Whole genome sequencing reveals insights into antibiotic resistant Klebsiella grimontii novel sequence type ST350 isolated from a wastewater source in South Africa

Klebsiella grimontii is a recently identified species that has been implicated in clinical infections. Few or no reports on environmental K. grimontii exist from Africa. This study was part of a broader longitudinal research that aimed to assess the distribution, antibiotic resistance patterns, and...

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Bibliographic Details
Published in:Journal of biotech research 2022-01, Vol.13, p.40-45
Main Authors: Mbanga, Joshua, Amoako, Daniel G, Abia, Akebe L K, Fatoba, Dorcas, Essack, Sabiha
Format: Article
Language:English
Subjects:
Antibiotic resistance
Antibiotics
Bioinformatics
Drug resistance
Gene sequencing
Genes
Genomes
Genomic analysis
Genomics
Infections
Insertion sequences
Klebsiella
Nucleotide sequence
Pathogens
Phylogenetics
Plasmids
Resistance factors
River systems
Rivers
Virulence
Virulence factors
Wastewater treatment
Wastewater treatment plants
Water treatment
Whole genome sequencing
β Lactamase
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Summary:Klebsiella grimontii is a recently identified species that has been implicated in clinical infections. Few or no reports on environmental K. grimontii exist from Africa. This study was part of a broader longitudinal research that aimed to assess the distribution, antibiotic resistance patterns, and genomics of Enterobacterales obtained from raw and treated wastewater and the associated river water of a wastewater treatment plant (WWTP) in KwaZulu-Natal, South Africa. We reported the genomics of an antibiotic resistant Klebsiella grimontii isolate obtained from the raw influent of the WWTP. Following phenotypic characterisation and antibiotic susceptibility testing, the isolate was sequenced on an Illumina MiSeq machine. Raw reads were assembled de novo by using SPAdes (v3.6.2) prior to bioinformatics analysis. The assembled K. grimontii INF139 genome was 6,369,878 bp, with 113 contiguous sequences (>200 bp) and 55.4 % GC content. The isolate was assigned a novel sequence type ST350. Genomic analysis revealed the presence of chromosomally encoded ß-lactamase (blaOXY-6-i) and fluoroquinolone (oqxB) resistance genes. Virulence factors encoding antiphagocytic, iron acquisition, and Intracellular survival properties were identified. Mobilome analysis revealed the presence of plasmid replicons (ColRNAI, FIA (pBK30683), IncFII, IncFII(Yp)) and insertion sequences (ISIX2, ISSen9, ISIS, IS1A). To our knowledge, this is the first description of antibiotic resistant K. grimontii from the water environment from Africa. The presence of this antibiotic resistant and potentially pathogenic isolate in the water environment is worrying as it may be disseminated into river systems used by informal settlements.
ISSN:1944-3285