Breaking the ICE: an easy workflow for identifying and analyzing integrative and conjugative elements in bacterial genomes

Gonçalves, Osiel Silva; Assis, Jéssica Catarine Silva de; Santana, Mateus Ferreira

doi:10.1007/s10142-022-00903-2

Cited by 7 publications

(4 citation statements)

References 44 publications

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“…The genomes of A. cacticida strains were additionally screened for the presence of self-transmissible mobile elements such as integrative conjugative elements (ICEs) and integrative mobile elements (IMEs) that are known to affect the pathogenicity and lifestyle of phytopathogens ( Gonçalves et al., 2022 ). Five different ICE elements were found, harboring genetic determinants of T4SS, and five putative IME elements ( Supplementary Table 12 ).…”

Section: Resultsmentioning

confidence: 99%

Comprehensive phenomic and genomic studies of the species, Pectobacterium cacticida and proposal for reclassification as Alcorniella cacticida comb. nov

Jonca,

Pirhonen,

Waleron

et al. 2024

Front. Plant Sci.

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IntroductionPectobacterium cacticida was identified as the causative agent of soft rot disease in cacti. Due to a high potential of spread in the face of global warming, the species poses a significant threat to horticultural and crop industry. The aim of this study was to revise the genomic, physiology and virulence characteristics of P. cacticida and update its phylogenetic position within the Pectobacterium genus.MethodsWhole genome sequences of five P. cacticida strains were obtained and subjected to comprehensive genomic and phylogenomic data analyses. We assessed the presence of virulence determinants and genes associated with host and environmental adaptation. Lipidomic analysis, as well as biochemical and phenotypic assays were performed to correlate genomic findings.ResultsPhylogenomic analysis revealed that P. cacticida forms a distinct lineage within the Pectobacterium genus. Genomic evaluation uncovered 516 unique proteins, most of which were involved in cellular metabolism. They included genes of carbohydrate metabolism and transport and ABC transporters. The main differing characteristics from other Pectobacterium species were the lack of a myo-inositol degradation pathway and the presence of the malonate decarboxylase gene. All tested strains were pathogenic towards Opuntia spp., chicory, Chinese cabbage, and potato, but exhibited only mild pathogenicity towards carrot.DiscussionThis study sheds light into the genomic characteristics of P. cacticida and highlights the pathogenic potential of the species. Unique genes found in P. cacticida genomes possibly enhance the species’ survival and virulence. Based on phylogenomic analyses, we propose the reclassification of P. cacticida to a new genus, Alcorniella comb. nov.

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Section: Resultsmentioning

confidence: 99%

Comprehensive phenomic and genomic studies of the species, Pectobacterium cacticida and proposal for reclassification as Alcorniella cacticida comb. nov

Jonca,

Pirhonen,

Waleron

et al. 2024

Front. Plant Sci.

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“…No match was found with the three insertions either querying the ICEberg database [ 22 ] or running PHASTER for phage search [ 23 ]. However, putative attL and attR sites were found in the flaking regions of the insertions, suggesting they could be integrative conjugative elements (ICE) [ 24 , 25 ]. The comparison of CDS regions of the putative ICEs is depicted in Fig.…”

Section: Resultsmentioning

confidence: 99%

Klebsiella pneumoniae carrying multiple alleles of antigen 43-encoding gene of Escherichia coli associated with biofilm formation

Tambassi

Passarini

Menozzi

et al. 2023

Eur J Clin Microbiol Infect Dis

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A clinical strain of Klebsiella pneumoniae typed as sequence type 307 carrying three different alleles of the flu gene encoding the Escherichia coli virulence factor antigen 43 associated with biofilm formation was detected and characterized. The flu alleles are located in the chromosome inside putative integrative conjugative elements. The strain displays the phenotypes associated with Ag43, i.e. bi-phasic colony morphology and enhanced biofilm production. Furthermore, the strain produces low amount of capsule known to affect Ag43 function. Analysis of 1431 worldwide deposited genomes revealed that 3.7% Klebsiella pneumoniae carry one or two flu alleles.

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“…IMEs carry ARGs and may play a major role in the dissemination of ARGs [317,318]. Identifying and annotating new putative ICEs and IMEs in bacterial chromosomes in silico remains challenging [319,320]. Nonetheless, ICEs and IMEs have been suggested to be more phylogenetically widespread than conjugative plasmids [316,318,321].…”

Section: Integrative and Conjugative Elements (Ices)mentioning

confidence: 99%

Horizontal Gene Transfer of Antibiotic Resistance Genes in Biofilms

2023

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Most bacteria attach to biotic or abiotic surfaces and are embedded in a complex matrix which is known as biofilm. Biofilm formation is especially worrisome in clinical settings as it hinders the treatment of infections with antibiotics due to the facilitated acquisition of antibiotic resistance genes (ARGs). Environmental settings are now considered as pivotal for driving biofilm formation, biofilm-mediated antibiotic resistance development and dissemination. Several studies have demonstrated that environmental biofilms can be hotspots for the dissemination of ARGs. These genes can be encoded on mobile genetic elements (MGEs) such as conjugative and mobilizable plasmids or integrative and conjugative elements (ICEs). ARGs can be rapidly transferred through horizontal gene transfer (HGT) which has been shown to occur more frequently in biofilms than in planktonic cultures. Biofilm models are promising tools to mimic natural biofilms to study the dissemination of ARGs via HGT. This review summarizes the state-of-the-art of biofilm studies and the techniques that visualize the three main HGT mechanisms in biofilms: transformation, transduction, and conjugation.

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Breaking the ICE: an easy workflow for identifying and analyzing integrative and conjugative elements in bacterial genomes

Cited by 7 publications

References 44 publications

Comprehensive phenomic and genomic studies of the species, Pectobacterium cacticida and proposal for reclassification as Alcorniella cacticida comb. nov

Comprehensive phenomic and genomic studies of the species, Pectobacterium cacticida and proposal for reclassification as Alcorniella cacticida comb. nov

Klebsiella pneumoniae carrying multiple alleles of antigen 43-encoding gene of Escherichia coli associated with biofilm formation

Horizontal Gene Transfer of Antibiotic Resistance Genes in Biofilms

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