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.