Articoli di riviste: "Integrative conjugative element (ICE)"

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Iannelli, Francesco, Francesco Santoro, Marco R. Oggioni e Gianni Pozzi. "Nucleotide Sequence Analysis of Integrative Conjugative Element Tn5253of Streptococcus pneumoniae". Antimicrobial Agents and Chemotherapy 58, n. 2 (2 dicembre 2013): 1235–39. http://dx.doi.org/10.1128/aac.01764-13.

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ABSTRACTConjugative transposon Tn5253, an integrative conjugative element (ICE) ofStreptococcus pneumoniaecarrying thecatandtet(M) genes, was shown to be 64,528 bp in size and to contain 79 open reading frames, of which only 38 could be annotated. Two distinct genetic elements were found integrated into Tn5253: Tn5251(18,033 bp), of the Tn916-Tn1545family of ICEs, and Ωcat(pC194) (7,627 bp), which could not conjugate but was capable of intracellular mobility by excision, circularization, and integration by homologous recombination. The highest conjugation frequency of Tn5253was observed whenStreptococcus pyogeneswas the donor (6.7 × 10−3transconjugants/donor).

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Libante, Virginie, Nazim Sarica, Abbas Mohamad Ali, Chloé Gapp, Anissa Oussalah, Gérard Guédon, Nathalie Leblond-Bourget e Sophie Payot. "Mobilization of IMEs Integrated in the oriT of ICEs Involves Their Own Relaxase Belonging to the Rep-Trans Family of Proteins". Genes 11, n. 9 (26 agosto 2020): 1004. http://dx.doi.org/10.3390/genes11091004.

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Integrative mobilizable elements (IMEs) are widespread but very poorly studied integrated elements that can excise and hijack the transfer apparatus of co-resident conjugative elements to promote their own spreading. Sixty-four putative IMEs, harboring closely related mobilization and recombination modules, were found in 14 Streptococcus species and in Staphylococcus aureus. Fifty-three are integrated into the origin of transfer (oriT) of a host integrative conjugative element (ICE), encoding a MobT relaxase and belonging to three distant families: ICESt3, Tn916, and ICE6013. The others are integrated into an unrelated IME or in chromosomal sites. After labeling by an antibiotic resistance gene, the conjugative transfer of one of these IMEs (named IME_oriTs) and its host ICE was measured. Although the IME is integrated in an ICE, it does not transfer as a part of the host ICE (no cis-mobilization). The IME excises and transfers separately from the ICE (without impacting its transfer rate) using its own relaxase, distantly related to all known MobT relaxases, and integrates in the oriT of the ICE after transfer. Overall, IME_oriTs use MobT-encoding ICEs both as hosts and as helpers for conjugative transfer. As half of them carry lsa(C), they actively participate in the dissemination of lincosamide–streptogramin A–pleuromutilin resistance among Firmicutes.

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Del Grosso, Maria, Romina Camilli, Ermanno Rizzi, Alessandro Pietrelli, Gianluca De Bellis e Annalisa Pantosti. "ICESpy009, a Conjugative Genetic Element Carryingmef(E) in Streptococcus pyogenes". Antimicrobial Agents and Chemotherapy 60, n. 7 (11 aprile 2016): 3906–12. http://dx.doi.org/10.1128/aac.03082-15.

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ABSTRACTEfflux-mediated macrolide resistance due tomef(E) andmel, carried by the mega element, is common inStreptococcus pneumoniae, for which it was originally characterized, but it is rare inStreptococcus pyogenes. InS. pyogenes, mega was previously found to be enclosed in Tn2009, a composite genetic element of the Tn916family containingtet(M) and conferring erythromycin and tetracycline resistance. In this study,S. pyogenesisolates containingmef(E), apparently not associated with other resistance determinants, were examined to characterize the genetic context of mega. By whole-genome sequencing of one isolate, MB56Spyo009, we identified a novel composite integrative and conjugative element (ICE) carrying mega, designated ICESpy009, belonging to the ICESa2603 family. ICESpy009 was 55 kb long, contained 61 putative open reading frames (ORFs), and was found to be integrated intohylA, a novel integration site for the ICESa2603 family. The modular organization of the ICE was similar to that of members of the ICESa2603 family carried by different streptococcal species. In addition, a novel cluster of accessory resistance genes was found inside a region that encloses mega. PCR mapping targeting ICESpy009 revealed the presence of a similar ICE in five other isolates under study. While in three isolates the integration site was the same as that of ICESpy009, in two isolates the ICE was integrated intorplL, the typical integration site of the ICESa2603 family. ICESpy009 was able to transfer macrolide resistance by conjugation to bothS. pyogenesandS. pneumoniae, showing the first evidence of the transferability of mega fromS. pyogenes.

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Giovanetti, Eleonora, Andrea Brenciani, Erika Tiberi, Alessandro Bacciaglia e Pietro Emanuele Varaldo. "ICESp2905, theerm(TR)-tet(O) Element of Streptococcus pyogenes, Is Formed by Two Independent Integrative and Conjugative Elements". Antimicrobial Agents and Chemotherapy 56, n. 1 (10 ottobre 2011): 591–94. http://dx.doi.org/10.1128/aac.05352-11.

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ABSTRACTIn ICESp2905, a widespreaderm(TR)- andtet(O)-carrying genetic element ofStreptococcus pyogenes, the two resistance determinants are contained in separate fragments inserted into a scaffold of clostridial origin. ICESp2905(∼65.6 kb) was transferable not only in its regular form but also in a defective form lacking theerm(TR) fragment (ICESp2906, ∼53.0 kb). Theerm(TR) fragment was also an independent integrative and conjugative element (ICE) (ICESp2907, ∼12.6 kb). ICESp2905thus results from one ICE (ICESp2907) being integrated into another (ICESp2906).

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Michael, G. B., K. Kadlec, M. T. Sweeney, E. Brzuszkiewicz, H. Liesegang, R. Daniel, R. W. Murray, J. L. Watts e S. Schwarz. "ICEPmu1, an integrative conjugative element (ICE) of Pasteurella multocida: structure and transfer". Journal of Antimicrobial Chemotherapy 67, n. 1 (14 ottobre 2011): 91–100. http://dx.doi.org/10.1093/jac/dkr411.

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Auchtung, Jennifer M., Naira Aleksanyan, Artemisa Bulku e Melanie B. Berkmen. "Biology of ICE Bs1 , an integrative and conjugative element in Bacillus subtilis". Plasmid 86 (luglio 2016): 14–25. http://dx.doi.org/10.1016/j.plasmid.2016.07.001.

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Calcutt, Michael J., Michelle S. Lewis e Kim S. Wise. "Molecular Genetic Analysis of ICEF, an Integrative Conjugal Element That Is Present as a Repetitive Sequence in the Chromosome of Mycoplasma fermentans PG18". Journal of Bacteriology 184, n. 24 (15 dicembre 2002): 6929–41. http://dx.doi.org/10.1128/jb.184.24.6929-6941.2002.

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ABSTRACT Mycoplasma genomes contain compact gene sets that approach the minimal complement necessary for life and reflect multiple evolutionary instances of genomic reduction. Lateral gene transfer may play a critical role in shaping the mobile gene pool in these organisms, yet complex mobile elements have not been reported within this genus. We describe here a large (∼23-kb) genetic element with unique features that is present in four copies in the Mycoplasma fermentans PG18 chromosome, accounting for approximately 8% of the genome. These novel elements, designated ICEF (integrative conjugal elements of M. fermentans), resemble conjugative, self-transmissible integrating elements (constins) in that circular, nonreplicative extrachromosomal forms occur in which the left and right termini of the integrated element are juxtaposed and separated by a coupling sequence derived from direct repeats flanking chromosomal copies of ICEF as a result of target site duplication. ICEF contain multiple similarly oriented open reading frames (ORFs), of which some have homology to products of known conjugation genes but others have no known counterparts. Surprisingly, unlike other constins, ICEF lack homologs of known integrases, transposases, or recombinases, suggesting that a novel enzyme may be employed for integration-excision. Skewed distribution and varied sites of chromosomal integration among M. fermentans isolates suggest a role for ICEF in promoting genomic and phenotypic variation in this species. Identification of homologs of terminal ICEF ORFs in two additional mycoplasma species indicates that ICEF is the prototype member of a family of ICE-related elements that may be widespread among pathogenic mycoplasmas infecting diverse vertebrate hosts.

