Draft genome sequence of a multidrug-resistant Escherichia coli ST189 carrying several acquired antimicrobial resistance genes obtained from Brazilian soil.

OBJECTIVES

This study reports the draft genome sequence of a multidrug-resistant Escherichia coli isolate obtained from a Brazilian soil sample.

METHODS

The E. coli genome was sequenced using an Illumina MiSeq platform. De novo genome assembly was performed using SPAdes v.3.9. The draft genome sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). The resistome, virulome and mobilome were identified using tools available from the Center for Genomic Epidemiology.

RESULTS

The genome presented 5613 protein-coding sequences and a GC content of 50.3%. Resistome analysis showed antimicrobial resistance genes to β-lactams (blaTEM-1B), tetracyclines [tet(A) and tet(34)], aminoglycosides (aadA1, aadA5 and aadA24), phenicols (floR), sulfonamides (sul2 and sul3), trimethoprim (dfrA17) and macrolides [mdf(A)]. For quinolone resistance, mutations in the quinolone resistance-determining regions of GyrA (Ser83Leu; Asp87Tyr) and ParC (Ser80Ile; Glu62Lys) were detected. Plasmid incompatibility (Inc) groups were detected, including ColpVC, IncN3, IncP1 and IncF [F113:A8:B20], with IncF113 being a new allele. The isolate belongs to ST189 (CC165), serotype O80:H26-fimH54 and presents some virulence genes (lpfA, iss and gad).

CONCLUSION

This is the first draft genome sequence of an E. coli ST189 isolate of serotype O80:H26-fimH54 obtained from soil. This draft genome sequence can be used to compare antimicrobial-resistant E. coli isolates obtained from different sources.