Genome sequence of carbapenem-resistant Citrobacter koseri carrying blaOXA-181 isolated from sewage sludge

Mutshiene Deogratias Ekwanzala; John Barr Dewar; Ilunga Kamika; Maggy Ndombo Benteke Momba

doi:10.1016/j.jgar.2019.07.011

Genome sequence of carbapenem-resistant Citrobacter koseri carrying bla_OXA-181 isolated from sewage sludge

J Glob Antimicrob Resist. 2020 Mar:20:94-97. doi: 10.1016/j.jgar.2019.07.011. Epub 2019 Jul 16.

Authors

Mutshiene Deogratias Ekwanzala¹, John Barr Dewar², Ilunga Kamika³, Maggy Ndombo Benteke Momba⁴

Affiliations

¹ Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Arcadia Campus, Pretoria, South Africa. Electronic address: ekwanzala.md@gmail.com.
² Department of Life and Consumer Sciences, University of South Africa, Florida Campus, Johannesburg, South Africa.
³ Department of Environmental Sciences, University of South Africa, Science Campus, Johannesburg, South Africa.
⁴ Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Arcadia Campus, Pretoria, South Africa. Electronic address: mombamnb@tut.ac.za.

PMID: 31323426
DOI: 10.1016/j.jgar.2019.07.011

Abstract

Objectives: This study reported the resistome content of sewage sludge-isolated carbapenem-resistant Citrobacter koseri (C. koseri) carrying bla_OXA-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 (bla_MAL-1 and bla_OXA-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 bla_KPC-2 and bla_OXA-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 bla_OXA-181; therefore, C. koseri AS1 is the first of its kind. This study also highlighted the resistome contents of C. koseri genomes.

Keywords: Citrobacter koseri; Resistome; Whole genome sequencing; bla(OXA-181).

Publication types

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

MeSH terms

Bacterial Proteins / genetics
Carbapenems / pharmacology*
Citrobacter koseri / classification*
Citrobacter koseri / drug effects
Citrobacter koseri / genetics
Citrobacter koseri / isolation & purification
Drug Resistance, Multiple, Bacterial
Fosfomycin / pharmacology
Genome Size
Genome, Bacterial
High-Throughput Nucleotide Sequencing
Microbial Sensitivity Tests
Phylogeny
Plasmids / genetics
Sewage / microbiology*
Whole Genome Sequencing / methods*
beta-Lactamases / genetics*

Substances

Bacterial Proteins
Carbapenems
Sewage
Fosfomycin
beta-Lactamases