by beta-lactam hydrolysing enzymes, specifically the extended-spectrum beta-lactamases (ESBLs), AmpC beta-lactamases and carbapenemases. Resistance is constantly spreading and evolving, predominantly attributed to several high-risk clonal lineages. High-risk clonal lineages are those with an enhanced ability to disseminate and survive in multiple settings and cause antibiotic resistant infection. The aim of this study was to characterise and investigate the molecular epidemiology and beta-lactam resistance of invasive K. pneumoniae isolates from a private laboratory in Gauteng, South Africa. A total of 154 K. pneumoniae isolates isolated from invasive specimens including blood, tissue and fluid were collected between 2021 and 2022 from a private laboratory in Pretoria. Specimens originated from patients in hospitals in Johannesburg, Pretoria and Emalahleni. Antibiotic susceptibility profiles for isolates were obtained using Vitek 2. Disc xv diffusion tests phenotypically confirmed the production of ESBLs, AmpCs and carbapenemases by K. pneumoniae isolates. Phenotypically confirmed isolates underwent polymerase chain reaction (PCR) assays for the detection of specific resistance genes. All K. pneumoniae isolates were genotyped by pulsed field gel electrophoresis (PFGE) and subsequently a dendrogram was constructed using the PFGE profile of each isolate. Major and minor PFGE clusters were identified, and one representative isolate per cluster was chosen from six of the clusters to undergo whole genome sequencing (WGS). The majority of the K. pneumoniae isolates originated from specimens taken from patients in intensive care unit hospital wards, predominantly representing bloodstream infections. High levels of resistance toward multiple antibiotic classes were observed, with 107 (70%) isolates classified as MDR. Amongst all K. pneumoniae isolates, 99 (64%) were phenotypically confirmed ESBL producers, 18 (12%) AmpC producers and 55 (36%) carbapenemase producers. Resistance genes detected included beta-lactamase (bla) sulfhydryl variant (SHV) in 95 isolates (49%), Temoneira (blaTEM) in 60 isolates (39%), the ESBL cefotaximase-Munich (blaCTX-M-15) in 68 isolates (44%), Dhahran (blaDHA) AmpC in seven isolates (5%), and the carbapenemases, oxacillinase-48-like (blaOXA-48-like) in 65 isolates (42%), New Delhi metallo beta-lactamase (blaNDM) in 21 isolates (14%) and K. pneumoniae carbapenemase (blaKPC) in seven isolates (5%). A rare genotype of triple carbapenemase production was detected in two isolates. Within the dendrogram, nine minor PFGE clusters were identified. The six representative isolates from clusters Minor A, Minor C, Minor F, Minor G, Minor H and Minor I that underwent WGS belonged to sequence types (ST) 307 (n = 3), ST2497 (n = 2) and ST3559 (n = 1). The ST307 isolates carried the blaOXA-181 variant. The ST2497 isolates were positive for yersiniabactin, as well as MDR, characterised by the blaOXA-232 variant. The ST3559 isolate was unique in carrying the blaDHA-1 AmpC. The high-risk clones detected in this study are evidence to the local epidemiology of K. pneumoniae in the private healthcare sector of South Africa and represent a major healthcare crisis. Surveillance and molecular epidemiological studies allow insight into current state of affairs regarding HAIs, and are vital in implementing measures to curb spread and outbreaks, as well as developing effective treatment models for highly resistant strains.