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

• DOI: 10.1099/mgen.0.000331
• Publication Date: 2020-01-31T16:13:25Z
• Authors: Cheryll M. Sia; David R. Greig; Martin Day; Hassan Hartman; Anais Painset; Michel Doumith; Daniele Meunier; Claire Jenkins; Marie Anne Chattaway; Katie L. Hopkins; Neil Woodford; Gauri Godbole; Timothy J. Dallman
• Keywords: 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

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.