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Whole Genome Sequencing of Candida glabrata for Detection of Markers of Antifungal Drug Resistance
Published on: December 28, 2017
Genome sequence of carbapenem-resistant Citrobacter koseri carrying blaOXA-181 isolated from sewage sludge
Mutshiene Deogratias Ekwanzala1, John Barr Dewar2, Ilunga Kamika3
1Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Arcadia Campus, Pretoria, South Africa.
Objectives:
This study reported the resistome content of sewage sludge-isolated carbapenem-resistant Citrobacter koseri (C. koseri) carrying blaOXA-181. It also provided a general phylogenomic analysis highlighting antibiotic resistance genes (ARGs), plasmids and pathogenicity of C. koseri genomes.
Methods:
The carbapenem-resistantC. koseri AS1 strain was isolated from sewage sludge on CHROMagar™ mSuperCARBA™ media. Whole genome sequencing of C. koseri AS1 was performed using an HiSeq X™ Ten instrument. Additional C. koseri genomes were downloaded from National Center for Biotechnology Information (NCBI). Phylogenomic analysis was established through CSI Phylogeny. ARGs, plasmids and pathogenicity were identified using ResFinder 3.1, PlasmidFinder 2.0 and PathogenFinder 1.1, respectively.
Results:
The phylogenomic tree indicated a polyclonal pattern ofC. koseri genomes. Resistome analysis of C. koseri AS1 revealed β-lactam resistance genes (blaMAL-1 and blaOXA-181) as well as a fosfomycin resistance gene (fosA7). Three plasmids (ColKP3, ColRNAI and IncX30) were identified in the C. koseri AS1 genome. In addition, 25 ARGs were found in downloaded genomes. Of these, clinically significant ARGs such as blaKPC-2 and blaOXA-48 were found in two and four genomes, respectively. Assessment of the genomes using PathogenFinder revealed all genomes as putative human pathogens.
Conclusions:
It is believed that noC. koseri genome has been reported to carry blaOXA-181; therefore, C. koseri AS1 is the first of its kind. This study also highlighted the resistome contents of C. koseri genomes.
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