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McKeithen-Mead, Saria A., e Alan D. Grossman. "Timing of integration into the chromosome is critical for the fitness of an integrative and conjugative element and its bacterial host". PLOS Genetics 19, n. 2 (13 febbraio 2023): e1010524. http://dx.doi.org/10.1371/journal.pgen.1010524.

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Integrative and conjugative elements (ICEs) are major contributors to genome plasticity in bacteria. ICEs reside integrated in the chromosome of a host bacterium and are passively propagated during chromosome replication and cell division. When activated, ICEs excise from the chromosome and may be transferred through the ICE-encoded conjugation machinery into a recipient cell. Integration into the chromosome of the new host generates a stable transconjugant. Although integration into the chromosome of a new host is critical for the stable acquisition of ICEs, few studies have directly investigated the molecular events that occur in recipient cells during generation of a stable transconjugant. We found that integration of ICEBs1, an ICE of Bacillus subtilis, occurred several generations after initial transfer to a new host. Premature integration in new hosts led to cell death and hence decreased fitness of the ICE and transconjugants. Host lethality due to premature integration was caused by rolling circle replication that initiated in the integrated ICEBs1 and extended into the host chromosome, resulting in catastrophic genome instability. Our results demonstrate that the timing of integration of an ICE is linked to cessation of autonomous replication of the ICE, and that perturbing this linkage leads to a decrease in ICE and host fitness due to a loss of viability of transconjugants. Linking integration to cessation of autonomous replication appears to be a conserved regulatory scheme for mobile genetic elements that both replicate and integrate into the chromosome of their host.

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Levicán, Gloria J., Assaf Katz, Jorge H. Valdés, Raquel Quatrini, David S. Holmes e O. Orellana. "A 300 kpb Genome Segment, Including a Complete Set of tRNA Genes, is Dispensable for Acidithiobacillus Ferrooxidans". Advanced Materials Research 71-73 (maggio 2009): 187–90. http://dx.doi.org/10.4028/www.scientific.net/amr.71-73.187.

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The genome sequences from two strains of the acidophilic, autotrophic, chemolithotrophic proteobacterium A. ferrooxidans are available from genome databases. Bioinformatic sequence comparison revealed the existence in one strain of a putative integrative conjugative element (ICE), containing an entire set of clustered tRNA genes. ICE is missing in the other strain, suggesting that this element as well as the tRNA genes cluster is dispensable for the bacterium. Bioinformatic predictions suggest that the tRNA genes cluster might mainly contribute to the translation of ICE encoded genes.

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Aberkane, Salim, Fabrice Compain, Dominique Decré, Chloé Dupont, Chrislène Laurens, Marion Vittecoq, Alix Pantel et al. "High Prevalence of SXT/R391-Related Integrative and Conjugative Elements CarryingblaCMY-2in Proteus mirabilis Isolates from Gulls in the South of France". Antimicrobial Agents and Chemotherapy 60, n. 2 (7 dicembre 2015): 1148–52. http://dx.doi.org/10.1128/aac.01654-15.

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ABSTRACTThe genetic structures involved in the dissemination ofblaCMY-2carried byProteus mirabilisisolates recovered from different gull species in the South of France were characterized and compared to clinical isolates.blaCMY-2was identified inP. mirabilisisolates from 27/93 yellow-legged gulls and from 37/65 slender-billed gulls. It was carried by a conjugative SXT/R391-like integrative and conjugative element (ICE) in all avian strains and in 3/7 human strains. Two clinical isolates had the same genetic background as six avian isolates.

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Bean, Emily L., Calvin Herman, Mary E. Anderson e Alan D. Grossman. "Biology and engineering of integrative and conjugative elements: Construction and analyses of hybrid ICEs reveal element functions that affect species-specific efficiencies". PLOS Genetics 18, n. 5 (18 maggio 2022): e1009998. http://dx.doi.org/10.1371/journal.pgen.1009998.

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Integrative and conjugative elements (ICEs) are mobile genetic elements that reside in a bacterial host chromosome and are prominent drivers of bacterial evolution. They are also powerful tools for genetic analyses and engineering. Transfer of an ICE to a new host involves many steps, including excision from the chromosome, DNA processing and replication, transfer across the envelope of the donor and recipient, processing of the DNA, and eventual integration into the chromosome of the new host (now a stable transconjugant). Interactions between an ICE and its host throughout the life cycle likely influence the efficiencies of acquisition by new hosts. Here, we investigated how different functional modules of two ICEs, Tn916 and ICEBs1, affect the transfer efficiencies into different host bacteria. We constructed hybrid elements that utilize the high-efficiency regulatory and excision modules of ICEBs1 and the conjugation genes of Tn916. These elements produced more transconjugants than Tn916, likely due to an increase in the number of cells expressing element genes and a corresponding increase in excision. We also found that several Tn916 and ICEBs1 components can substitute for one other. Using B. subtilis donors and three Enterococcus species as recipients, we found that different hybrid elements were more readily acquired by some species than others, demonstrating species-specific interactions in steps of the ICE life cycle. This work demonstrates that hybrid elements utilizing the efficient regulatory functions of ICEBs1 can be built to enable efficient transfer into and engineering of a variety of other species.

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Sulser, Sandra, Andrea Vucicevic, Veronica Bellini, Roxane Moritz, François Delavat, Vladimir Sentchilo, Nicolas Carraro e Jan Roelof van der Meer. "A bistable prokaryotic differentiation system underlying development of conjugative transfer competence". PLOS Genetics 18, n. 6 (28 giugno 2022): e1010286. http://dx.doi.org/10.1371/journal.pgen.1010286.

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The mechanisms and impact of horizontal gene transfer processes to distribute gene functions with potential adaptive benefit among prokaryotes have been well documented. In contrast, little is known about the life-style of mobile elements mediating horizontal gene transfer, whereas this is the ultimate determinant for their transfer fitness. Here, we investigate the life-style of an integrative and conjugative element (ICE) within the genus Pseudomonas that is a model for a widespread family transmitting genes for xenobiotic compound metabolism and antibiotic resistances. Previous work showed bimodal ICE activation, but by using single cell time-lapse microscopy coupled to combinations of chromosomally integrated single copy ICE promoter-driven fluorescence reporters, RNA sequencing and mutant analysis, we now describe the complete regulon leading to the arisal of differentiated dedicated transfer competent cells. The regulon encompasses at least three regulatory nodes and five (possibly six) further conserved gene clusters on the ICE that all become expressed under stationary phase conditions. Time-lapse microscopy indicated expression of two regulatory nodes (i.e., bisR and alpA-bisDC) to precede that of the other clusters. Notably, expression of all clusters except of bisR was confined to the same cell subpopulation, and was dependent on the same key ICE regulatory factors. The ICE thus only transfers from a small fraction of cells in a population, with an estimated proportion of between 1.7–4%, which express various components of a dedicated transfer competence program imposed by the ICE, and form the centerpiece of ICE conjugation. The components mediating transfer competence are widely conserved, underscoring their selected fitness for efficient transfer of this class of mobile elements.

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Tardy, Florence, Virginie Mick, Emilie Dordet-Frisoni, Marc Serge Marenda, Pascal Sirand-Pugnet, Alain Blanchard e Christine Citti. "Integrative Conjugative Elements Are Widespread in Field Isolates of Mycoplasma Species Pathogenic for Ruminants". Applied and Environmental Microbiology 81, n. 5 (19 dicembre 2014): 1634–43. http://dx.doi.org/10.1128/aem.03723-14.

