Comparative Analysis of AbaR-Type Genomic Islands Reveals Distinct Patterns of Genetic Features in Elements with Different Backbones

Abstract

AbaR-type genomic islands (AbaRs) are prevalent and associated with multiple antimicrobial resistance in Acinetobacter baumannii. AbaRs feature varied structural configurations involving different but closely related backbones with acquisition of diverse mobile genetic elements (MGEs) and antimicrobial resistance genes. This study aimed to understand the structural modulation patterns of AbaRs. A total of 442 intact AbaRs, including nonresistance but closely related islands, were mapped to backbones Tn6019, Tn6022, Tn6172/Tn6173, and AbGRI1-0 followed by alien sequence characterization. Genetic configurations were then examined and compared. The AbaRs fall into 53 genetic configurations, among which 26 were novel, including one Tn6019-type, nine Tn6022-type, three Tn6172/Tn6173-type, nine AbGRI1-type, and four new transposons that could not be mapped to the known backbones. The newly identified genetic configurations involved insertions of novel MGEs like ISAcsp2, ISAba42, ISAba17, and ISAba10, novel structural modulations driven by known MGEs such as ISCR2, Tn2006, and even another AbaR, and different backbone deletions. Recombination events in AbGRI1-type elements were also examined by identifying hybrid sequences from different backbones. Moreover, we found that the content and context features of AbaRs including the profiles of the MGEs driving the plasticity of these elements and the consequently acquired antimicrobial resistance genes, insertion sites, and clonal distribution displayed backbone-specific patterns. This study provides a comprehensive view of the genetic features of AbaRs. IMPORTANCE AbaR-type genomic islands (AbaRs) are well-known elements that can cause antimicrobial resistance in Acinetobacter baumannii. These elements contain diverse and complex genetic configurations involving different but related backbones with acquisition of diverse mobile genetic elements and antimicrobial resistance genes. Understanding their structural diversity is far from complete. In this study, we performed a large-scale comparative analysis of AbaRs, including nonresistance but closely related islands. Our findings offered a comprehensive and interesting view of their genetic features, which allowed us to correlate the structural modulation signatures, antimicrobial resistance patterns, insertion loci, as well as host clonal distribution of these elements to backbone types. This study provides insights into the evolution of these elements, explains the association between their antimicrobial resistance gene profiles and clonal distribution, and could facilitate establishment of a more proper nomenclature than the term “AbaR” that has been variously used.

Genomic rearrangements of mobile genetic elements associated with carbapenem resistance of Acinetobacter baumannii

“…Interestingly, the remaining two genomes (AB02, AB13) carried novel Tn6022-derived, plasmid linker and Tn6172-derived elements. Insertion of a single copy of Tn2006 and △ISCR2-△Tn10-MARR like region in Tn6172 as described earlier by Dexi Bi and colleagues was observed in both the genomes (Bi et al, 2020). However, one minor difference identified between both genomes where one carried blaPER-1 within class 1 integron of Tn6172-derived element whilst another was found to carry class 1 integron and devoid of blaPER-1 (Figure 4D & 4E).…”

“…AbaR island commonly disrupt the chromosomal comM gene, which is an insertion hotspot (Bi et al, 2020). Analysis of the 17 CRAB genomes revealed the presence of resistance p1AB28 Size -99090bp islands with a range of AMR genes along with its associated transposons and insertion elements in 15 genomes while absent in two genomes.…”

Interbacterial Transfer of Carbapenem Resistance and Large Antibiotic Resistance Islands by Natural Transformation in Pathogenic Acinetobacter

“…Genomics studies suggests that Ab-RI were initially introduced into A. baumannii through plasmid conjugation, with subsequent insertion in the chromosome ( 12 , 13 ). Ab-RI retain the features of ancestral Tn 7 elements ( 47 ), and although transposition activity tested with AbaR1 was not detectable ( 48 ), Ab-RI are found inserted in over 50 chromosomal insertion sites ( 9 ). Yet the vast majority of Ab-RI appear to be inserted in a specific locus, the comM gene ( 9 , 11 , 12 ), which encodes a putative helicase involved in natural transformation ( 35 , 49 , 50 ).…”

Coming from the Wild: Multidrug Resistant Opportunistic Pathogens Presenting a Primary, Not Human-Linked, Environmental Habitat

“…Notably, ARGs acquired by A. baumannii are frequently clustered, forming part of genomic islands, dubbed AbaRs. These AbaRs [ 146 ] present backbones resembling Tn 6019 , Tn 6022 and Tn 6172 transposons [ 150 ] and seem to be clone-specific [ 151 ]. This feature may mean that, once an AbaR has been acquired, its mobilization to another phylogenomic A. baumannii group could be limited.…”