Journal of global antimicrobial resistance · 2019
Draft genome sequence of a multidrug-resistant tetA/IncF-harbouring Escherichia coli ST906 obtained from a soil cultivated with jaboticaba (Plinia cauliflora).
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Furlan João Pedro Rueda, Stehling Eliana Guedes
Аннотация
OBJECTIVES: The aim of this study was to report the draft genome sequence of a multidrug-resistant (MDR) Escherichia coli isolate obtained from a jaboticaba (Plinia cauliflora) culture soil in Brazil.
METHODS: The whole genome of E. coli strain S376 was sequenced on an Illumina MiSeq platform and was assembled using SPAdes v.3.9. All data analyses were performed using tools from the Center for Genomic Epidemiology and Geneious v.11.1.5 software. The genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v.3.2.
RESULTS: A total of 4854 protein-coding sequences were identified, with a GC content of 50.4%. Resistome analysis showed acquired antimicrobial resistance genes to β-lactams (blaTEM-116), tetracyclines [tetA and tet(34)], aminoglycosides (aadA1), trimethoprim (dfrA1) and macrolides (mphA). Mutations in the quinolone resistance-determining region (QRDR) of GyrA, ParC and ParE were detected. Three plasmid incompatibility groups were detected [IncFII (allele 24), IncFIB (allele 1) and ColRNAl]. In silico analysis showed the tetA and mphA are located inside the IncF plasmid. This isolate was classified as ST906 (singleton), serotype O156:H23-fimH61, commensal phylogroup B1 and presented various virulence genes, including iroN, ipfA, cma, gad and iss.
CONCLUSION: This is the first report of a draft genome sequence of a MDR E. coli ST906 serotype O156:H23-fimH61 obtained from a Brazilian soil. This draft genome sequence can be used to compare MDR E. coli isolated from different sources and to better understand the spread of this clone worldwide.
METHODS: The whole genome of E. coli strain S376 was sequenced on an Illumina MiSeq platform and was assembled using SPAdes v.3.9. All data analyses were performed using tools from the Center for Genomic Epidemiology and Geneious v.11.1.5 software. The genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v.3.2.
RESULTS: A total of 4854 protein-coding sequences were identified, with a GC content of 50.4%. Resistome analysis showed acquired antimicrobial resistance genes to β-lactams (blaTEM-116), tetracyclines [tetA and tet(34)], aminoglycosides (aadA1), trimethoprim (dfrA1) and macrolides (mphA). Mutations in the quinolone resistance-determining region (QRDR) of GyrA, ParC and ParE were detected. Three plasmid incompatibility groups were detected [IncFII (allele 24), IncFIB (allele 1) and ColRNAl]. In silico analysis showed the tetA and mphA are located inside the IncF plasmid. This isolate was classified as ST906 (singleton), serotype O156:H23-fimH61, commensal phylogroup B1 and presented various virulence genes, including iroN, ipfA, cma, gad and iss.
CONCLUSION: This is the first report of a draft genome sequence of a MDR E. coli ST906 serotype O156:H23-fimH61 obtained from a Brazilian soil. This draft genome sequence can be used to compare MDR E. coli isolated from different sources and to better understand the spread of this clone worldwide.