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Abstract
Infection with multiple drug resistant (MDR) Escherichia coli poses a life threat to immunocompromised pediatric cancer patients. Our aim is to genotypically characterize the plasmids harbored in MDR E. coli isolates recovered from bacteremic patients of Children’s Cancer Hospital in Egypt 57357 (CCHE 57357). In this study, 21 carbapenem-resistant E. coli (CRE) isolates were selected that exhibit Quinolones and Aminoglycosides resistance. Plasmid shot-gun sequencing was performed using Illumina next- generation sequencing platform. Isolates demonstrated resistant to all beta-lactams, carbapenems, aminoglycosides and quinolones. Of the 32 antimicrobial resistant genes identified that exceeded the analysis cutoff coverage, the highest represented genes were aph(6)-Id, sul2, aph(3″)-Ib, aph(3′)-Ia, sul1, dfrA12, TEM-220, NDM-11. Isolates employed a wide array of resistance mechanisms including antibiotic efflux, antibiotic inactivation, antibiotic target replacements and antibiotic target alteration. Sequenced isolates displayed diverse insertion sequences, including IS26, suggesting dynamic reshuffling of the harbored plasmids. Most isolates carried plasmids originating from other bacterial species suggesting a possible horizontal gene transfer. Only two isolates showed virulence factors with iroA gene cluster which was found in only one of them. Outside the realms of nosocomial infections among patients in hospitals, our results indicate a transfer of resistant genes and plasmids across different organisms.
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1 Children’s cancer hospital Egypt 57357, Molecular Microbiology Unit, Cairo, Egypt (GRID:grid.428154.e); Cairo University, Department of clinical pathology, Faculty of Medicine, Cairo, Egypt (GRID:grid.7776.1) (ISNI:0000 0004 0639 9286)
2 Children’s cancer hospital Egypt 57357, Genomics Program, Cairo, Egypt (GRID:grid.428154.e)
3 Bioinformatics Group, Center of Informatics Sciences (CIS), Nile University, Giza, Egypt (GRID:grid.440877.8)
4 Cairo University, Department of clinical pathology, Faculty of Medicine, Cairo, Egypt (GRID:grid.7776.1) (ISNI:0000 0004 0639 9286); Children’s cancer hospital Egypt 57357, Microbiology Unit, Cairo, Egypt (GRID:grid.428154.e)
5 Children’s cancer hospital Egypt 57357, Infectious disease unit, Cairo, Egypt (GRID:grid.428154.e); Cairo University, Department of pediatric oncology, National cancer Institute, Cairo, Egypt (GRID:grid.7776.1) (ISNI:0000 0004 0639 9286)
6 Children’s cancer hospital Egypt 57357, Genomics Program, Cairo, Egypt (GRID:grid.428154.e); Ain Shams University, Department of Biochemistry, Faculty of Science, Cairo, Egypt (GRID:grid.7269.a) (ISNI:0000 0004 0621 1570)