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

• Published in: Microorganisms (Basel) 2020-01, Vol.8 (1), p.137
• Main Authors: Ramsamy, Yogandree, Mlisana, Koleka P., Allam, Mushal, Amoako, Daniel G., Abia, Akebe L. K., Ismail, Arshad, Singh, Ravesh, Kisten, Theroshnie, Swe Han, Khine Swe, Muckart, David J. Jackson, Hardcastle, Timothy, Suleman, Moosa, Essack, Sabiha Y.
• Format: Article
• Language: English
• Subjects: Antibiotics; Bacteria; Carbapenemase; Carbapenems; Drug resistance; Enzymes; Epidemics; Epidemiology; extensively drug-resistant; Genetic testing; Genomes; Genomic analysis; Genomics; Horizontal transfer; Hospitals; Identification; Infections; Klebsiella; Klebsiella pneumoniae; Laboratories; Microorganisms; mobile genetic elements; Mutation; Nucleotide sequence; Pathogens; Patients; phylogenomic; Plasmids; south africa; Trauma; β-Lactam antibiotics
• ISSN: 2076-2607; 2076-2607
• DOI: 10.3390/microorganisms8010137

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.