Draft genome sequence of a blaNDM-1- and blaOXA-244-carrying multidrug-resistant Escherichia coli D: ST69 clinical isolate from Egypt

Authors: SOLIMAN, AHMED - University Of Hiroshima; RAMADAN, HAZEM - Mansoura University; ZARAD, HODA - University Of Hiroshima; NARIYA, HIROFUMI - University Of Hiroshima; SHIMAMOTO, TOSHI - University Of Hiroshima; Hiott, Lari; Jackson, Charlene; Frye, Jonathan; SHIMAMOTO, TADASHI - University Of Hiroshima

Submitted to: Journal of Global Antimicrobial Resistance
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/14/2020
Publication Date: 7/29/2020
Citation: Soliman, A., Ramadan, H., Zarad, H., Nariya, H., Shimamoto, T., Hiott, L.M., Jackson, C.R., Frye, J.G., Shimamoto, T. 2020. Draft genome sequence of a blaNDM-1- and blaOXA-244-carrying multidrug-resistant Escherichia coli D: ST69 clinical isolate from Egypt. Journal of Global Antimicrobial Resistance. 22:832-834. https://doi.org/10.1016/j.jgar.2020.07.015.
DOI: https://doi.org/10.1016/j.jgar.2020.07.015

Interpretive Summary: Antibiotics belonging to the carbapenem class of antibiotics are often the last line of defense in treatment of human infections. Although carbapenems are not prescribed for use in food animal production, resistance mechanisms for carbapenems exist from both human and animal sources and is cause for concern. In a study on antimicrobial resistance in Escherichia coli from Egypt, a clinical strain was isolated and analyzed using antimicrobial susceptibility testing, conjugation experiments and whole genome sequencing to provide valuable insight into its resistome and genetic background. The isolate was resistant to two carbapenems, meropenem and doripenem. One carbapenem resistance gene was located on the chromosome while the second gene was located on a conjugative plasmid. Multiple acquired antimicrobial resistance genes were also detected conferring resistance to macrolide, quinolone, trimethoprim, ß-lactam, and aminoglycoside antibiotics. Results further identified that the spread of this E. coli genetic type could be related to localization of the carbapenem resistance genes on mobile genetic elements. This data will provide a basis for comparison of resistance genes and mobile elements from human and food animal origin which will be useful for researchers and policy makers as antimicrobial use for the One Health initiative is evaluated.

Technical Abstract: Objective: To describe the first draft genome sequence of a multidrug-resistant Escherichia coli D: ST69 clinical isolate from Egypt carrying blaNDM-1- and blaOXA-244. Material and Methods: The strain was isolated in December 2014 from a wound pus swab of a male patient in the city of Kafr El-Sheikh, Egypt using MacConkey agar containing 2 µg/ml meropenem. PCR screening and partial DNA sequencing was performed to confirm the detection of blaNDM-1 and blaOXA-244. The isolate was then subjected to antimicrobial susceptibility testing, conjugation experiments and whole genomic sequencing using Illumina MiSeq platform. Results: The draft genome of the strain, designated HR14_AS, was 5.08 Mbp in size containing a total of 90 contigs encoding 4677 predicted genes with an average G+C content of 50.7%. Isolate HR14_AS belonged to sequence type (ST) ST69 (phylogroup D) and exhibited multidrug resistant phenotypes with a minimum inhibitory concentration of 64 and 32 µg/ml for meropenem and doripenem, respectively. Multiple acquired antimicrobial resistance genes conferring resistance to macrolides (mdf(A)), quinolones (aac(6')-Ib-cr, and qnrS1), trimethoprim (dfrA14), ß-lactams (blaNDM-1, blaOXA-244, blaCTX-M-15, blaOXA-9, and blaTEM-1B), and aminoglycosides (aac(3)-IId, aac(6')-Ib, aadA1, and aph(3')-VI) were detected. The blaOXA-244, and blaNDM-1 were located on the chromosome (Tn6237) and on an IncI1 type self-conjugative plasmid of >93-kb in size, respectively. Conclusion: Here we reported the first draft genome sequence of a multidrug-resistant E. coli D: ST69 carrying blaNDM-1- and blaOXA-244. Beside the clonal expansion of the E. coli ST38 pandemic clone, this study further identified that the spread of OXA-244-E. coli could be related to the mobilization of the IS1R-made composite transposon (Tn6237) carrying blaOXA-244.