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ABSTRACTComparative genomics have revealed massive horizontal gene transfer (HGT) betweenMycoplasmaspecies sharing common ruminant hosts. Further results pointed toward an integrative conjugative element (ICE) as an important contributor of HGT in the small-ruminant-pathogenMycoplasma agalactiae. To estimate the prevalence of ICEs in ruminant mycoplasmas, we surveyed their occurrence in a collection of 166 field strains representing 4 (sub)species that are recognized as major pathogens. Based on available sequenced genomes, we first defined the conserved, minimal ICE backbone as composed of 4 coding sequences (CDSs) that are evenly distributed and predicted to be essential for ICE chromosomal integration-excision and horizontal transfer. Screening of the strain collection revealed that these 4 CDSs are well represented in ruminantMycoplasmaspecies, suggesting widespread occurrence of ICEs. Yet their prevalence varies within and among species, with no correlation found with the individual strain history. Extrachromosomal ICE forms were also often detected, suggesting that ICEs are able to circularize in all species, a first and essential step in ICE horizontal transfer. Examination of the junction of the circular forms and comparative sequence analysis of conserved CDSs clearly pointed toward two types of ICE, thehominisandspiroplasmatypes, most likely differing in their mechanism of excision-integration. Overall, our data indicate the occurrence and maintenance of functional ICEs in a large number of field isolates of ruminant mycoplasmas. These may contribute to genome plasticity and gene exchanges and, presumably, to the emergence of diverse genotypes within pathogenic mycoplasmas of veterinary importance.

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Shang, Yanhong, Dexi Li, Wenbo Hao, Stefan Schwarz, Xinxin Shan, Bianzhi Liu, Su-Mei Zhang, Xin-Sheng Li e Xiang-Dang Du. "A prophage and two ICESa2603-family integrative and conjugative elements (ICEs) carrying optrA in Streptococcus suis". Journal of Antimicrobial Chemotherapy 74, n. 10 (17 luglio 2019): 2876–79. http://dx.doi.org/10.1093/jac/dkz309.

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Abstract Objectives To investigate the presence and transfer of the oxazolidinone/phenicol resistance gene optrA and identify the genetic elements involved in the horizontal transfer of the optrA gene in Streptococcus suis. Methods A total of 237 S. suis isolates were screened for the presence of the optrA gene by PCR. Whole-genome DNA of three optrA-positive strains was completely sequenced using the Illumina MiSeq and Pacbio RSII platforms. MICs were determined by broth microdilution. Transferability of the optrA gene in S. suis was investigated by conjugation. The presence of circular intermediates was examined by inverse PCR. Results The optrA gene was present in 11.8% (28/237) of the S. suis strains. In three strains, the optrA gene was flanked by two copies of IS1216 elements in the same orientation, located either on a prophage or on ICESa2603-family integrative and conjugative elements (ICEs), including one tandem ICE. In one isolate, the optrA-carrying ICE transferred with a frequency of 2.1 × 10−8. After the transfer, the transconjugant displayed elevated MICs of the respective antimicrobial agents. Inverse PCRs revealed that circular intermediates of different sizes were formed in the three optrA-carrying strains, containing one copy of the IS1216E element and the optrA gene alone or in combination with other resistance genes. Conclusions A prophage and two ICESa2603-family ICEs (including one tandem ICE) associated with the optrA gene were identified in S. suis. The association of the optrA gene with the IS1216E elements and its location on either a prophage or ICEs will aid its horizontal transfer.

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Bidet, Philippe, Romain Basmaci, Julien Guglielmini, Catherine Doit, Christelle Jost, André Birgy e Stéphane Bonacorsi. "Genome Analysis of Kingella kingae Strain KWG1 Reveals How a β-Lactamase Gene Inserted in the Chromosome of This Species". Antimicrobial Agents and Chemotherapy 60, n. 1 (16 novembre 2015): 703–8. http://dx.doi.org/10.1128/aac.02192-15.

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ABSTRACTWe describe the genome of a penicillinase-producingKingella kingaestrain (KWG1), the first to be isolated in continental Europe, whoseblaTEM-1gene was, for the first time in this species, found to be chromosomally inserted. TheblaTEMgene is located in an integrative and conjugative element (ICE) inserted in Met-tRNA and comprising genes that encode resistance to sulfonamides, streptomycin, and tetracycline. This ICE is homologous to resistance-conferring plasmids ofK. kingaeand other Gram-negative bacteria.

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Roche, David, Maud Fléchard, Nathalie Lallier, Maryline Répérant, Annie Brée, Géraldine Pascal, Catherine Schouler e Pierre Germon. "ICEEc2, a New Integrative and Conjugative Element Belonging to the pKLC102/PAGI-2 Family, Identified in Escherichia coli Strain BEN374". Journal of Bacteriology 192, n. 19 (30 luglio 2010): 5026–36. http://dx.doi.org/10.1128/jb.00609-10.

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ABSTRACT The diversity of the Escherichia coli species is in part due to the large number of mobile genetic elements that are exchanged between strains. We report here the identification of a new integrative and conjugative element (ICE) of the pKLC102/PAGI-2 family located downstream of the tRNA gene pheU in the E. coli strain BEN374. Indeed, this new region, which we called ICEEc2, can be transferred by conjugation from strain BEN374 to the E. coli strain C600. We were also able to transfer this region into a Salmonella enterica serovar Typhimurium strain and into a Yersinia pseudotuberculosis strain. This transfer was then followed by the integration of ICEEc2 into the host chromosome downstream of a phe tRNA gene. Our data indicated that this transfer involved a set of three genes encoding DNA mobility enzymes and a type IV pilus encoded by genes present on ICEEc2. Given the wide distribution of members of this family, these mobile genetic elements are likely to play an important role in the diversification of bacteria.

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Han, Xiaoyan, Xiang-Dang Du, Luke Southey, Dieter M. Bulach, Torsten Seemann, Xu-Xia Yan, Trudi L. Bannam e Julian I. Rood. "Functional Analysis of a Bacitracin Resistance Determinant Located on ICECp1, a Novel Tn916-Like Element from a Conjugative Plasmid in Clostridium perfringens". Antimicrobial Agents and Chemotherapy 59, n. 11 (17 agosto 2015): 6855–65. http://dx.doi.org/10.1128/aac.01643-15.

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ABSTRACTBacitracins are mixtures of structurally related cyclic polypeptides with antibiotic properties. They act by interfering with the biosynthesis of the bacterial cell wall. In this study, we analyzed an avian necrotic enteritis strain ofClostridium perfringensthat was resistant to bacitracin and produced NetB toxin. We identified a bacitracin resistance locus that resembled a bacitracin resistance determinant fromEnterococcus faecalis. It contained the structural genesbcrABDand a putative regulatory gene,bcrR. Mutagenesis studies provided evidence that bothbcrAandbcrBare essential for bacitracin resistance, and that evidence was supported by the results of experiments in which the introduction of both thebcrAandbcrBgenes into a bacitracin-susceptibleC. perfringensstrain was required to confer bacitracin resistance. The wild-type strain was shown to contain at least three large, putatively conjugative plasmids, and thebcrRABDlocus was localized to an 89.7-kb plasmid, pJIR4150. This plasmid was experimentally shown to be conjugative and was sequenced. The sequence revealed that it also carries atpeLtoxin gene and is related to the pCW3 family of conjugative antibiotic resistance and toxin plasmids fromC. perfringens. Thebcrgenes were located on a genetic element, ICECp1, which is related to the Tn916family of integrative conjugative elements (ICEs). ICECp1appears to be the first Tn916-like element shown to confer bacitracin resistance. In summary, we identified in a toxin-producingC. perfringensstrain a novel mobile bacitracin resistance element which was experimentally shown to be essential for bacitracin resistance and is carried by a putative ICE located on a conjugative plasmid.

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Kong, Ling-Han, Rong Xiang, Yu-Long Wang, Shun-Kang Wu, Chang-Wei Lei, Zhuang-Zhuang Kang, Yan-Peng Chen, Xiao-Lan Ye, Yan Lai e Hong-Ning Wang. "Integration of the blaNDM-1 carbapenemase gene into a novel SXT/R391 integrative and conjugative element in Proteus vulgaris". Journal of Antimicrobial Chemotherapy 75, n. 6 (10 marzo 2020): 1439–42. http://dx.doi.org/10.1093/jac/dkaa068.

