Genomic Analysis of Carbapenemase-Producing Extensively Drug-Resistant Klebsiella pneumoniae Isolates Reveals the Horizontal Spread of p18-43_01 Plasmid Encoding blaNDM-1 in South Africa.
Yogandree RamsamyKoleka P MlisanaMushal AllamDaniel Gyamfi AmoakoAkebe L K AbiaArshad IsmailRavesh SinghTheroshnie KistenKhine Swe HanDavid J Jackson MuckartTimothy Craig HardcastleMoosa SulemanSabiha Y EssackPublished in: Microorganisms (2020)
Whole-genome sequence (WGS) analyses were employed to investigate the genomic epidemiology of extensively drug-resistant Klebsiella pneumoniae strains, focusing on the carbapenem resistance-encoding determinants, mobile genetic support, clonal and epidemiological relationships. A total of ten isolates were obtained from patients admitted to the intensive care unit (ICU) in a public hospital in South Africa. Five isolates were from rectal swabs of colonized patients and five from blood cultures of patients with invasive carbapenem-resistant infections. Following microbial identification and antibiotic susceptibility tests, the isolates were subjected to WGS on the Illumina MiSeq platform. All the isolates showed genotypic resistance to tested β-lactams (NDM-1, OXA-1, CTX-M-15, TEM-1B, SHV-1) and other antibiotics. All but one isolate belonged to the ST152 with a novel sequence type, ST3136, differing by a single-locus variant. The isolates had the same plasmid multilocus sequence type (IncF[K12:A-:B36]) and capsular serotype (KL149), supporting the epidemiological linkage between the clones. Resistance to carbapenems in the 10 isolates was conferred by the blaNDM-1 mediated by the acquisition of multi-replicon [ColRNAI, IncFIB(pB171), Col440I, IncFII, IncFIB(K) and IncFII(Yp)] p18-43_01 plasmid. These findings suggest that the acquisition of blaNDM-1-bearing plasmid structure (p18-43_01), horizontal transfer and clonal dissemination facilitate the spread of carbapenemases in South Africa. This emphasizes the importance of targeted infection control measures to prevent dissemination.
Keyphrases
- klebsiella pneumoniae
- multidrug resistant
- drug resistant
- escherichia coli
- acinetobacter baumannii
- south africa
- gram negative
- genetic diversity
- crispr cas
- healthcare
- end stage renal disease
- gene expression
- hiv positive
- intensive care unit
- emergency department
- heavy metals
- mental health
- newly diagnosed
- copy number
- peritoneal dialysis
- genome wide
- ejection fraction
- high throughput
- risk assessment
- hiv infected
- single cell
- men who have sex with men
- antiretroviral therapy
- acute care
- mechanical ventilation
- dengue virus
- bioinformatics analysis