Phylogenetic analysis of integrases of Acinetobacter baumannii genomic islands

Genomic islands of closely related S. meliloti and S. medicae species were evaluated and homologous sequences were identified; it has been suggested that horizontal gene transfer occurs at homologous tRNA sites.

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

mSphere ◽

10.1128/msphere.00349-20 ◽

2020 ◽

Vol 5 (3) ◽

Author(s):

Dexi Bi ◽

Jiayi Zheng ◽

Ruting Xie ◽

Yin Zhu ◽

Rong Wei ◽

...

Keyword(s):

Comparative Analysis ◽

Antimicrobial Resistance ◽

Acinetobacter Baumannii ◽

Resistance Genes ◽

Genomic Islands ◽

Content Type ◽

Antimicrobial Resistance Genes ◽

Genetic Features ◽

Clonal Distribution ◽

Structural Modulation

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.

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Salmonella Genomic Island 1B Variant Found in a Sequence Type 117 Avian Pathogenic Escherichia coli Isolate

mSphere ◽

10.1128/msphere.00169-19 ◽

2019 ◽

Vol 4 (3) ◽

Cited By ~ 6

Author(s):

Max Laurence Cummins ◽

Piklu Roy Chowdhury ◽

Marc Serge Marenda ◽

Glenn Francis Browning ◽

Steven Philip Djordjevic

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Acinetobacter Baumannii ◽

Genome Sequencing ◽

Genomic Island ◽

Sequence Type ◽

Genomic Islands ◽

Content Type ◽

E Coli ◽

Antimicrobial Resistance Genes

ABSTRACT Salmonella genomic island 1 (SGI1) is an integrative genetic island first described in Salmonella enterica serovars Typhimurium DT104 and Agona in 2000. Variants of it have since been described in multiple serovars of S. enterica, as well as in Proteus mirabilis, Acinetobacter baumannii, Morganella morganii, and several other genera. The island typically confers resistance to older, first-generation antimicrobials; however, some variants carry blaNDM-1, blaVEB-6, and blaCTX-M15 genes that encode resistance to frontline, clinically important antibiotics, including third-generation cephalosporins. Genome sequencing studies of avian pathogenic Escherichia coli (APEC) identified a sequence type 117 (ST117) isolate (AVC96) with genetic features found in SGI1. The complete genome sequence of AVC96 was assembled from a combination of Illumina and single-molecule real-time (SMRT) sequence data. Analysis of the AVC96 chromosome identified a variant of SGI1-B located 18 bp from the 3′ end of trmE, also known as the attB site, a known hot spot for the integration of genomic islands. This is the first report of SGI1 in wild-type E. coli. The variant, here named SGI1-B-Ec1, was otherwise unremarkable, apart from the identification of ISEc43 in open reading frame (ORF) S023. IMPORTANCE SGI1 and variants of it carry a variety of antimicrobial resistance genes, including those conferring resistance to extended-spectrum β-lactams and carbapenems, and have been found in diverse S. enterica serovars, Acinetobacter baumannii, and other members of the Enterobacteriaceae. SGI1 integrates into Gram-negative pathogenic bacteria by targeting a conserved site 18 bp from the 3′ end of trmE. For the first time, we describe a novel variant of SGI1 in an avian pathogenic Escherichia coli isolate. The presence of SGI1 in E. coli is significant because it represents yet another lateral gene transfer mechanism to enhancing the capacity of E. coli to acquire and propagate antimicrobial resistance and putative virulence genes. This finding underscores the importance of whole-genome sequencing (WGS) to microbial genomic epidemiology, particularly within a One Health context. Further studies are needed to determine how widespread SGI1 and variants of it may be in Australia.

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Spreading of AbaR-type Genomic Islands in Multidrug Resistance Acinetobacter baumannii Strains Belonging to Different Clonal Complexes

Current Microbiology ◽

10.1007/s00284-013-0326-5 ◽

2013 ◽

Vol 67 (1) ◽

pp. 9-14 ◽

Cited By ~ 26

Author(s):

María Soledad Ramírez ◽

Elisabet Vilacoba ◽

María Silvina Stietz ◽

Andrea Karina Merkier ◽

Paola Jeric ◽

...

Keyword(s):

Multidrug Resistance ◽

Acinetobacter Baumannii ◽

Genomic Islands

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AbaR-Type Genomic Islands in Non-baumannii Acinetobacter Species Isolates from South Korea

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01175-15 ◽

2015 ◽

Vol 59 (9) ◽

pp. 5824-5826 ◽

Cited By ~ 8

Author(s):

Dae Hun Kim ◽

Kwan Soo Ko

Keyword(s):

South Korea ◽

Acinetobacter Baumannii ◽

Genomic Islands ◽

Asian Countries ◽

Acinetobacter Species ◽

Content Type ◽

South Korean

ABSTRACTTo investigate the presence and structure of AbaR-type genomic islands (GIs) in non-Acinetobacter baumanniiisolates, a total of 155 non-baumannii Acinetobacterisolates from a South Korean hospital were analyzed. GIs were found in threeAcinetobacter nosocomialisand twoAcinetobacter seifertiiisolates. Their structures were similar to those inA. baumanniiisolates from Asian countries, including South Korea. The existence of AbaR-type GIs in non-baumannii Acinetobacterisolates is believed to be due to interspecies transfer of GI.

