Comparative genomic analysis of Acinetobacter spp. plasmids originating from clinical settings and environmental habitats

Ileana P Salto,Andreas Schlüter,Daniel Wibberg,Gonzalo Torres Tejerizo,Mariano Pistorio,Alfred Pühler

doi:10.1038/s41598-018-26180-3

Abstract

Bacteria belonging to the genus Acinetobacter have become of clinical importance over the last decade due to the development of a multi-resistant phenotype and their ability to survive under multiple environmental conditions. The development of these traits among Acinetobacter strains occurs frequently as a result of plasmid-mediated horizontal gene transfer. In this work, plasmids from nosocomial and environmental Acinetobacter spp. collections were separately sequenced and characterized. Assembly of the sequenced data resulted in 19 complete replicons in the nosocomial collection and 77 plasmid contigs in the environmental collection. Comparative genomic analysis showed that many of them had conserved backbones. Plasmid coding sequences corresponding to plasmid specific functions were bioinformatically and functionally analyzed. Replication initiation protein analysis revealed the predominance of the Rep_3 superfamily. The phylogenetic tree constructed from all Acinetobacter Rep_3 superfamily plasmids showed 16 intermingled clades originating from nosocomial and environmental habitats. Phylogenetic analysis of relaxase proteins revealed the presence of a new sub-clade named MOBQAci, composed exclusively of Acinetobacter relaxases. Functional analysis of proteins belonging to this group showed that they behaved differently when mobilized using helper plasmids belonging to different incompatibility groups.

Highlights

The genetic and functional diversity of bacteria facilitates their adaptation to different environments
Antibiotic multi-resistant phenotypes have had a significant impact over the last decade since they have appeared in bacteria associated with nosocomial infections in hospitals and intensive care units (ICUs)[10,11,12]
The nosocomial collection consisted of 64 multi-resistant Acinetobacter spp. isolates from five different hospitals, and the environmental collection consisted of 59 Acinetobacter spp. bacteria isolated from La Plata city ground soil and water samples

Summary

Introduction

The genetic and functional diversity of bacteria facilitates their adaptation to different environments. Plasmids are selfish genetic elements that undergo autonomous and self-controlled replication[7] These molecules represent assemblies of different functional modules such as replication, mobilization and maintenance, as well as accessory genes that may provide adaptive advantages to host bacteria, such as pathogenicity/virulence determinants, xenobiotic compound degradation or antimicrobial resistance mechanisms[8]. Replicon pIH1 pIH2 pIH3 phIH4 phIH5 pIH6 pIH7 pIH8 pIH9 phIH10 pIH11 pIH12 pIH13 pIH14 pIH15 pIH16 pIH17 pIH18 pIH19 When these genes enter MGEs such as plasmids, information spreads rapidly among bacterial communities, giving rise to multi-resistant bacteria epidemics[13,14,15,16]. Since plasmids are able to self-replicate, transfer, persist and even acquire new genes within their backbones, they can be considered as specialized HGT vehicles, and have become an important target of research to design new strategies for the control of antimicrobial resistance dissemination[17,18]

Methods

Results

Conclusion