AUTHOR=Soliman Ahmed M. , Ramadan Hazem , Yu Liansheng , Hisatsune Junzo , Sugai Motoyuki , Elnahriry Shimaa S. , Nariya Hirofumi , El-Domany Ramadan A. , Shimamoto Toshi , Jackson Charlene R. , Shimamoto Tadashi 

TITLE=Complete genome sequences of two Escherichia coli clinical isolates from Egypt carrying mcr-1 on IncP and IncX4 plasmids

JOURNAL=Frontiers in Microbiology

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.989045

DOI=10.3389/fmicb.2022.989045

ISSN=1664-302X

ABSTRACT=<p>Colistin is a last-resort antibiotic used in the treatment of multidrug resistant Gram-negative bacteria. However, the activity and efficacy of colistin has been compromised by the worldwide spread of the mobile colistin resistance genes (<italic>mcr-1</italic> to <italic>mcr-10</italic>). In this study, two clinical <italic>Escherichia coli</italic> strains, named <italic>Ec</italic>CAI51, and <italic>Ec</italic>CAI73, harbored <italic>mcr-1</italic>, showed multidrug-resistant phenotypes (with colistin MIC = 4 μg/ml), and belonged to phylogroup D: multilocus sequence type 1011 (ST1011) and phylogroup A: ST744, respectively. Findings revealed the existence of <italic>mcr-1</italic> gene on two conjugable plasmids, pAMS-51-MCR1 (∼122 kb IncP) and pAMS-73-MCR1 (∼33 kb IncX4), in <italic>Ec</italic>CAI51, and <italic>Ec</italic>CAI73, respectively. The <italic>mcr-1</italic>-<italic>pap2</italic> element was detected in the two plasmids. Additionally, the composite transposon (IS<italic>Apl1</italic>-IS<italic>5D</italic>-<italic>pap2</italic>-<italic>mcr-1</italic>-IS<italic>Apl1</italic>) was identified only in pAMS-51-MCR1 suggesting the potential for horizontal gene transfer. The two strains carried from 16 to 18 different multiple acquired antimicrobial resistance genes (ARGs). Additionally, two different multireplicon virulence plasmids (∼117 kb pAMS-51-Vr and ∼226 kb pAMS-73-Vr) carrying the <italic>sit</italic> operon, the Salmochelin siderophore <italic>iroBCDE</italic> operon and other several virulence genes were identified from the two strains. Hierarchical clustering of core genome MLST (HierCC) revealed clustering of <italic>Ec</italic>CAI73, and <italic>Ec</italic>CAI51 with global <italic>E. coli</italic> lineages at HC levels of 50 (HC50) to 100 (HC100) core genome allelic differences. To the best of our knowledge, this study presented the first complete genomic sequences of <italic>mcr-1</italic>-carrying IncP and IncX4 plasmids from human clinical <italic>E. coli</italic> isolates in Egypt. In addition, the study illustrated the <italic>mcr-1</italic> broad dissemination in diverse plasmids and dissimilar <italic>E. coli</italic> clones.</p>