Spread of Plasmid-Encoded NDM-1 and GES-5 Carbapenemases among Extensively Drug-Resistant and Pandrug-Resistant Clinical Enterobacteriaceae in Durban, South Africa

Torunn Pedersen; John Osei Sekyere; Usha Govinden; Krishnee Moodley; Audun Sivertsen; Ørjan Samuelsen; Sabiha Yusuf Essack; Arnfinn Sundsfjord

doi:10.1128/AAC.02178-17

Spread of Plasmid-Encoded NDM-1 and GES-5 Carbapenemases among Extensively Drug-Resistant and Pandrug-Resistant Clinical Enterobacteriaceae in Durban, South Africa

Antimicrob Agents Chemother. 2018 Apr 26;62(5):e02178-17. doi: 10.1128/AAC.02178-17. Print 2018 May.

Authors

Torunn Pedersen¹, John Osei Sekyere², Usha Govinden², Krishnee Moodley³, Audun Sivertsen⁴, Ørjan Samuelsen^{4

5}, Sabiha Yusuf Essack⁴, Arnfinn Sundsfjord^{4

6}

Affiliations

¹ Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway torunn.annie.pedersen@uit.no.
² Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
³ Department of Clinical Microbiology, Lancet Laboratories, KwaZulu Natal, Durban, South Africa.
⁴ Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway.
⁵ Department of Pharmacy, Faculty of Health Sciences, University of Tromsø-The Arctic University of Norway, Tromsø, Norway.
⁶ Department of Medical Biology, Faculty of Health Sciences, University of Tromsø-The Arctic University of Norway, Tromsø, Norway.

Abstract

Whole-genome sequence analyses revealed the presence of bla_NDM-1 (n = 31), bla_GES-5 (n = 8), bla_OXA-232 (n = 1), or bla_NDM-5 (n = 1) in extensively drug-resistant and pandrug-resistant Enterobacteriaceae organisms isolated from in-patients in 10 private hospitals (2012 to 2013) in Durban, South Africa. Two novel NDM-1-encoding plasmids from Klebsiella pneumoniae were circularized by PacBio sequencing. In p19-10_01 [IncFIB(K); 223.434 bp], bla_NDM-1 was part of a Tn1548-like structure (16.276 bp) delineated by IS26 The multireplicon plasmid p18-43_01 [IncR_1/IncFIB(pB171)/IncFII(Yp); 212.326 bp] shared an 80-kb region with p19-10_01, not including the bla_NDM-1-containing region. The two plasmids were used as references for tracing NDM-1-encoding plasmids in the other genome assemblies. The p19-10_01 sequence was detected in K. pneumoniae (n = 7) only, whereas p18-43_01 was tracked to K. pneumoniae (n = 4), Klebsiella michiganensis (n = 1), Serratia marcescens (n = 11), Enterobacter spp. (n = 7), and Citrobacter freundii (n = 1), revealing horizontal spread of this bla_NDM-1-bearing plasmid structure. Global phylogeny showed clustering of the K. pneumoniae (18/20) isolates together with closely related carbapenemase-negative ST101 isolates from other geographical origins. The South African isolates were divided into three phylogenetic subbranches, where each group had distinct resistance and replicon profiles, carrying either p19-10_01, p18-10_01, or pCHE-A1 (8,201 bp). The latter plasmid carried bla_GES-5 and aacA4 within an integron mobilization unit. Our findings imply independent plasmid acquisition followed by local dissemination. Additionally, we detected bla_OXA-232 carried by pPKPN4 in K. pneumoniae (ST14) and bla_NDM-5 contained by a pNDM-MGR194-like genetic structure in Escherichia coli (ST167), adding even more complexity to the multilayer molecular mechanisms behind nosocomial spread of carbapenem-resistant Enterobacteriaceae in Durban, South Africa.

Keywords: Enterobacteriaceae; GES-5; NDM-1; carbapenemases; plasmid-mediated resistance.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Anti-Bacterial Agents / pharmacology
Bacterial Proteins / genetics
Bacterial Proteins / metabolism*
Citrobacter freundii / drug effects
Citrobacter freundii / enzymology
Citrobacter freundii / genetics
Enterobacter / drug effects
Enterobacter / enzymology
Enterobacter / genetics
Klebsiella pneumoniae / drug effects
Klebsiella pneumoniae / enzymology*
Klebsiella pneumoniae / genetics*
Microbial Sensitivity Tests
Phylogeny
Plasmids / genetics*
Serratia marcescens / drug effects
Serratia marcescens / enzymology
Serratia marcescens / genetics
beta-Lactamases / genetics
beta-Lactamases / metabolism*

Substances

Anti-Bacterial Agents
Bacterial Proteins
beta-Lactamases
beta-lactamase NDM-1
carbapenemase