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Abstract Objectives To characterize the genetic environment of the carbapenem resistance determinant in Proteus vulgaris of swine origin. Methods The carbapenem-resistant P. vulgaris strain BC22 was isolated from a faecal swab from a diseased pig with diarrhoea in Sichuan Province of China in 2018. The presence of carbapenemase genes was screened by PCR. WGS and bioinformatics analysis were performed to analyse the genetic environment of the carbapenem resistance determinant. Results P. vulgaris strain BC22 was found to harbour the carbapenemase gene blaNDM-1. WGS data revealed that blaNDM-1 was located in a truncated ISAba125 composite transposon. The carbapenem resistance gene blaNDM-1 and 20 other resistance genes, including the multiresistance gene cfr and the bifunctional aminoglycoside/quinolone resistance gene aac(6′)-lb-cr, were located in a novel SXT/R391 integrative and conjugative element (ICE). This new SXT/R391 ICE of 148.7 kb was chromosomally located, and could be transferred to Escherichia coli. Conclusions Here, we report a carbapenemase gene, blaNDM-1, integrated into an SXT/R391 ICE. Our study highlights that this SXT/R391 ICE may facilitate the dissemination of clinically important resistance genes such as blaNDM-1, cfr and aac(6′)-lb-cr.

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Delavat, François, Sara Mitri, Serge Pelet e Jan Roelof van der Meer. "Highly variable individual donor cell fates characterize robust horizontal gene transfer of an integrative and conjugative element". Proceedings of the National Academy of Sciences 113, n. 24 (31 maggio 2016): E3375—E3383. http://dx.doi.org/10.1073/pnas.1604479113.

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Horizontal gene transfer is an important evolutionary mechanism for bacterial adaptation. However, given the typical low transfer frequencies in a bacterial population, little is known about the fate and interplay of donor cells and the mobilized DNA during transfer. Here we study transfer of an integrative and conjugative element (ICE) among individual live bacterial cells. ICEs are widely distributed mobile DNA elements that are different than plasmids because they reside silent in the host chromosome and are maintained through vertical descent. Occasionally, ICEs become active, excise, and transmit their DNA to a new recipient, where it is reintegrated. We develop a fluorescent tool to differentiate excision, transfer, and reintegration of a model ICE named ICEclc(for carrying theclcgenes for chlorocatechol metabolism) among singlePseudomonascells by using time-lapse microscopy. We find that ICEclcactivation is initiated in stationary phase cells, but excision and transfer predominantly occur only when such cells have been presented with new nutrients. Donors with activated ICE develop a number of different states, characterized by reduced cell division rates or growth arrest, persistence, or lysis, concomitant with ICE excision, and likely, ICE loss or replication. The donor cell state transitions can be described by using a stochastic model, which predicts that ICE fitness is optimal at low initiation rates in stationary phase. Despite highly variable donor cell fates, ICE transfer is remarkably robust overall, with 75% success after excision. Our results help to better understand ICE behavior and shed a new light on bacterial cellular differentiation during horizontal gene transfer.

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Lei, Chang-Wei, An-Yun Zhang, Hong-Ning Wang, Bi-Hui Liu, Li-Qin Yang e Yong-Qiang Yang. "Characterization of SXT/R391 Integrative and Conjugative Elements in Proteus mirabilis Isolates from Food-Producing Animals in China". Antimicrobial Agents and Chemotherapy 60, n. 3 (11 gennaio 2016): 1935–38. http://dx.doi.org/10.1128/aac.02852-15.

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SXT/R391 integrative and conjugative elements (ICEs) were detected in 8 out of 125Proteus mirabilisisolates from food-producing animals in China. Whole-genome sequencing revealed that seven ICEs were identical to ICEPmiJpn1, carrying the cephalosporinase geneblaCMY-2. Another one, designated ICEPmiChn1, carried five resistance genes. All eight ICEs could be transferred toEscherichia colivia conjugation. The results highlight the idea that animal farms are important reservoir of the SXT/R391 ICE-containingP. mirabilis.

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Davies, Mark R., Josephine Shera, Gary H. Van Domselaar, Kadaba S. Sriprakash e David J. McMillan. "A Novel Integrative Conjugative Element Mediates Genetic Transfer from Group G Streptococcus to Other β-Hemolytic Streptococci". Journal of Bacteriology 191, n. 7 (23 gennaio 2009): 2257–65. http://dx.doi.org/10.1128/jb.01624-08.

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ABSTRACT Lateral gene transfer is a significant contributor to the ongoing evolution of many bacterial pathogens, including β-hemolytic streptococci. Here we provide the first characterization of a novel integrative conjugative element (ICE), ICESde3396, from Streptococcus dysgalactiae subsp. equisimilis (group G streptococcus [GGS]), a bacterium commonly found in the throat and skin of humans. ICESde3396 is 64 kb in size and encodes 66 putative open reading frames. ICESde3396 shares 38 open reading frames with a putative ICE from Streptococcus agalactiae (group B streptococcus [GBS]), ICESa2603. In addition to genes involves in conjugal processes, ICESde3396 also carries genes predicted to be involved in virulence and resistance to various metals. A major feature of ICESde3396 differentiating it from ICESa2603 is the presence of an 18-kb internal recombinogenic region containing four unique gene clusters, which appear to have been acquired from streptococcal and nonstreptococcal bacterial species. The four clusters include two cadmium resistance operons, an arsenic resistance operon, and genes with orthologues in a group A streptococcus (GAS) prophage. Streptococci that naturally harbor ICESde3396 have increased resistance to cadmium and arsenate, indicating the functionality of genes present in the 18-kb recombinogenic region. By marking ICESde3396 with a kanamycin resistance gene, we demonstrate that the ICE is transferable to other GGS isolates as well as GBS and GAS. To investigate the presence of the ICE in clinical streptococcal isolates, we screened 69 isolates (30 GGS, 19 GBS, and 20 GAS isolates) for the presence of three separate regions of ICESde3396. Eleven isolates possessed all three regions, suggesting they harbored ICESde3396-like elements. Another four isolates possessed ICESa2603-like elements. We propose that ICESde3396 is a mobile genetic element that is capable of acquiring DNA from multiple bacterial sources and is a vehicle for dissemination of this DNA through the wider β-hemolytic streptococcal population.

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Burrus, Vincent, e Matthew K. Waldor. "Formation of SXT Tandem Arrays and SXT-R391 Hybrids". Journal of Bacteriology 186, n. 9 (1 maggio 2004): 2636–45. http://dx.doi.org/10.1128/jb.186.9.2636-2645.2004.

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ABSTRACT SXT is an integrative and conjugative element (ICE) isolated from Vibrio cholerae. This ∼100-kb ICE encodes resistance to multiple antibiotics and integrates site specifically into the chromosome. SXT excises from the chromosome to form a circular but nonreplicative extrachromosomal molecule that is required for its transfer. Here we found that a significant fraction of freshly isolated SXT exconjugants contained tandem SXT arrays. There was heterogeneity in the size of the SXT arrays detected in single exconjugant colonies. Some arrays consisted of more than five SXTs arranged in tandem. These extended arrays were unstable and did not persist during serial passages. The mechanism accounting for the generation of SXT arrays is unknown; however, array formation was not dependent upon recA and appeared to depend on conjugative transfer. While such arrays did not alter the transfer frequency of wild-type SXT, they partially complemented the transfer deficiency of a Δxis SXT mutant, which is ordinarily unable to generate the extrachromosomal intermediate required for SXT transfer. Exconjugants derived from donor strains that harbored tandem arrays of SXT and R391, an SXT-related element, contained functional hybrid elements that arose from recA-independent recombination between the two ICEs. Thus, arrays of SXT-related elements promote the creation of novel ICEs.

23

Mingoia, Marina, Eleonora Morici, Gianluca Morroni, Eleonora Giovanetti, Maria Del Grosso, Annalisa Pantosti e Pietro E. Varaldo. "Tn5253Family Integrative and Conjugative Elements Carryingmef(I) andcatQDeterminants in Streptococcus pneumoniae and Streptococcus pyogenes". Antimicrobial Agents and Chemotherapy 58, n. 10 (28 luglio 2014): 5886–93. http://dx.doi.org/10.1128/aac.03638-14.

