New insights regarding Acinetobacter genomic island-related elements

Siébor, Eliane; Neuwirth, Catherine

doi:10.1016/j.ijantimicag.2020.106117

Cited by 5 publications

(13 citation statements)

References 17 publications

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“…All of them harbor a DNA recombination module ( int and xis genes) encoding an integrase belonging to the tyrosine-recombinase family and an excisionase, a replication module consisting of a rep gene encoding a replicase and an ORF encoding a transcriptional regulator, transcriptional activator genes ( sgaC and usually sgaD ) encoding the sgaDC heterodimeric complex belonging to the FlhDC family, some genes involved in conjugation ( traN , traG , and usually traH ), and mobilization genes ( mpsB / mpsA ) ( de Curraize et al, 2021 ). The SGI1-REs are not able to self-transfer; however, they harbor AcaCD binding sites indicating that they are mobilizable by IncC conjugative plasmids ( Douard et al, 2010 ; Carraro et al, 2014 , 2017 ; Siebor et al, 2016 ; Lei et al, 2018 ; Siebor and Neuwirth, 2020 ). The origin of transfer ( oriT ) is located upstream of mpsB / mpsA ( Kiss et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

“…The MDR region is generally inserted at the same position in SGI1 variants, PGI1 variants, and PGI2 variants. Nevertheless, five positions were detected in AGI1 variants ( Siebor and Neuwirth, 2020 ). Some differences also occur in their backbone.…”

Section: Introductionmentioning

confidence: 99%

“…The most-reported variation in the backbone of SGI1 variants is the deletion from within the traN to within S009 replaced by the insertion sequence IS 1359 (IS Vch4 ) characterizing the SGI1-HKL group ( de Curraize et al, 2020b ), and other deletions on either side of the MDR region insertion site often resulting from IS 26 -mediated events. A deletion also occurs between A022 and A025 in AGI1 variants, replaced by the insertion of a new ORF sharing nucleotide (nt) identity with a short segment from a Shewanella element that is a part of a GI that belongs to the same SGI1-RE family ( Siebor and Neuwirth, 2020 ; de Curraize et al, 2021 ). However, there are some differences among the SGI1/PGI1/PGI2/AGI1 backbones that are located upstream of the mobilization genes and the oriT .…”

Section: Introductionmentioning

confidence: 99%

“…Salmonella genomic island 1-related elements carrying antimicrobial resistance genes have been found mainly in the pathogenic strains of human or veterinary samples ( Siebor and Neuwirth, 2020 ; de Curraize et al, 2021 ). Only a few SGI1-REs that do not harbor any MDR region have been reported.…”

Section: Introductionmentioning

confidence: 99%

“…An SGI1-RE identified in Klebsiella pneumoniae consists of a region closely related to PGI2 and in parts closer to PGI1 ( Cummins et al, 2020 ). Most of an SGI1-RE found in Shewanella is closer to the AGI1 backbone ( Siebor and Neuwirth, 2020 ), and SGI1-REs found in Vibrio cholerae and Vibrio mimicus are closer to the PGI1 backbone ( de Curraize et al, 2021 ). Given that SGI1/PGI1/PGI2/AGI1 islands integrate at the 3′-end of the trmE gene and that many bacterial species carry the trmE gene, we suspect that SGI1-REs might be more widely distributed and that SGI1-REs with a new backbone might perhaps emerge.…”

Section: Introductionmentioning

confidence: 99%

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Overview of Salmonella Genomic Island 1-Related Elements Among Gamma-Proteobacteria Reveals Their Wide Distribution Among Environmental Species

Siébor

Neuwirth

2022

Front. Microbiol.

