Large-Scale Identification of AbaR-Type Genomic Islands in Acinetobacter baumannii Reveals Diverse Insertion Sites and Clonal Lineage-Specific Antimicrobial Resistance Gene Profiles
Large-Scale Identification of AbaR-Type Genomic Islands in Acinetobacter baumannii Reveals Diverse Insertion Sites and Clonal Lineage-Specific Antimicrobial Resistance Gene Profiles
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鲍曼不动杆菌中 AbaR 型基因组岛的大规模鉴定揭示了多种插入位点和克隆谱系特异性抗菌素耐药性基因谱
DOI：
10.1128/aac.02526-18
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发表时间：
2019-04-01
影响因子：
4.9
通讯作者：
Wei, Qing
中科院分区：
文献类型：
--
作者：
Bi, Dexi;Xie, Ruting;Wei, Qing
abar型基因组岛（AbaRs）是鲍曼不动杆菌耐药的重要基因。本研究对AbaRs进行了大规模鉴定，以了解其耐药基因的分布和组成。abar型基因组岛（AbaRs）是鲍曼不动杆菌耐药的重要基因。本研究对AbaRs进行了大规模鉴定，以了解其耐药基因的分布和组成。我们鉴定了2.89 kb的左端和1.87 kb的右端保守序列（CSs），并开发了一种生物信息学方法来鉴定abar，使用CSs作为签名，在3148个公开可用的基因组中。abar在鲍曼不动杆菌中普遍存在，在2091个基因组中被发现。它们在其他不动杆菌种中稀少，仅局限于本属。来自111个完整基因组的结果显示，85%以上的abar位于染色体上。在所有已鉴定的CSs中，与反转重复序列相邻的外部侧翼被映射到一条不含abar的染色体上，或者在NCBI数据库中搜索空位点来定义插入位点。令人惊讶的是，共发现了84个不同起源的插入位点，其中51个分散在染色体上，20个质粒携带，12个位于噬菌体、转座子、ISAba1、复杂AbaRs和其他类型的基因组岛上，1个未被鉴定，其中一些与克隆谱系密切相关。最终，我们从70.9%（299/422）的完整AbaRs中发现了994个耐药基因，包括28个独特基因。抗性基因谱显示出明显的克隆谱系特异性模式，突出了全球克隆1 （GC1）和GC2中AbaRs的明显特征。在GC2中，tet(B)基因对AbaRs具有高度特异性。综上所述，AbaRs在染色体和移动遗传元件（MGEs）上具有不同的插入位点，并且在不同的克隆谱系中表现出不同的抗微生物基因谱。
AbaR-type genomic islands (AbaRs) are important elements responsible for antimicrobial resistance in Acinetobacter baumannii. This study performed a large-scale identification of AbaRs to understand their distribution and compositions of antimicrobial resistance genes. ABSTRACT AbaR-type genomic islands (AbaRs) are important elements responsible for antimicrobial resistance in Acinetobacter baumannii. This study performed a large-scale identification of AbaRs to understand their distribution and compositions of antimicrobial resistance genes. We identified 2.89-kb left-end and 1.87-kb right-end conserved sequences (CSs) and developed a bioinformatics approach to identify AbaRs, using the CSs as signatures, in 3,148 publicly available genomes. AbaRs were prevalent in A. baumannii, being found in 2,091 genomes. They were sparse in other Acinetobacter species and confined only to this genus. Results from 111 complete genomes showed that over 85% of AbaRs resided on chromosomes. The external flanks adjacent to the inverted repeats available in all identified CSs were mapped to an AbaR-free chromosome or searched in the NCBI database for empty loci to define insertion sites. Surprisingly, 84 insertion sites with diverse origins were revealed, including 51 scattered on the chromosome, 20 plasmid borne, 12 located on prophages, transposons, ISAba1, complex AbaRs, and genomic islands of other types, and one uncharacterized, and some were strongly associated with clonal lineages. Finally, we found 994 antimicrobial resistance genes covering 28 unique genes from 70.9% (299/422) of intact AbaRs currently available. The resistance gene profiles displayed an apparent clonal lineage-specific pattern, highlighting the distinct features of AbaRs in global clone 1 (GC1) and GC2. The tet(B) gene was highly specific to the AbaRs in GC2. In conclusion, AbaRs have diverse insertion sites on the chromosome and mobile genetic elements (MGEs) and display distinct antimicrobial resistance gene profiles in different clonal lineages.