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ABSTRACTThe linkage between the macrolide efflux genemef(I) and the chloramphenicol inactivation genecatQwas first described inStreptococcus pneumoniae(strain Spn529), where the two genes are located in a module designated IQ element. Subsequently, two different defective IQ elements were detected inStreptococcus pyogenes(strains Spy029 and Spy005). The genetic elements carrying the three IQ elements were characterized, and all were found to be Tn5253family integrative and conjugative elements (ICEs). The ICE fromS. pneumoniae(ICESpn529IQ) was sequenced, whereas the ICEs fromS. pyogenes(ICESpy029IQ and ICESpy005IQ, the first Tn5253-like ICEs reported in this species) were characterized by PCR mapping, partial sequencing, and restriction analysis. ICESpn529IQ and ICESpy029IQ were found to share theintSp23FST81integrase gene and an identical Tn916fragment, whereas ICESpy005IQ hasint5252and lacks Tn916. All three ICEs were found to lack the linearized pC194 plasmid that is usually associated with Tn5253-like ICEs, and all displayed a single copy of a toxin-antitoxin operon that is typically contained in the direct repeats flanking the excisable pC194 region when this region is present. Two different insertion sites of the IQ elements were detected, one in ICESpn529IQ and ICESpy029IQ, and another in ICESpy005IQ. The chromosomal integration of the three ICEs was site specific, depending on the integrase (intSp23FST81orint5252). Only ICESpy005IQ was excised in circular form and transferred by conjugation. By transformation,mef(I) andcatQwere cotransferred at a high frequency fromS. pyogenesSpy005 and at very low frequencies fromS. pneumoniaeSpn529 andS. pyogenesSpy029.

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Haskett, Timothy L., Jason J. Terpolilli, Amanuel Bekuma, Graham W. O’Hara, John T. Sullivan, Penghao Wang, Clive W. Ronson e Joshua P. Ramsay. "Assembly and transfer of tripartite integrative and conjugative genetic elements". Proceedings of the National Academy of Sciences 113, n. 43 (12 ottobre 2016): 12268–73. http://dx.doi.org/10.1073/pnas.1613358113.

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Integrative and conjugative elements (ICEs) are ubiquitous mobile genetic elements present as “genomic islands” within bacterial chromosomes. Symbiosis islands are ICEs that convert nonsymbiotic mesorhizobia into symbionts of legumes. Here we report the discovery of symbiosis ICEs that exist as three separate chromosomal regions when integrated in their hosts, but through recombination assemble as a single circular ICE for conjugative transfer. Whole-genome comparisons revealed exconjugants derived from nonsymbiotic mesorhizobia received three separate chromosomal regions from the donorMesorhizobium ciceriWSM1271. The three regions were each bordered by two nonhomologous integrase attachment (att) sites, which together comprised three homologous pairs ofattLandattRsites. Sequential recombination between eachattLandattRpair produced correspondingattPandattBsites and joined the three fragments to produce a single circular ICE, ICEMcSym1271. A plasmid carrying the threeattPsites was used to recreate the process of tripartite ICE integration and to confirm the role of integrase genesintS,intM, andintGin this process. Nine additional tripartite ICEs were identified in diverse mesorhizobia and transfer was demonstrated for three of them. The transfer of tripartite ICEs to nonsymbiotic mesorhizobia explains the evolution of competitive but suboptimal N2-fixing strains found in Western Australian soils. The unheralded existence of tripartite ICEs raises the possibility that multipartite elements reside in other organisms, but have been overlooked because of their unusual biology. These discoveries reveal mechanisms by which integrases dramatically manipulate bacterial genomes to allow cotransfer of disparate chromosomal regions.

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Haenni, Marisa, Estelle Saras, Stéphane Bertin, Pierre Leblond, Jean-Yves Madec e Sophie Payot. "Diversity and Mobility of Integrative and Conjugative Elements in Bovine Isolates of Streptococcusagalactiae, S. dysgalactiae subsp. dysgalactiae, and S. uberis". Applied and Environmental Microbiology 76, n. 24 (15 ottobre 2010): 7957–65. http://dx.doi.org/10.1128/aem.00805-10.

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ABSTRACT Bovine isolates of S treptococcus agalactiae (n = 76), S treptococcus dysgalactiae subsp. dysgalactiae (n = 32), and S treptococcus uberis (n = 101) were analyzed for the presence of different integrative and conjugative elements (ICEs) and their association with macrolide, lincosamide, and tetracycline resistance. The diversity of the isolates included in this study was demonstrated by multilocus sequence typing for S. agalactiae and pulsed-field gel electrophoresis for S. dysgalactiae and S. uberis. Most of the erythromycin-resistant strains carry an ermB gene. Five strains of S. uberis that are resistant to lincomycin but susceptible to erythromycin carry the lin(B) gene, and one has both linB and lnuD genes. In contrast to S. uberis, most of the S. agalactiae and S. dysgalactiae tetracycline-resistant isolates carry a tet(M) gene. A tet(S) gene was also detected in the three species. A Tn916-related element was detected in 30 to 50% of the tetracycline-resistant strains in the three species. Tetracycline resistance was successfully transferred by conjugation to an S. agalactiae strain. Most of the isolates carry an ICE integrated in the rplL gene. In addition, half of the S. agalactiae isolates have an ICE integrated in a tRNA lysine (tRNALys) gene. Such an element is also present in 20% of the isolates of S. dysgalactiae and S. uberis. A circular form of these ICEs was detected in all of the isolates tested, indicating that these genetic elements are mobile. These ICEs could thus also be a vehicle for horizontal gene transfer between streptococci of animal and/or human origin.

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Dimopoulou, Ioanna D., Sofia I. Kartali, Rosalind M. Harding, Tim E. A. Peto e Derrick W. Crook. "Diversity of antibiotic resistance integrative and conjugative elements among haemophili". Journal of Medical Microbiology 56, n. 6 (1 giugno 2007): 838–46. http://dx.doi.org/10.1099/jmm.0.47125-0.

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The objective of this study was to investigate the sequence diversity in a single country of a family of integrative and conjugative elements (ICEs) that are vectors of antibiotic resistance in Haemophilus influenzae and Haemophilus parainfluenzae, and test the hypothesis that they emerged from a single lineage. Sixty subjects aged 9 months – 13 years were recruited and oropharyngeal samples cultured. Up to 10 morphologically distinct Pasteurellaceae spp. were purified, and then the species were determined and differentiated by partial sequence analysis of 16S rDNA and mdh, respectively. ICEs were detected by PCR directed at five genes distributed evenly across the ICE. These amplicons were sequenced and aligned by the neighbour-joining algorithm. A total of 339 distinguishable isolates were cultured. ICEs with all 5 genes present were found in 9 of 110 (8 %) H. influenzae and 21 of 211 (10 %) H. parainfluenzae, respectively. ICEs were not detected among the other Pasteurellaceae. A total of 20 of 60 (33 %) children carried at least 1 oropharyngeal isolate with an ICE possessing all 5 genes. One of the five genes, integrase, however, consisted of two lineages, one of which was highly associated with H. influenzae. The topology of neighbour-joining trees of the remaining four ICE genes was compared and showed a lack of congruence; though, the genes form a common pool among H. influenzae and H. parainfluenzae. This family of antibiotic resistance ICEs was prevalent among the children studied, was genetically diverse, formed a large gene pool, transferred between H. influenzae and H. parainfluenzae, lacked population structure and possessed features suggestive of panmixia, all indicating it has not recently emerged from a single source.

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Pavlovic, Guillaume, Vincent Burrus, Brigitte Gintz, Bernard Decaris e Gérard Guédon. "Evolution of genomic islands by deletion and tandem accretion by site-specific recombination: ICESt1-related elements from Streptococcus thermophilus". Microbiology 150, n. 4 (1 aprile 2004): 759–74. http://dx.doi.org/10.1099/mic.0.26883-0.