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The aim of this study was to perform an in silico analysis of the available whole-genome sequencing data to detect syntenic genomic islands (GIs) having homology to Salmonella genomic island 1 (SGI1), analyze the genetic variations of their backbone, and determine their relatedness. Eighty-nine non-redundant SGI1-related elements (SGI1-REs) were identified among gamma-proteobacteria. With the inclusion of the thirty-seven backbones characterized to date, seven clusters were identified based on integrase homology: SGI1, PGI1, PGI2, AGI1 clusters, and clusters 5, 6, and 7 composed of GIs mainly harbored by waterborne or marine bacteria, such as Vibrio, Shewanella, Halomonas, Idiomarina, Marinobacter, and Pseudohongiella. The integrase genes and the backbones of SGI1-REs from clusters 6 and 7, and from PGI1, PGI2, and AGI1 clusters differed significantly from those of the SGI1 cluster, suggesting a different ancestor. All backbones consisted of two parts: the part from attL to the origin of transfer (oriT) harbored the DNA recombination, transfer, and mobilization genes, and the part from oriT to attR differed among the clusters. The diversity of SGI1-REs resulted from the recombination events between GIs of the same or other families. The oriT appeared to be a high recombination site. The multi-drug resistant (MDR) region was located upstream of the resolvase gene. However, most SGI1-REs in Vibrio, Shewanella, and marine bacteria did not harbor any MDR region. These strains could constitute a reservoir of SGI1-REs that could be potential ancestors of SGI1-REs encountered in pathogenic bacteria. Furthermore, four SGI1-REs did not harbor a resolvase gene and therefore could not acquire an integron. The presence of mobilization genes and AcaCD binding sites indicated that their conjugative transfer could occur with helper plasmids. The plasticity of SGI1-REs contributes to bacterial adaptation and evolution. We propose a more relevant classification to categorize SGI1-REs into different clusters based on their integrase gene similarity.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Overview of Salmonella Genomic Island 1-Related Elements Among Gamma-Proteobacteria Reveals Their Wide Distribution Among Environmental Species

Siébor

Neuwirth

2022

Front. Microbiol.

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Genomic islands related to Salmonella genomic island 1; integrative mobilisable elements in trmE mobilised in trans by A/C plasmids

Curraize

Siébor

Neuwirth

2021

Plasmid

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Genomic islands and their role in fitness traits of two key sepsis-causing bacterial pathogens

Ilyas

Purkait

Atmakuri

2022

Briefings in Functional Genomics

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To survive and establish a niche for themselves, bacteria constantly evolve. Toward that, they not only insert point mutations and promote illegitimate recombinations within their genomes but also insert pieces of ‘foreign’ deoxyribonucleic acid, which are commonly referred to as ‘genomic islands’ (GEIs). The GEIs come in several forms, structures and types, often providing a fitness advantage to the harboring bacterium. In pathogenic bacteria, some GEIs may enhance virulence, thus altering disease burden, morbidity and mortality. Hence, delineating (i) the GEIs framework, (ii) their encoded functions, (iii) the triggers that help them move, (iv) the mechanisms they exploit to move among bacteria and (v) identification of their natural reservoirs will aid in superior tackling of several bacterial diseases, including sepsis. Given the vast array of comparative genomics data, in this short review, we provide an overview of the GEIs, their types and the compositions therein, especially highlighting GEIs harbored by two important pathogens, viz. Acinetobacter baumannii and Klebsiella pneumoniae, which prominently trigger sepsis in low- and middle-income countries. Our efforts help shed some light on the challenges these pathogens pose when equipped with GEIs. We hope that this review will provoke intense research into understanding GEIs, the cues that drive their mobility across bacteria and the ways and means to prevent their transfer, especially across pathogenic bacteria.

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New insights regarding Acinetobacter genomic island-related elements

Cited by 5 publications

References 17 publications

Overview of Salmonella Genomic Island 1-Related Elements Among Gamma-Proteobacteria Reveals Their Wide Distribution Among Environmental Species

Overview of Salmonella Genomic Island 1-Related Elements Among Gamma-Proteobacteria Reveals Their Wide Distribution Among Environmental Species

Genomic islands related to Salmonella genomic island 1; integrative mobilisable elements in trmE mobilised in trans by A/C plasmids

Genomic islands and their role in fitness traits of two key sepsis-causing bacterial pathogens

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