Acinetobacter Plasmids: Diversity and Development of Classification Strategies

Abstract

Bacteria of the genus Acinetobacter , with their numerous species common in various habitats, play a significant role as pathogens. Their ability to adapt to different living conditions is largely due to the presence of numerous plasmids containing the necessary adaptive genes. At the same time the diversity of Acinetobacter plasmids and their evolutionary dynamics have not been sufficiently studied. Here, we characterized 44 plasmids isolated from five permafrost Acinetobacter lwoffii strains, examined their relationship with plasmids of modern Acinetobacter strains and identified groups of related plasmids. For this purpose, we have developed a combined approach for classifying all known Acinetobacter plasmids. The classification took into account the size of plasmids, the presence and structure of the rep and mob genes, as well as the structure of their backbone and accessory regions. Based on the analysis, 19 major groups (lineages) of plasmids were identified, of which more than half were small plasmids. The plasmids of each group have common features of the organization of the backbone region with a DNA identity level of at least 80%. In addition, plasmids of the same group have similarities in the organization of accessory regions. We also described a number of plasmids with a unique structure. The presence of plasmids in clinical strains that are closely related to those of environmental permafrost strains provides evidence of the origin of the former from the latter.

Ubiquitous Conjugative Mega-Plasmids of Acinetobacter Species and Their Role in Horizontal Transfer of Multi-Drug Resistance

“…Later, thanks to the complete sequencing of pALWED1.1 (287,631 bp) it became possible to study the structure of extended plasmid regions containing determinants of resistance to heavy metal salts ( Mindlin et al, 2016 ). Finally, due to the appearance of a large number of complete genomes of Àcinetobacter plasmids, it became clear that pALWED1.1 is a typical representative of an extensive group of plasmids, designated III-4a ( Ghaly et al, 2020 ; Mindlin et al, 2020 ). However, the structure of the backbone region of the plasmids of this group remained unexplored.…”

“…The number of sequenced Acinetobacter plasmids in genomic databases has exceeded 3,000 and continues to grow rapidly. It should be noted that the genus Acinetobacter is characterized by the presence of numerous plasmids in the same strain ( Feng et al, 2016 ; Brovedan et al, 2019 ; Mindlin et al, 2020 ), and most of them contain the relaxase gene ( mobA ), which suggests their potential ability to be mobilized ( Francia et al, 2004 ; Garcillán-Barcia et al, 2009 ). Large conjugative plasmids are usually found in the study of clinical antibiotic-resistant strains of Acinetobacter , but only some of them are studied in detail.…”

“…Its relaxase gene belongs to the MOB P family. In the work of Mindlin et al (2020) , this group of plasmids was designated III-1a. In contrast, neither the relaxase gene nor the gene encoding the replication initiator protein could be identified in the third group of conjugative mega-plasmids, represented by the prototype plasmid pA297-3 ( Hamidian et al, 2016 ; Nigro and Hall, 2017 ).…”

“…At the end of 2020, another group of Acinetobcater conjugative plasmids was discovered simultaneously by two teams of researchers ( Ghaly et al, 2020 ; Mindlin et al, 2020 ). In Mindlin et al (2020) , this group was designated III-4a.…”

“…At the end of 2020, another group of Acinetobcater conjugative plasmids was discovered simultaneously by two teams of researchers ( Ghaly et al, 2020 ; Mindlin et al, 2020 ). In Mindlin et al (2020) , this group was designated III-4a. It includes mega-plasmids with the size of about 300 kb, which also do not contain known replicase and relaxase genes.…”