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The 34 734-bp integrative and potentially conjugative element (putative ICE) ICESt1 has been previously found to be site-specifically integrated in the 3′ end of the fda locus of Streptococcus thermophilus CNRZ368. Four types of genomic islands related to ICESt1 are integrated in the same position in seven other strains of S. thermophilus. One of these elements, ICESt3, harbours conjugation and recombination modules closely related to those of ICESt1 and excises by site-specific recombination. Two other types of elements, CIME19258 and CIME302, are flanked by site-specific attachment sites closely related to attL and attR of ICESt1 and ICESt3, whereas ΔCIME308 only possesses a putative attR site; none of these three elements carry complete conjugation and recombination modules. ICESt1 contains a functional internal recombination site, attL′, that is almost identical to attL of CIME19258. The recombination between attL′ and attR of ICESt1 leads to the excision of the expected circular molecule (putative ICE); a cis-mobilizable element (CIME) flanked by an attL site and an attB′ site remains integrated into the 3′ end of fda. Furthermore, sequences that could be truncated att sites were found within ICESt1, ICESt3 and CIME302. All together, these data suggest that these genomic islands evolved by deletion and tandem accretion of ICEs and CIMEs resulting from site-specific recombination. A model for this evolution is proposed and its application to other genomic islands is discussed.

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Burrus, Vincent, Roberto Quezada-Calvillo, Joeli Marrero e Matthew K. Waldor. "SXT-Related Integrating Conjugative Element in New World Vibrio cholerae". Applied and Environmental Microbiology 72, n. 4 (aprile 2006): 3054–57. http://dx.doi.org/10.1128/aem.72.4.3054-3057.2006.

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ABSTRACT SXT-related integrating conjugative elements (ICEs) became prevalent in Asian Vibrio cholerae populations after V. cholerae O139 emerged. Here, we describe an SXT-related ICE, ICEVchMex1, in a Mexican environmental V. cholerae isolate. Identification of ICEVchMex1 represents the first description of an SXT-related ICE in the Western Hemisphere. The significant differences between the SXT and ICEVchMex1 genomes suggest that these ICEs have evolved independently.

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Dangla-Pélissier, Gauthier, Nicolas Roux, Victoria Schmidt, Gaël Chambonnier, Moly Ba, Corinne Sebban-Kreuzer, Sophie de Bentzmann, Caroline Giraud e Christophe Bordi. "The horizontal transfer of Pseudomonas aeruginosa PA14 ICE PAPI-1 is controlled by a transcriptional triad between TprA, NdpA2 and MvaT". Nucleic Acids Research 49, n. 19 (13 ottobre 2021): 10956–74. http://dx.doi.org/10.1093/nar/gkab827.

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Abstract Pseudomonas aeruginosa is a major cause of nosocomial infections, particularly in immunocompromised patients or in individuals with cystic fibrosis. Genome sequences reveal that most P. aeruginosa strains contain a significant number of accessory genes gathered in genomic islands. Those genes are essential for P. aeruginosa to invade new ecological niches with high levels of antibiotic usage, like hospitals, or to survive during host infection by providing pathogenicity determinants. P. aeruginosa pathogenicity island 1 (PAPI-1), one of the largest genomic islands, encodes several putative virulence factors, including toxins, biofilm genes and antibiotic-resistance traits. The integrative and conjugative element (ICE) PAPI-1 is horizontally transferable by conjugation via a specialized GI-T4SS, but the mechanism regulating this transfer is currently unknown. Here, we show that this GI-T4SS conjugative machinery is directly induced by TprA, a regulator encoded within PAPI-1. Our data indicate that the nucleotide associated protein NdpA2 acts in synergy with TprA, removing a repressive mechanism exerted by MvaT. In addition, using a transcriptomic approach, we unravelled the regulon controlled by Ndpa2/TprA and showed that they act as major regulators on the genes belonging to PAPI-1. Moreover, TprA and NdpA2 trigger an atypical biofilm structure and enhance ICE PAPI-1 transfer.

30

Bean, Emily L., Lisa K. McLellan e Alan D. Grossman. "Activation of the integrative and conjugative element Tn916 causes growth arrest and death of host bacteria". PLOS Genetics 18, n. 10 (24 ottobre 2022): e1010467. http://dx.doi.org/10.1371/journal.pgen.1010467.

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Integrative and conjugative elements (ICEs) serve as major drivers of bacterial evolution. These elements often confer some benefit to host cells, including antibiotic resistance, metabolic capabilities, or pathogenic determinants. ICEs can also have negative effects on host cells. Here, we investigated the effects of the ICE (conjugative transposon) Tn916 on host cells. Because Tn916 is active in a relatively small subpopulation of host cells, we developed a fluorescent reporter system for monitoring activation of Tn916 in single cells. Using this reporter, we found that cell division was arrested in cells of Bacillus subtilis and Enterococcus faecalis (a natural host for Tn916) that contained an activated (excised) Tn916. Furthermore, most of the cells with the activated Tn916 subsequently died. We also observed these phenotypes on the population level in B. subtilis utilizing a modified version of Tn916 that can be activated in the majority of cells. We identified two genes (orf17 and orf16) in Tn916 that were sufficient to cause growth defects in B. subtilis and identified a single gene, yqaR, that is in a defective phage (skin) in the B. subtilis chromosome that was required for this phenotype. These three genes were only partially responsible for the growth defect caused by Tn916, indicating that Tn916 possesses multiple mechanisms to affect growth and viability of host cells. These results highlight the complex relationships that conjugative elements have with their host cells and the interplay between mobile genetic elements.

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Eidam, C., A. Poehlein, A. Leimbach, G. B. Michael, K. Kadlec, H. Liesegang, R. Daniel et al. "Analysis and comparative genomics of ICEMh1, a novel integrative and conjugative element (ICE) of Mannheimia haemolytica". Journal of Antimicrobial Chemotherapy 70, n. 1 (18 settembre 2014): 93–97. http://dx.doi.org/10.1093/jac/dku361.

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32

Libante, Virginie, Yves Nombre, Charles Coluzzi, Johan Staub, Gérard Guédon, Marcelo Gottschalk, Sarah Teatero, Nahuel Fittipaldi, Nathalie Leblond-Bourget e Sophie Payot. "Chromosomal Conjugative and Mobilizable Elements in Streptococcus suis: Major Actors in the Spreading of Antimicrobial Resistance and Bacteriocin Synthesis Genes". Pathogens 9, n. 1 (25 dicembre 2019): 22. http://dx.doi.org/10.3390/pathogens9010022.

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Streptococcus suis is a zoonotic pathogen suspected to be a reservoir of antimicrobial resistance (AMR) genes. The genomes of 214 strains of 27 serotypes were screened for AMR genes and chromosomal Mobile Genetic Elements (MGEs), in particular Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs). The functionality of two ICEs that host IMEs carrying AMR genes was investigated by excision tests and conjugation experiments. In silico search revealed 416 ICE-related and 457 IME-related elements. These MGEs exhibit an impressive diversity and plasticity with tandem accretions, integration of ICEs or IMEs inside ICEs and recombination between the elements. All of the detected 393 AMR genes are carried by MGEs. As previously described, ICEs are major vehicles of AMR genes in S. suis. Tn5252-related ICEs also appear to carry bacteriocin clusters. Furthermore, whereas the association of IME-AMR genes has never been described in S. suis, we found that most AMR genes are actually carried by IMEs. The autonomous transfer of an ICE to another bacterial species (Streptococcus thermophilus)—leading to the cis-mobilization of an IME carrying tet(O)—was obtained. These results show that besides ICEs, IMEs likely play a major role in the dissemination of AMR genes in S. suis.

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McLeod, Sarah M., Vincent Burrus e Matthew K. Waldor. "Requirement for Vibrio cholerae Integration Host Factor in Conjugative DNA Transfer". Journal of Bacteriology 188, n. 16 (15 agosto 2006): 5704–11. http://dx.doi.org/10.1128/jb.00564-06.

