WHOLE-GENOME SEQUENCING ANALYSIS OF TWO Escherichia coli WITH PLASMID-MEDIATED QUINOLONE RESISTANCE

PEREIRA E; RIAÑO D; GABRIEL GUTKIND; DI CONZA JOSÉ; RINCÓN GIOVANNA

Congreso; 1st WBDS-LA (Women in Bioinformatics & Data Science LA); 2020

Plasmid Mediated Quinolone Resistance (PMQR) determinants have spread throughout the world, and their relationship with other resistance genes has been found. These genes include qnr, aac(6')-Ib-cr, qepA, and oqxAB efflux pumps and confer a decrease in sensitivity to this class of antimicrobials. The aim of this study was to analyze two PMQR-carrying E. coli using a next-generation sequencing-based analysis. These clinical? isolates were initially tested by PCR for PMQR, one of them (C27) presented qepA and the other (C29) displayed qnrS. Whole genome sequencing were obtained using Illumina platform. The resulting raw readings were processed by FastQC, SPAdes, and Prokka. Identification and typing analysis tools included MLST 2.0, 16S-based identification, and EzBioCloud ANI calculator were used. Antibiotic resistance genes were identified with Resfinder and TrueBacID-Genome. The assembly of the two genomes resulted in the identification of E. coli C27, ANI 98.57%, ANI coverage (86%), 16S rDNA 99.84%, ST131, wzy O25, fliC H4, genome length 5433910 bp, contigs 155, the GC content is 50.84% and Q30 is 96.08%. Plasmid Inc Type detected were IncA/c2, IncI2, IncI1, IncFII (95.75% ID) (psE11) and IncFIB 98% ID (AP001918); In addition to qepA4 the following resistance genes were found: aadA2, aph(3'')-Ib, aph(6)-Id, blaCMY-2, blaCTX-M-2, dfrA1, dfrA12, floR, sul1, sul2 and tet(A). On the other hand, and E. coli C29 showed ANI 97.17%, ANI coverage (83.3%), 16s 98.98 %, ST38, wzy O7 (99.9%ID) fliC H18 (96.7%), genome length 5008994 bp, contigs 218, the GC content is 51.046% and Q30 is 93.048 %. Plasmid Contig Inc Type: IncX1(98,6% ID), Col (BS512,) resistance genes: aph(6)-Id, blaCMY-2, blaTEM-1B, dfrA14, qnrS1, sul3, tet(A). In conclusion, the sequencing of the entire genome is an important tool that allows the detection of genes of interest, as well as the characterization of multi-resistant isolates as E. coli C27 y C29.