ABSTRACT
Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.
Subject(s)
Anti-Bacterial Agents , Sewage , Anti-Bacterial Agents/pharmacology , Drug Resistance, Bacterial/genetics , Genomics , MetagenomeSubject(s)
Escherichia coli Infections , Escherichia coli Proteins , Animals , Anti-Bacterial Agents/pharmacology , Carbapenems/pharmacology , Chickens , Colistin/pharmacology , Drug Resistance, Bacterial , Escherichia coli/genetics , Escherichia coli Infections/veterinary , Escherichia coli Proteins/genetics , Microbial Sensitivity Tests , Plasmids , Poultry Diseases/microbiologyABSTRACT
Background and aimPlasmid-mediated colistin resistance mechanisms have been identified worldwide in the past years. A multiplex polymerase chain reaction (PCR) protocol for detection of all currently known transferable colistin resistance genes (mcr-1 to mcr-5, and variants) in Enterobacteriaceae was developed for surveillance or research purposes. Methods: We designed four new primer pairs to amplify mcr-1, mcr-2, mcr-3 and mcr-4 gene products and used the originally described primers for mcr-5 to obtain a stepwise separation of ca 200 bp between amplicons. The primer pairs and amplification conditions allow for single or multiple detection of all currently described mcr genes and their variants present in Enterobacteriaceae. The protocol was validated testing 49 European Escherichia coli and Salmonella isolates of animal origin. Results: Multiplex PCR results in bovine and porcine isolates from Spain, Germany, France and Italy showed full concordance with whole genome sequence data. The method was able to detect mcr-1, mcr-3 and mcr-4 as singletons or in different combinations as they were present in the test isolates. One new mcr-4 variant, mcr-4.3, was also identified. Conclusions: This method allows rapid identification of mcr-positive bacteria and overcomes the challenges of phenotypic detection of colistin resistance. The multiplex PCR should be particularly interesting in settings or laboratories with limited resources for performing genetic analysis as it provides information on the mechanism of colistin resistance without requiring genome sequencing.
Subject(s)
Anti-Bacterial Agents/pharmacology , Colistin/pharmacology , Enterobacteriaceae/drug effects , Enterobacteriaceae/genetics , Escherichia coli Proteins/genetics , Plasmids/genetics , Salmonella/drug effects , Salmonella/genetics , Enterobacteriaceae/isolation & purification , Enterobacteriaceae Infections/drug therapy , Enterobacteriaceae Infections/microbiology , Escherichia coli Proteins/metabolism , Humans , Membrane Proteins , Microbial Sensitivity Tests , Multiplex Polymerase Chain Reaction , Plasmids/metabolism , Salmonella/isolation & purification , Transferases (Other Substituted Phosphate Groups)ABSTRACT
In August 2017, an outbreak of six listeriosis cases in Denmark was traced to cold-smoked salmon, using epidemiological investigations and whole-genome sequencing (WGS) analyses. Exchange of genome sequences allowed identification in France of a food isolate from a salmon-derived product and a human isolate from 2016 within the same cgMLST cluster as the Danish isolates (L2-SL8-ST8-CT771). The salmon product came from a third European Union country. WGS can rapidly link human cases and food isolates across Europe.
