Comparative Analysis of AbaR-Type Genomic Islands Reveals Distinct Patterns of Genetic Features in Elements with Different Backbones
Open Access
- 1 May 2020
- journal article
- research article
- Published by American Society for Microbiology in mSphere
- Vol. 5 (3)
- https://doi.org/10.1128/mSphere.00349-20
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.Funding Information
- Science and Technology Commission of Shanghai Municipality (19430750600)
- Pandeng Research Foundation of Shanghai Tenth People's Hospital (2018SYPDRC015)
- National Natural Science Foundation of China (81772849)
- National Natural Science Foundation of China (81702037)
This publication has 26 references indexed in Scilit:
- Large-Scale Identification of AbaR-Type Genomic Islands in Acinetobacter baumannii Reveals Diverse Insertion Sites and Clonal Lineage-Specific Antimicrobial Resistance Gene ProfilesAntimicrobial Agents and Chemotherapy, 2019
- AbGRI1-5, a novel AbGRI1 variant in anAcinetobacter baumanniiGC2 isolate from Adelaide, AustraliaJournal of Antimicrobial Chemotherapy, 2018
- The resistance gene complement of D4, a multiply antibiotic-resistant ST25Acinetobacter baumanniiisolate, resides in two genomic islands and a plasmidJournal of Antimicrobial Chemotherapy, 2016
- Evolution of AbGRI2-0, the Progenitor of the AbGRI2 Resistance Island in Global Clone 2 of Acinetobacter baumanniiAntimicrobial Agents and Chemotherapy, 2016
- Mapping the resistance-associated mobilome of a carbapenem-resistantKlebsiella pneumoniaestrain reveals insights into factors shaping these regions and facilitates generation of a ‘resistance-disarmed’ model organismJournal of Antimicrobial Chemotherapy, 2015
- Spread of Carbapenem-Resistant Acinetobacter baumannii Global Clone 2 in Asia and AbaR-Type Resistance IslandsAntimicrobial Agents and Chemotherapy, 2013
- Complete Genome Analysis of Three Acinetobacter baumannii Clinical Isolates in China for Insight into the Diversification of Drug Resistance ElementsPLOS ONE, 2013
- AbaR4-Type Resistance Island Including the bla OXA-23 Gene in Acinetobacter nosocomialis IsolatesAntimicrobial Agents and Chemotherapy, 2012
- Antibiotic resistance islands in A320 (RUH134), the reference strain for Acinetobacter baumannii global clone 2Journal of Antimicrobial Chemotherapy, 2011
- Diversity and Evolution of AbaR Genomic Resistance Islands in Acinetobacter baumannii Strains of European Clone IAntimicrobial Agents and Chemotherapy, 2011