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.
Highlights
Escherichia coli represents the most frequent sources of blood stream and urinary tract infections worldwide
There has been a particular concern regarding the increase in Extended-Spectrum Beta-Lactamase (ESBL)-producing and carbapenem-resistant E. coli. carbapenem-resistant E. coli (CRE) have become resistant to the majority of available antibiotics, including carbapenems which are a last-resort treatment for multidrug-resistant pathogens
We describe the use of comparative genomics to track plasmid-mediated antibiotic resistance gene distribution in Multiple Drug Resistance (MDR) E. coli isolated from bacteremic patients through 2016–2017, at the Children’s Cancer Hospital in Egypt 57357 (CCHE)
Summary
Escherichia coli represents the most frequent sources of blood stream and urinary tract infections worldwide. Carbapenem-resistant E. coli (CRE) have become resistant to the majority of available antibiotics, including carbapenems which are a last-resort treatment for multidrug-resistant pathogens. This is often accompanied by resistance to fluoroquinolones and aminoglycosides[3,4]. Integrons and plasmids frequently carry Multiple Drug Resistance (MDR) genetic motifs. These elements can be transferred from foodborne pathogens to human pathogens, increasing their virulence[7]. This method has enabled the rapid propagation of AMR among several pathogenic bacterial genera to humans, including E. coli[8]. We describe the use of comparative genomics to track plasmid-mediated antibiotic resistance gene distribution in MDR E. coli isolated from bacteremic patients through 2016–2017, at the Children’s Cancer Hospital in Egypt 57357 (CCHE)
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