Genomic and antimicrobial resistance genes diversity in multidrug-resistant CTX-M-positive isolates of Escherichia coli at a health care facility in Jeddah

Background: Whole genome sequencing has revolutionized epidemiological investigations of multidrug-resistant pathogenic bacteria worldwide. Aim of this study was to perform comprehensive characterization of ESBL-positive isolates of Escherichia coli obtained from clinical samples at the King Abdulaziz University Hospital utilizing whole genome sequencing. Methods: Isolates were identified by MALDI-TOF mass spectrometry. Genome sequencing was performed using a paired-end strategy on the MiSeq platform. Results: Nineteen isolates were clustered into different clades in a phylogenetic tree based on single nucleotide polymorphisms in core genomes. Seventeen sequence types were identified in the extended-spectrum p-lactamase (ESBL)-positive isolates, and 11 subtypes were identified based on distinct types of fimH alleles. Forty-one acquired resistance genes were found in the 19 genomes. The bla(CTX-M-15) gene, which encodes ESBL, was found in 15 isolates and was the most predominant resistance gene. Other antimicrobial resistance genes (ARGs) found in the isolates were associated with resistance to tetracycline ( tetA), aminoglycoside [aph(3 '')-Ib, and aph(6)-Id], and sulfonamide (sul1, and sul2). Nonsynonymous chromosomal mutations in the housekeeping genes parC and gyrA were commonly found in several genomes. Conclusion: Several other ARGs were found in CTX-M-positive E. coli isolates confer resistance to clinically important antibiotics used to treat infections caused by Gram-negative bacteria. (C) 2019 The Authors. Published by Elsevier Limited on behalf of King Saud Bin Abdulaziz University for Health Sciences.