A global survey of Salmonella plasmids and their associations with antimicrobial resistance

Abstract

Plasmids are the primary vector for horizontal transfer of antimicrobial resistance (AMR) within bacterial populations. We applied the MOB-suite, a toolset for reconstructing and typing plasmids, to 150 767 publicly available Salmonella whole-genome sequencing samples covering 1204 distinct serovars to produce a large-scale population survey of plasmids based on the MOB-suite plasmid nomenclature. Reconstruction yielded 183 017 plasmids representing 1044 primary MOB-clusters and 830 potentially novel MOB-clusters. Replicon and relaxase typing were able to type 83.4 and 58 % of plasmids, respectively, compared to 99.9 % for MOB-clusters. Within this work, we developed an approach to characterize the horizonal transfer of MOB-clusters and AMR genes across different serotypes, as well as the diversity of MOB-cluster associations with AMR genes. Aggregating conjugative mobility predictions provided by the MOB-suite and their corresponding serovar entropy demonstrated that non-mobilizable plasmids were associated with fewer serotypes compared to mobilizable or conjugative MOB-clusters. The host-range predictions for MOB-clusters also showed differences between the mobility classes, with mobilizable MOB-clusters accounting for 88.3 % of the multi-phyla (broad-host-range) predictions compared to 3 and 8.6 % for conjugative and non-mobilizable, respectively. A total of 296 (22 %) of identified MOB-clusters were associated with at least one resistance gene, indicating that the majority of Salmonella plasmids are not involved in AMR dissemination. Shannon entropy analysis of horizontal transfer of AMR genes across serovars and MOB-clusters demonstrated that horizonal transfer of genes is higher between serovars compared to transfer between different MOB-clusters. In addition to the population structure characterization based on primary MOB-clusters, we characterized a multi-plasmid outbreak responsible for the global dissemination of bla _CMY-2 across different serotypes using higher resolution MOB-suite secondary cluster codes. The plasmid characterization approach developed here can be applied to different organisms to identify plasmids and genes which pose high risks for horizontal transfer.

Keywords: Salmonella; antimicrobial resistance; horizontal transfer; mobile genetic elements; plasmids.

Fig. 1.

Overall plasmid analytical workflow.

Fig. 2.

Scatter plot of individual MOB-clusters coloured based on their overall mobility class prediction. The y-axis is the log-scale number of occurrences of a MOB-cluster in the dataset and the x-axis is the serovar entropy (nats) based on sistr predictions. Box plots are presented for the marginal distributions for each axis.

Fig. 3.

Sunburst plot of individual NCBI resistance genes grouped by drug class and coloured based on the proportion of occurrences of the gene associated with the chromosome or a plasmid.

Fig. 4.

Relationship between serovar and MOB-cluster entropy (nats) for individual NCBI-curated resistance genes. The size of each circle represents the abundance of the gene in the dataset and colours indicate the percentage of samples associated with human sources.

Fig. 5.

Sunburst plot of the bla _CMY-2 (n=4116) multi-plasmid outbreak with the inner ring showing association between chromosome or plasmid contig sequences. The middle ring shows the primary MOB-cluster and outer ring shows the secondary MOB-cluster associated with the gene.

Fig. 6.

Relationship between serovar entropy (nats) and proportion of members containing at least one NCBI resistance gene for individual MOB-clusters. The size of the circles represents the abundance of the MOB-cluster and overall mobility prediction is used to colour the circles.