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ABSTRACT The requirement for host factors in the transmission of integrative and conjugative elements (ICEs) has not been extensively explored. Here we tested whether integration host factor (IHF) or Fis, two host-encoded nucleoid proteins, are required for transfer of SXT, a Vibrio cholerae-derived ICE that can be transmitted to many gram-negative species. Fis did not influence the transfer of SXT to or from V. cholerae. In contrast, IHF proved to be required for V. cholerae to act as an SXT donor. In the absence of IHF, V. cholerae displayed a modest defect for serving as an SXT recipient. Surprisingly, SXT integration into or excision from the V. cholerae chromosome, which requires an SXT-encoded integrase related to λ integrase, did not require IHF. Therefore, the defect in SXT transmission in the V. cholerae IHF mutant is probably not related to IHF's ability to promote DNA recombination. The V. cholerae IHF mutant was also highly impaired as a donor of RP4, a broad-host-range conjugative plasmid. Thus, the V. cholerae IHF mutant appears to have a general defect in conjugation. Escherichia coli IHF mutants were not impaired as donors or recipients of SXT or RP4, indicating that IHF is a V. cholerae-specific conjugation factor.

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Xu, Jinpeng, Haiyan Jia, Guanghui Cui, Huixian Tong, Jianchao Wei, Donghua Shao, Ke Liu, Yafeng Qiu, Beibei Li e Zhiyong Ma. "ICEAplChn1, a novel SXT/R391 integrative conjugative element (ICE), carrying multiple antibiotic resistance genes in Actinobacillus pleuropneumoniae". Veterinary Microbiology 220 (luglio 2018): 18–23. http://dx.doi.org/10.1016/j.vetmic.2018.05.002.

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Marenda, Marc, Valérie Barbe, Géraldine Gourgues, Sophie Mangenot, Evelyne Sagne e Christine Citti. "A New Integrative Conjugative Element Occurs in Mycoplasma agalactiae as Chromosomal and Free Circular Forms". Journal of Bacteriology 188, n. 11 (1 giugno 2006): 4137–41. http://dx.doi.org/10.1128/jb.00114-06.

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ABSTRACT An integrative conjugative element, ICEA, was characterized in Mycoplasma agalactiae strain 5632, in which it occurs as multiple chromosomal copies and as a free circular form. The distribution of ICEA sequences in M. agalactiae strains and their occurrence in Mycoplasma bovis suggest the spreading of the element within or between species.

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He, Dandan, Liangliang Wang, Shiyu Zhao, Lanping Liu, Jianhua Liu, Gongzheng Hu e Yushan Pan. "A novel tigecycline resistance gene, tet(X6), on an SXT/R391 integrative and conjugative element in a Proteus genomospecies 6 isolate of retail meat origin". Journal of Antimicrobial Chemotherapy 75, n. 5 (4 febbraio 2020): 1159–64. http://dx.doi.org/10.1093/jac/dkaa012.

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Abstract Objectives To characterize a novel tigecycline resistance gene, tet(X6), and a novel SXT-related integrative and conjugative element (ICE), ICEPgs6Chn1, found in a tigecycline-resistant Proteus genomospecies 6 strain, T60. Methods Strain T60 was identified by the VITEK 2 system, biochemical reactions and an SNP-based approach. The genetic profile of strain T60 was determined by WGS analysis. ICEPgs6Chn1 was analysed by PCR, conjugation experiments and bioinformatics tools. tet(X6) was characterized by cloning and protein structure prediction. Results Strain T60 was resistant to ampicillin, tetracycline, tigecycline, florfenicol, colistin and kanamycin, but susceptible to cefotaxime; it also exhibited high MICs of eravacycline (32 mg/L) and omadacycline (>64 mg/L). Only one chromosome was identified and tet(X6) was located in chromosomal ICEPgs6Chn1, a member of the SXT/R391 ICE family, of 114 368 bp and encoding the antimicrobial resistance genes floR, strB, strA, aph(3′)-Ia, aac(3)-IV, aph(4)-Ia, tet(X6) and sul2. The circular intermediate of ICEPgs6Chn1 was detected by PCR and sequencing, but conjugation experiments showed that it was not self-transmissible. Cloning of the novel gene tet(X6) and protein structure prediction revealed that Tet(X6) confers tigecycline resistance. Conclusions To our knowledge, this is the first report of a novel SXT/R391 ICE in a Proteus genomospecies 6 strain. Importantly, a novel high-level tigecycline resistance gene, tet(X6), emerged for the first time in the SXT/R391 element of Proteus genomospecies 6, revealing that ICEs may serve as an important platform for the accumulation of antibiotic resistance genes.

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Adabi, M., B. Bakhshi, H. Goudarzi e M. R. Pourshafie. "Integrating Conjugative Element (ICE) among Environmental and Clinical Isolates of Vibrio cholerae". International Journal of Infectious Diseases 12 (dicembre 2008): e119. http://dx.doi.org/10.1016/j.ijid.2008.05.297.

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Nonaka, Lisa, Michiaki Masuda e Hirokazu Yano. "Atypical integrative element with strand-biased circularization activity assists interspecies antimicrobial resistance gene transfer from Vibrio alfacsensis". PLOS ONE 17, n. 8 (2 agosto 2022): e0271627. http://dx.doi.org/10.1371/journal.pone.0271627.

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The exchange of antimicrobial resistance (AMR) genes between aquaculture and terrestrial microbial populations has emerged as a serious public health concern. However, the nature of the mobile genetic elements in marine bacteria is poorly documented. To gain insight into the genetic mechanisms underlying AMR gene transfer from marine bacteria, we mated a multidrug-resistant Vibrio alfacsensis strain with an Escherichia coli strain, and then determined the complete genome sequences of the donor and the transconjugant strains. Sequence analysis revealed a conjugative multidrug resistance plasmid in the donor strain, which was integrated into the chromosome of the recipient. The plasmid backbone in the transconjugant chromosome was flanked by two copies of a 7.1 kb unclassifiable integrative element harboring a β-lactamase gene. The 7.1 kb element and the previously reported element Tn6283 share four coding sequences, two of which encode the catalytic R-H-R-Y motif of tyrosine recombinases. Polymerase chain reaction and sequencing experiments revealed that these elements generate a circular copy of one specific strand without leaving an empty site on the donor molecule, in contrast to the movement of integron gene cassettes or ICE/IMEs discovered to date. These elements are termed SEs (strand-biased circularizing integrative elements): SE-6945 (the 7.1 kb element) and SE-6283 (Tn6283). The copy number and location of SE-6945 in the chromosome affected the antibiotic resistance levels of the transconjugants. SEs were identified in the genomes of other Vibrio species. Overall, these results suggest that SEs are involved in the spread of AMR genes among marine bacteria.

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Osorio, Carlos R., Joeli Marrero, Rachel A. F. Wozniak, Manuel L. Lemos, Vincent Burrus e Matthew K. Waldor. "Genomic and Functional Analysis of ICEPdaSpa1, a Fish-Pathogen-Derived SXT-Related Integrating Conjugative Element That Can Mobilize a Virulence Plasmid". Journal of Bacteriology 190, n. 9 (7 marzo 2008): 3353–61. http://dx.doi.org/10.1128/jb.00109-08.

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ABSTRACT Integrating conjugative elements (ICEs) are self-transmissible mobile elements that transfer between bacteria via conjugation and integrate into the host chromosome. SXT and related ICEs became prevalent in Asian Vibrio cholerae populations in the 1990s and play an important role in the dissemination of antibiotic resistance genes in V. cholerae. Here, we carried out genomic and functional analyses of ICEPdaSpa1, an SXT-related ICE derived from a Spanish isolate of Photobacterium damselae subsp. piscicida, the causative agent of fish pasteurellosis. The ∼102-kb DNA sequence of ICEPdaSpa1 shows nearly 97% DNA sequence identity to SXT in genes that encode essential ICE functions, including integration and excision, conjugal transfer, and regulation. However, ∼25 kb of ICEPdaSpa1 DNA, including a tetracycline resistance locus, is not present in SXT. Most ICEPdaSpa1-specific DNA is inserted at loci where other SXT-related ICEs harbor element-specific DNA. ICEPdaSpa1 excises itself from the chromosome and is transmissible to other Photobacterium strains, as well as to Escherichia coli, in which it integrates into prfC. Interestingly, the P. damselae virulence plasmid pPHDP10 could be mobilized from E. coli in an ICEPdaSpa1-dependent fashion via the formation of a cointegrate between pPHDP10 and ICEPdaSpa1. pPHDP10-Cm integrated into ICEPdaSpa1 in a non-site-specific fashion independently of RecA. The ICEPdaSpa1::pPHDP10 cointegrates were stable, and markers from both elements became transmissible at frequencies similar to those observed for the transfer of ICEPdaSpa1 alone. Our findings reveal the plasticity of ICE genomes and demonstrate that ICEs can enable virulence gene transfer.

