The characterization of mobile colistin resistance (mcr) genes among 33 000 Salmonella enterica genomes from routine public health surveillance in England

0301 basic medicine Drug Resistance Animal/epidemiology Salmonella enterica/classification Microbial Sensitivity Tests 03 medical and health sciences Bacterial Proteins Salmonella Drug Resistance, Bacterial Environmental Microbiology Animals Humans Public Health Surveillance England/epidemiology Phylogeny MCR and WGS Plasmids/genetics Salmonella Infections, Animal 0303 health sciences Genome Bacterial Proteins/genetics Colistin Anti-Bacterial Agents/metabolism Bacterial Salmonella Infections/epidemiology Salmonella enterica Colistin/pharmacology Anti-Bacterial Agents 3. Good health England Salmonella Infections Food Microbiology Genome, Bacterial Research Article Plasmids
DOI: 10.1099/mgen.0.000331 Publication Date: 2020-01-31T16:13:25Z
ABSTRACT
To establish the prevalence of mobile colistin resistance (mcr) genes amongst Salmonella enterica isolates obtained through public health surveillance in England (April 2014 to September 2017), 33 205 S . enterica genome sequences obtained from human, food, animal and environmental isolates were screened for the presence of mcr variants 1 to 8. The mcr-positive genomes were assembled, annotated and characterized according to plasmid type. Nanopore sequencing was performed on six selected isolates with putative novel plasmids, and phylogenetic analysis was used to provide an evolutionary context for the most commonly isolated clones. Fifty-two mcr-positive isolates were identified, of which 32 were positive for mcr-1, 19 for mcr-3 and 1 for mcr-5. The combination of Illumina and Nanopore sequencing identified three novel mcr-3 plasmids and one novel mcr-5 plasmid, as well as the presence of chromosomally integrated mcr-1 and mcr-3. Monophasic S. enterica serovar Typhimurium accounted for 27/52 (52 %) of the mcr-positive isolates, with the majority clustering in clades associated with travel to Southeast Asia. Isolates in these clades were associated with a specific plasmid range and an additional extended-spectrum beta-lactamase genotype. Routine whole-genome sequencing for public health surveillance provides an effective screen for novel and emerging antimicrobial determinants, including mcr. Complementary long-read technologies elucidated the genomic context of resistance determinants, offering insights into plasmid dissemination and linkage to other resistance genes.
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