Complete Nucleotide Sequence of Plasmids of Two Escherichia coli Strains Carrying bla NDM- 5 and bla NDM - 5 and bla OXA - 181 From the Same Patient

Vittoria Mattioni Marchetti; Ibrahim Bitar; Alessandra Mercato; Elisabetta Nucleo; Annalisa Bonomini; Palmino Pedroni; Jaroslav Hrabak; Roberta Migliavacca

doi:10.3389/fmicb.2019.03095

Complete Nucleotide Sequence of Plasmids of Two Escherichia coli Strains Carrying bla _NDM- ₅ and bla _NDM _- ₅ and bla _OXA _- ₁₈₁ From the Same Patient

Front Microbiol. 2020 Jan 21:10:3095. doi: 10.3389/fmicb.2019.03095. eCollection 2019.

Authors

Vittoria Mattioni Marchetti¹, Ibrahim Bitar^{2

3}, Alessandra Mercato¹, Elisabetta Nucleo¹, Annalisa Bonomini⁴, Palmino Pedroni⁴, Jaroslav Hrabak^{2

3}, Roberta Migliavacca¹

Affiliations

¹ Department of Clinical Surgical Diagnostic and Pediatric Sciences, Unit of Microbiology and Clinical Microbiology, University of Pavia, Pavia, Italy.
² Department of Microbiology, Faculty of Medicine in Pilsen, University Hospital in Pilsen, Charles University, Pilsen, Czechia.
³ Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia.
⁴ Clinical Microbiology Laboratory, "AO Desenzano del Garda," Brescia, Italy.

Abstract

Aim of this study was to genetically characterize two carbapenemase-producing Escherichia coli strains obtained from a pediatric patient affected by diarrhea, expressing OXA-181 and/or NDM-5 type enzymes. The above microorganisms were collected in the same Desenzano hospital (Northern Italy) where the bla _NDM- ₅ gene was detected for the first time in Italy 3 years ago. One strain (5P), belonged to sequence type ST405/ST477 (according to Pasture/Oxford schemes) and serotype O102:H6. It was characterized by a 130562 bp multi-replicon plasmid IncFII/IncFIA/IncFIB (pVSI_NDM-5) enclosing two main antibiotic resistance islands: (i) ARI-I, 10030 bp in size, carried genes coding for β-lactam- (bla _OXA- ₁, bla _CTX-M- ₁₅), fluoroquinolone/aminoglycoside- (aac(6')-lb-cr) and phenicol- resistance (catB3), (ii) ARI-II, 15326 bp in size, carried genes coding for sulfonamide- (sul1), β-lactam- (bla _NDM- ₅, bla _TEM- ₁ _B), phenicol- (catB3), trimethoprim- (dfrA17), antiseptic- (qacEΔ1), and aminoglycoside- (aadA5, rmtB) resistance. The other isolate (5M), belonged to sequence type ST2659/ST759 and serotype O50/02:H18, and carried four plasmids: a 153866 bp multi-replicon IncFII/IncFIA/IncFIB (pISV_IncFII_NDM-5), an 89866 bp IncI1 plasmid, a 51480 bp IncX3 plasmid (pISV_IncX3_OXA181), and a 41143 bp IncI plasmid (pISV_IncI_CMY-42). pISV_IncFII_NDM-5 carried two main antibiotic resistance islands: (i) ARI-III, 12220 bp in size, carried genes coding for β-lactam- (bla _OXA- ₁), fluoroquinolone/aminoglycoside- (aac(6')-lb-cr), tetracycline- (tet(B)) and phenicol- resistance (catB3, catA1), and ii) ARI-IV, 26527 bp in size, carried determinants coding for macrolide- (erm(B), mph(A)), sulfonamide- (sul1), beta-lactam- (bla _NDM- ₅, bla _TEM- ₁ _B), trimethoprim- (dfrA14, dfrA12), antiseptic- (qacEΔ1), and aminoglycoside- resistance (aadA5). pISV_IncI_CMY-42 harbored the bla _CMY- ₄₂ gene coding for beta-lactam resistance, pISV_IncX3_OXA181 harbored genes encoding fluoroquinolone- (qnrS1) and beta-lactams- resistance (bla _OXA- ₁₈₁). In conclusion, the detection of two different NDM-5 E. coli strains from a pediatric patient with a history of travel to the Far East countries strongly highlight an increasing trend and risk of importation from such areas.

Keywords: CMY-42; E. coli; NDM-5; OXA-181; WGS; plasmids.