Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction

• Published in: Scientific reports Vol. 7; no. 1; p. 15364
• Main Authors: Matamoros, Sébastien, van Hattem, Jarne M., Arcilla, Maris S., Willemse, Niels, Melles, Damian C., Penders, John, Vinh, Trung Nguyen, Thi Hoa, Ngo, Bootsma, Martin C. J., van Genderen, Perry J., Goorhuis, Abraham, Grobusch, Martin, Molhoek, Nicky, Oude Lashof, Astrid M. L., Stobberingh, Ellen E., Verbrugh, Henri A., de Jong, Menno D., Schultsz, Constance
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 10.11.2017; Nature Publishing Group
• Subjects: 45/23; 631/326/22/1434; 631/326/325/2482; Animal human relations; Animals; E coli; Escherichia coli; Escherichia coli - classification; Escherichia coli - growth & development; Escherichia coli - isolation & purification; Escherichia coli Proteins - genetics; Europe; Gene transfer; Gene Transfer, Horizontal; Genomes; Humanities and Social Sciences; Humans; Literature reviews; multidisciplinary; Phylogeny; Plasmids; Plasmids - genetics; Population structure; Science; Science (multidisciplinary); Europe
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-017-15539-7

To understand the dynamics behind the worldwide spread of the mcr-1 gene, we determined the population structure of Escherichia coli and of mobile genetic elements (MGEs) carrying the mcr-1 gene. After a systematic review of the literature we included 65 E. coli whole genome sequences (WGS), adding 6 recently sequenced travel related isolates, and 312 MLST profiles. We included 219 MGEs described in 7 Enterobacteriaceae species isolated from human, animal and environmental samples. Despite a high overall diversity, 2 lineages were observed in the E. coli population that may function as reservoirs of the mcr-1 gene, the largest of which was linked to ST10, a sequence type known for its ubiquity in human faecal samples and in food samples. No genotypic clustering by geographical origin or isolation source was observed. Amongst a total of 13 plasmid incompatibility types, the IncI2, IncX4 and IncHI2 plasmids accounted for more than 90% of MGEs carrying the mcr-1 gene. We observed significant geographical clustering with regional spread of IncHI2 plasmids in Europe and IncI2 in Asia. These findings point towards promiscuous spread of the mcr-1 gene by efficient horizontal gene transfer dominated by a limited number of plasmid incompatibility types.