Draft Genome Sequence Data of Multidrug-Resistant Escherichia coli CUK-76 Co-Harboring Class A and Class C β-Lactamases from Wastewater of India

The present study was performed to determine the antibiotic resistance genes (ARGs), virulence determinants, and mobile genetic elements in multidrug-resistant Escherichia coli CUK-76 isolated from wastewater in Himachal Pradesh, India. Whole genome sequencing was performed using the Illumina Miseq system, and the draft genome sequence was assembled by Unicycler v0.5.1 and annotated by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP v6.10). The bioinformatics-based prediction analysis was performed using ResFinder v4.7.2 and CARD v4.0.1 (antibiotic resistance genes), VirulenceFinder v2.0, VFDB and MGEFinder v1.0.3 (virulence determinants), PlasmidFinder v2.0.1 (plasmid sequences), MLST v2.0 (sequence type), ISFinder and TnCentral v2.0 (insertion sequences and transposons), PathogenFinder2 v0.6.0 (pathogenicity), RAST (subsystems category) and Phigaro (prophage sequences). The draft genome of E. coli CUK-76 strain comprised 4,607,136 bp with a GC content of 51%. Genome annotation revealed 4498 genes of which 4289 were protein-coding genes, 78 RNA genes, and 131 pseudogenes. It was related to sequence type ST949 and its predicted resistome consisted of blaCTX-M-15, blaTEM-1B (class A β-lactamase genes), blaEC-14 (class C β-lactamase gene), aph(6)-Id, aph(3″)-Ib, qnrS1, sul2, tet(A), and dfrA14 genes. Additionally, multiple virulence genes, two plasmid sequences viz. IncFIB(K) and IncFIB(AP001918), insertion sequences, transposons and prophage sequences were detected. The genomic dataset of this strain will be a valuable resource for comparative genomic studies on E. coli.