Investigation of mobile genetic elements and their association with antibiotic resistance genes in clinical pathogens worldwide

Abstract

Objectives: Antimicrobial-resistant bacteria are a major global health threat. Mobile genetic elements (MGEs) have been crucial for spreading resistance to new bacterial species, including human pathogens. Understanding how MGEs promote resistance could be essential for prevention. Here we present an investigation of MGEs and their association with resistance genes in pathogenic bacteria collected from 59 diagnostic units during 2020, representing a snapshot of clinical infections from 35 counties worldwide.

Methods: We analysed 3,095 whole-genome sequenced clinical bacterial isolates from over 100 species to study the relationship between resistance genes and MGEs. The mobiliome of Staphylococcus aureus, Enterococcus faecalis, Escherichia coli, and Klebsiella pneumoniae were further examined for geographic differences, as these species were prevalent in all countries. Genes potentially mobilized by MGEs were identified by finding DNA segments containing MGEs and ARGs preserved in multiple species. Network analysis was used to investigate potential MGE interactions, host range, and transmission pathways.

Results: The prevalence and diversity of MGEs and resistance genes varied among species, with E. coli and S. aureus carrying more diverse elements. MGE composition differed between bacterial lineages, indicating strong vertical inheritance. 102 MGEs associated with resistance were found in multiple species, and four of these elements seemed to be highly transmissible as they were found in different phyla. We identified 21 genomic regions containing resistance genes potentially mobilized by MGEs, highlighting their importance in transmitting genes to clinically significant bacteria.

Conclusion: Resistance genes are spread through various MGEs, including plasmids and transposons. Our findings suggest that multiple factors influence MGE prevalence and their transposability, thereby shaping the MGE population and transmission pathways. Some MGEs have a wider host range, which could make them more important for mobilizing genes. We also identified 103 resistance genes potentially mobilised by MGEs, which could increase their transmissibility to unrelated bacteria.

Fig 1. Geographic distribution of beta-lactamase gene families in E. coli.

Countries with resistance are coloured in blue. The pie chart shows the composition of gene families per country. Map was created using shapefiles from Natural Earth.

Fig 2. Geographic distribution of beta-lactamase gene families in K. pneumonia.

Countries with resistance are coloured in blue. The pie chart shows the composition of gene families per country. Map was created using shapefiles from Natural Earth.

Fig 3. Number of ARGs per species and their predicted location.

Fig 4. Number of ARGs mobilized by iMGEs per species.

Hatched bars denote that the ARG is located on a plasmid.

Fig 5. Heatmap describing the number of putative translocatable (pTU) units identified in all isolates.

Rows are the pTUs; columns show the genera of the additional ~2000 isolates. The top bar display species stratified into Gram+ (white) and Gram- (black).

Fig 6. The relative number of predicted iMGEs per type, genome location, and species.

The number of predicted iMGE is normalized to the number of species isolates. The bar colours show the number of MGEs predicted to be plasmid or chromosome borne. Plasmid annotation is based on annotations from plasmid prediction software.

Fig 7. Phylogenetic confinement of iMGEs.

Fig 8. Bacterial families constituting the three communities detected in the iMGE graph using the Louvain community detection method.

Communities are clusters within the graph of species densely connected by iMGEs. The bars depict the number of species coloured by their taxonomic family. Hatched bars indicate Gram- species.