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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

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Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
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Medical Microbiology, National Health Laboratory Services, Durban 4000, South Africa
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Medical Microbiology, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
4
Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa
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School of Clinical Medicine, Discipline of Anaesthetics & Critical Care, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
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Inkosi Albert Luthuli Central Hospital, Department of Critical Care, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
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Inkosi Albert Luthuli Central Hospital, Department of Surgery & Trauma Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
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Ahmed Al-Kadi Private Hospital, Durban 4000, South Africa
*
Authors to whom correspondence should be addressed.
Microorganisms 2020, 8(1), 137; https://doi.org/10.3390/microorganisms8010137
Received: 18 December 2019 / Revised: 11 January 2020 / Accepted: 17 January 2020 / Published: 17 January 2020
(This article belongs to the Special Issue Carbapenemase-producing Enterobacteriaceae)
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. View Full-Text
Keywords: genomics; carbapenemase; Klebsiella pneumoniae; extensively drug-resistant; mobile genetic elements; epidemiology; phylogenomic; South Africa genomics; carbapenemase; Klebsiella pneumoniae; extensively drug-resistant; mobile genetic elements; epidemiology; phylogenomic; South Africa
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Ramsamy, Y.; Mlisana, K.P.; Allam, M.; Amoako, D.G.; Abia, A.L.K.; Ismail, A.; Singh, R.; Kisten, T.; Swe Han, K.S.; Muckart, D.J.J.; Hardcastle, T.; Suleman, M.; Essack, S.Y. 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. Microorganisms 2020, 8, 137.

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