Whole-genome sequencing of multidrug-resistant Escherichia coli causing urinary tract infection in an immunocompromised patient: a case report.

BACKGROUND

Escherichia coli is a major human pathogen responsible for a broad range of clinical illnesses. It has been linked to endemic and epidemic nosocomial diseases caused by multidrug-resistant pathogens in Sudan as well as throughout the globe.

CASE PRESENTATION

A 76-year-old African woman arrived at Saad Rashwan Medical Centre complaining of backaches and discomfort during urination. Throughout the preceding 5 years, the patient had recurrent urinary tract infections. Following overnight incubation at 37 °C, Escherichia coli was found in her midstream urine specimen on cysteine lactose electrolyte deficient agar media. Minimum inhibitory concentration (colorimetric/turbidimetric method) was employed to test a wide range of antimicrobial drugs against this bacterial strain, and the results revealed significant multidrug resistance. QIAamp DNA Mini Kit was used to obtain DNA Template from the purified Escherichia coli (Qiagen, Hilden, Germany). The bacterial whole-genome sequence was done by Novogene company (Hong Kong) using Illumina HiSeq 2500 (Illumina, San Diego, CA, USA), followed by whole genome reconstructions, and identification of antibiotic-resistant genes. Phylogenetic analysis revealed that our strain was related to the Escherichia coli DSM30083 ( genome sequence ID: CP033092.2) from the USA. Our strain possessed the following antimicrobial-resistant genes: aminoglycoside (kdpE, baeR, cpxA, aadA5), nitroimidazole (msbA), phosphonic acid (mdtG), tetracycline (emrY), macrolide, penam, tetracycline, (evgA, TolC, H-NS), fluoroquinolone, cephalosporin, glycylcycline, penam, tetracycline, rifamycin, phenicol antibiotic, disinfecting agents and antiseptics (acrB; marA), sulfonamide (sul1), macrolide (Mrx), cephalosporin, penam (CTX-M-15), carbapenem, cephalosporin, and penam (OXA-1).

CONCLUSION

This study found that the isolated Escherichia coli strain had varied antimicrobial resistance genes on the basis of whole-genome sequencing and phenotypic resistance analyses. Whole-genome sequencing is critical for control and preventative methods to battle the growing threat of antimicrobial resistance. A larger investigation is recommended for improved generalization of results.