Mobile genetic elements driving antimicrobial resistance in Streptococcus pneumoniae
Gabriel Temitope Sunmonu a,b, Abiodun David Ogunniyi a,b,*, Anna E. Sheppard b,c,*
a School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia 5371, Australia
b Australian Centre for Antimicrobial Resistance Ecology, The University of Adelaide, South Australia, Australia
c School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
Mobile genetic elements (MGEs) are DNA segments that can move within and between bacterial genomes, playing a crucial role in the spread of antimicrobial resistance (AMR) genes among bacterial populations. Among these MGEs, integrative conjugative elements (ICEs) can transfer themselves from one bacterial cell to another through conjugation, while also being able to integrate into the host chromosome. In Streptococcus pneumoniae, ICEs have been identified as major vectors for the dissemination of AMR genes, enabling this pathogen to acquire resistance to multiple antibiotics through horizontal gene transfer. The acquisition of these ICEs carrying AMR genes has contributed significantly to the emergence of multidrug-resistant S. pneumoniae strains, which pose a serious clinical challenge worldwide. Previous sequence analysis of S. pneumoniae genomes indicated that the Tn916-related and Tn5253-related ICEs were key ICE driving acquired AMR in S. pneumoniae. The Tn916-related ICE was mostly responsible for the spread of macrolide and tetracycline resistance determinants in S. pneumoniae. In this study we sought to investigate MGEsassociated with AMR in S. pneumoniae.
We utilized publicly available S. pneumoniae genomes from the PubMLST database. From the 42,319 S. pneumoniae genomes in PubMLST, 39,138 passed initial assembly quality checks and were downloaded. Using MobileElementFinder, we identified integrative and conjugative elements (ICEs) in 12,539 of these sequences.
The most commonly identified ICE was Tn6009, with an average length of 1,888bp, which was present in 8,944 genomes but was rarely reported in the literature for S. pneumoniae.Further investigation revealed that truncated ICEs in the database with higher coverage percentage and identity were reported by MobileElementFinder over other more plausible ICEs with slightly lesser coverage percentage and identity. This highlights the need for meticulous database curation and scrutiny of computational results, as surface-level outputs may mask complex variations and biases that fundamentally alter scientific interpretations.