Occurrence of mcr-1.1-producing Escherichia coli in clinical settings in Tunisia

Abstract

Objective

Our study aims at characterizing a mcr-1-producing Escherichia coli ST224 clinical isolate collected at the University Hospital of Sahloul-Sousse from a joint infection.

Methods

Phenotypic characterization was performed using a Vitek-2 System. NGS was performed by short-read (150 bp paired-end reads) sequencing on a NovaSeq6000 platform, as well as by long-read sequencing using an ONT R10.4 flow cell. Hybrid assembly was achieved using the Flye de novo assembler, and analyses were performed using tools of the Center for Genomic Epidemiology. The mcr-1-carrying plasmid was compared by BLAST to similar plasmids recovered in the NCBI database and visualized by PROKSEE.

Results

The collected E. coli belonged to ST224 and was multi-drug resistant, remaining susceptible to carbapenems, amikacin, gentamicin, and sulfamethoxazole only. Resistances to last-generation cephalosporins (mediated by bla_CMY-2) and fluoroquinolones were chromosomally-encoded. The mcr-1.1 gene was carried by an Inc12 plasmid similar but not identical to published data, and that lacked the two copies of the ISApl1 element usually bracketing the mcr-1.1 and pap2 genes.

Conclusions

The dissemination of plasmid-encoded mcr-1 genes that can spread across species and sectors is a major health issue in countries such as Tunisia, where colistin is essential for the treatment of complicated human infections due to carbapenem-resistant Enterobacterales. Reporting all mcr-1-positive E. coli clinical isolates is thus important to understand the dynamic of spread of these resistant pathogens.