Pathogenomic Analysis of a Novel Extensively Drug-Resistant Citrobacter freundii Isolate Carrying a blaNDM-1 Carbapenemase in South Africa

Yogandree Ramsamy; Koleka P Mlisana; Daniel G Amoako; Mushal Allam; Arshad Ismail; Ravesh Singh; Akebe Luther King Abia; Sabiha Y Essack

doi:10.3390/pathogens9020089

Pathogenomic Analysis of a Novel Extensively Drug-Resistant Citrobacter freundii Isolate Carrying a bla_NDM-1 Carbapenemase in South Africa

Pathogens. 2020 Jan 31;9(2):89. doi: 10.3390/pathogens9020089.

Authors

Yogandree Ramsamy^{1

2

3}, Koleka P Mlisana², Daniel G Amoako⁴, Mushal Allam⁵, Arshad Ismail⁵, Ravesh Singh^{1

2}, Akebe Luther King Abia³, Sabiha Y Essack³

Affiliations

¹ Medical Microbiology, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa.
² National Health Laboratory Services, Durban 4000, South Africa.
³ Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa.
⁴ Infection Genomics and Applied Bioinformatics Division, Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa.
⁵ Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa.

Abstract

Pathogenomic analysis was performed on a novel carbapenem-resistant Citrobacter freundii isolate (H2730R) from a rectal swab of an adult male patient admitted to a tertiary hospital, Durban, South Africa. H2730R was identified using selective media and API 20e kit. Confirmatory identification and antibiotic susceptibility testing were performed using the VITEK II. H2730R was whole-genome sequenced on the Illumina MiSeq platform. H2730R was resistant to all tested antibiotics except tigecycline and was defined as ST498 by the C. freundii multilocus sequence typing (MLST) database. The estimated pathogenic potential predicted a higher probability (P_score ≈ 0.875), supporting H2730R as a human pathogen. H2730R harbored 25 putative acquired resistance genes, 4 plasmid replicons, 4 intact prophages, a class 1 integron (IntI1), 2 predominant insertion sequences (IS3 and IS5), numerous efflux genes, and virulome. BLASTn analysis of the bla_NDM-1 encoding contig (00022) and its flanking sequences revealed the bla_NDM-1 was located on a plasmid similar to the multireplicon p18-43_01 plasmid reported for the spread of carbapenem resistance in South Africa. Phylogenomic analysis showed clustering of H2730R with CF003/CF004 strains in the same clade, suggesting a possible association between C. freundii strains/clones. Acquiring the p18-43_01 plasmid containing bla_NDM-₁, the diversity, and complex resistome, virulome, and mobilome of this pathogen makes its incidence very worrying regarding mobilized resistance. This study presents the background genomic information for future surveillance and tracking of the spread of carbapenem-resistant Enterobacteriaceae in South Africa.

Keywords: Carbapenemase; Citrobacter freundii; Mobilome; Novel; Pathogenomics; South Africa; blaNDM-1.

Abstract

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