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Integrase-Controlled Excision of Metal-Resistance Genomic Islands in Acinetobacter baumannii

Genes ◽

10.3390/genes9070366 ◽

2018 ◽

Vol 9 (7) ◽

pp. 366 ◽

Cited By ~ 7

Author(s):

Zaaima AL-Jabri ◽

Roxana Zamudio ◽

Eva Horvath-Papp ◽

Joseph Ralph ◽

Zakariya AL-Muharrami ◽

...

Keyword(s):

Heavy Metal ◽

Acinetobacter Baumannii ◽

Core Genome ◽

Susceptibility Testing ◽

Gene Clusters ◽

Heavy Metal Resistance ◽

Metal Resistance ◽

Genomic Islands ◽

Genome Plasticity ◽

E Coli

Genomic islands (GIs) are discrete gene clusters encoding for a variety of functions including antibiotic and heavy metal resistance, some of which are tightly associated to lineages of the core genome phylogenetic tree. We have investigated the functions of two distinct integrase genes in the mobilization of two metal resistant GIs, G08 and G62, of Acinetobacter baumannii. Real-time PCR demonstrated integrase-dependent GI excision, utilizing isopropyl β-d-1-thiogalactopyranoside IPTG-inducible integrase genes in plasmid-based mini-GIs in Escherichia coli. In A. baumannii, integrase-dependent excision of the original chromosomal GIs could be observed after mitomycin C induction. In both E. coli plasmids and A. baumannii chromosome, the rate of excision and circularization was found to be dependent on the expression level of the integrases. Susceptibility testing in A. baumannii strain ATCC 17978, A424, and their respective ΔG62 and ΔG08 mutants confirmed the contribution of the GI-encoded efflux transporters to heavy metal decreased susceptibility. In summary, the data evidenced the functionality of two integrases in the excision and circularization of the two Acinetobacter heavy-metal resistance GIs, G08 and G62, in E. coli, as well as when chromosomally located in their natural host. These recombination events occur at different frequencies resulting in genome plasticity and may participate in the spread of resistance determinants in A. baumannii.

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Comparative and phylogenetic analysis of a novel family of Enterobacteriaceae-associated genomic islands that share a conserved excision/integration module

Scientific Reports ◽

10.1038/s41598-018-28537-0 ◽

2018 ◽

Vol 8 (1) ◽

Cited By ~ 8

Author(s):

Alejandro Piña-Iturbe ◽

Diego Ulloa-Allendes ◽

Catalina Pardo-Roa ◽

Irenice Coronado-Arrázola ◽

Francisco J. Salazar-Echegarai ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Genomic Islands

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Characterization of multidrug-resistant Acinetobacter baumannii strain ATCC BAA1605 using whole-genome sequencing

BMC Research Notes ◽

10.1186/s13104-021-05493-z ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Kah Ern Ten ◽

Muhammad Zarul Hanifah Md Zoqratt ◽

Qasim Ayub ◽

Hock Siew Tan

Keyword(s):

Whole Genome Sequencing ◽

Acinetobacter Baumannii ◽

Genome Sequencing ◽

Gc Content ◽

Multidrug Resistant ◽

Genomic Islands ◽

Whole Genome ◽

Strain Atcc ◽

Circular Chromosome ◽

Genome Data

Abstract Objective The nosocomial pathogen, Acinetobacter baumannii, has acquired clinical significance due to its ability to persist in hospital settings and survive antibiotic treatment, which eventually resulted in the rapid spread of this bacterium with antimicrobial resistance (AMR) phenotypes. This study used a multidrug-resistant A. baumannii (strain ATCC BAA1605) as a model to study the genomic features of this pathogen. Results One circular chromosome and one circular plasmid were discovered in the complete genome of A. baumannii ATCC BAA1605 using whole-genome sequencing. The chromosome is 4,039,171 bp long with a GC content of 39.24%. Many AMR genes, which confer resistance to major classes of antibiotics (beta-lactams, aminoglycosides, tetracycline, sulphonamides), were found on the chromosome. Two genomic islands were predicted on the chromosome, one of which (Genomic Island 1) contains a cluster of AMR genes and mobile elements, suggesting the possibility of horizontal gene transfer. A subtype I-F CRISPR-Cas system was also identified on the chromosome of A. baumannii ATCC BAA1605. This study provides valuable genome data that can be used as a reference for future studies on A. baumannii. The genome of A. baumannii ATCC BAA1605 has been deposited at GenBank under accession no. CP058625 and CP058626.

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