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Kireeva, A. G., O. V. Kalinina, A. M. Kiselev, N. I. Briko, E. V. Glushkova e A. V. Dmitriev. "AN OCCURRENCE OF ICE-emm12 GENETIC ELEMENT CONTAINING tetM AND ermB RESISTANCE GENES AMONG RUSSIAN AND VIETNAMESE GROUP A STREPTOCOCCAL STRAINS". Journal of microbiology epidemiology immunobiology, n. 2 (28 aprile 2018): 23–30. http://dx.doi.org/10.36233/0372-9311-2018-2-23-30.

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Aim. Goal of the study is characterization and analysis of an occurrence of ICE-emm12 genetic element associated with streptococcal outbreaks, among Vietnamese and Russian GAS strains. Materials and methods. A total of 96 strains isolated in 2007 - 2014 in Moscow, Saint-Petersburg and different provinces of Vietnam were studied. Molecular genetic experiments were done as previously described. Whole genome sequencing was done using MiSeq technology. Results. Complete genome sequencing of Vietnamese strain V31 revealed the presence of 61028 bp fragment homologous to integrative and conjugative element ICE-emm12 containing resistance genes to MLS-antibiotics (ermB) and tetracycline (tetM). This element was discovered in 12 (26,1%, types emm12.0, emm12.22) out of 46 Vietnamese strains, and 2 (4,0%, types emm12.0, emm88.2) out of 50 Russian strains. In 13 out of 14 strains, ICE-emm12 was integrated in RNA-methyltransferase gene, which is possibly the «hot spot» for recombination. In all the strains ICE-emm12 was present in two forms: integrated linearized form and excised circular form with potential to be horizontally transferred. Conclusion. The presence of ICE-emm12 containing antibiotic resistance genes and associated with streptococcal outbreaks in South East Asia, among Russian GAS strains together with the fact of intensive tourism industry indicate the need of molecular epidemiological surveillance for circulation of epidemiologically actual streptococcal clones in Russia.

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Berbel, Dàmaris, Jordi Càmara, Aida González-Díaz, Meritxell Cubero, Guillem López de Egea, Sara Martí, Fe Tubau, M. Angeles Domínguez e Carmen Ardanuy. "Deciphering mobile genetic elements disseminating macrolide resistance in Streptococcus pyogenes over a 21 year period in Barcelona, Spain". Journal of Antimicrobial Chemotherapy 76, n. 8 (20 maggio 2021): 1991–2003. http://dx.doi.org/10.1093/jac/dkab130.

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Abstract Objectives To phenotypically and genetically characterize the antibiotic resistance determinants and associated mobile genetic elements (MGEs) among macrolide-resistant (MR) Streptococcus pyogenes [Group A streptococci (GAS)] clinical isolates collected in Barcelona, Spain. Methods Antibiotic susceptibility testing was performed by microdilution. Isolates were emm and MLST typed and 55 were whole-genome sequenced to determine the nature of the macrolide resistance (MR) determinants and their larger MGE and chromosomal context. Results Between 1998 and 2018, 142 of 1028 GAS (13.8%) were MR. Among 108 isolates available for molecular characterization, 41.7% had cMLSB, 30.5% iMLSB and 27.8% M phenotype. Eight erm(B)-containing strains were notable in having an MDR phenotype conferred by an MGE encoding several antibiotic resistance genes. MR isolates were comprised of several distinct genetic lineages as defined by the combination of emm and ST. Although most lineages were only transiently present, the emm11/ST403 clone persisted throughout the period. Two lineages, emm9/ST75 with erm(B) and emm77/ST63 with erm(TR), emerged in 2016–18. The erm(B) was predominantly encoded on the Tn916 family of transposons (21/31) with different genetic contexts, and in other MGEs (Tn6263, ICESpHKU372 and one harbouring an MDR cluster called ICESp1070HUB). The erm(TR) was found in ICESp2905 (8/17), ICESp1108-like (4/17), ICESpHKU165 (3/17) and two structures described in this study (IMESp316HUB and ICESp3729HUB). The M phenotype [mef(A)-msr(D)] was linked to phage φ1207.3. Eight integrative conjugative element/integrative mobilizable element (ICE/IME) cluster groups were classified on the basis of gene content within conjugation modules. These groups were found among MGEs, which corresponded with the MR-containing element or the site of integration. Conclusions We detected several different MGEs harbouring erm(B) or erm(TR). This is the first known description of Tn6263 in GAS and three MGEs [IMESp316HUB, ICESp3729HUB and ICESp1070HUB] associated with MR. Periods of high MR rates in our area were mainly associated with the expansion of certain predominant lineages, while in low MR periods different sporadic and low prevalence lineages were more frequent.

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Grim, Christopher J., Nur A. Hasan, Elisa Taviani, Bradd Haley, Jongsik Chun, Thomas S. Brettin, David C. Bruce et al. "Genome Sequence of Hybrid Vibrio cholerae O1 MJ-1236, B-33, and CIRS101 and Comparative Genomics with V. cholerae". Journal of Bacteriology 192, n. 13 (26 marzo 2010): 3524–33. http://dx.doi.org/10.1128/jb.00040-10.

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ABSTRACT The genomes of V ibrio cholerae O1 Matlab variant MJ-1236, Mozambique O1 El Tor variant B33, and altered O1 El Tor CIRS101 were sequenced. All three strains were found to belong to the phylocore group 1 clade of V. cholerae, which includes the 7th-pandemic O1 El Tor and serogroup O139 isolates, despite displaying certain characteristics of the classical biotype. All three strains were found to harbor a hybrid variant of CTXΦ and an integrative conjugative element (ICE), leading to their establishment as successful clinical clones and the displacement of prototypical O1 El Tor. The absence of strain- and group-specific genomic islands, some of which appear to be prophages and phage-like elements, seems to be the most likely factor in the recent establishment of dominance of V. cholerae CIRS101 over the other two hybrid strains.

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Schubert, Sören, Severin Dufke, Johanna Sorsa e Jürgen Heesemann. "A novel integrative and conjugative element (ICE) of Escherichia coli: the putative progenitor of the Yersinia high-pathogenicity island". Molecular Microbiology 51, n. 3 (15 dicembre 2003): 837–48. http://dx.doi.org/10.1046/j.1365-2958.2003.03870.x.

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Michael, G. B., K. Kadlec, M. T. Sweeney, E. Brzuszkiewicz, H. Liesegang, R. Daniel, R. W. Murray, J. L. Watts e S. Schwarz. "ICEPmu1, an integrative conjugative element (ICE) of Pasteurella multocida: analysis of the regions that comprise 12 antimicrobial resistance genes". Journal of Antimicrobial Chemotherapy 67, n. 1 (14 ottobre 2011): 84–90. http://dx.doi.org/10.1093/jac/dkr406.

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Abbott, Zachary D., Kaitlin J. Flynn, Brenda G. Byrne, Sampriti Mukherjee, Daniel B. Kearns e Michele S. Swanson. "csrTRepresents a New Class ofcsrA-Like Regulatory Genes Associated with Integrative Conjugative Elements of Legionella pneumophila". Journal of Bacteriology 198, n. 3 (23 novembre 2015): 553–64. http://dx.doi.org/10.1128/jb.00732-15.

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ABSTRACTBacterial evolution is accelerated by mobile genetic elements. To spread horizontally and to benefit the recipient bacteria, genes encoded on these elements must be properly regulated. Among the legionellae are multiple integrative conjugative elements (ICEs) that each encode a paralog of the broadly conserved regulatorcsrA. Using bioinformatic analyses, we deduced that specificcsrAparalogs are coinherited with particular lineages of the type IV secretion system that mediates horizontal spread of its ICE, suggesting a conserved regulatory interaction. As a first step to investigate the contribution ofcsrAregulators to this class of mobile genetic elements, we analyzed here the activity of thecsrAparalog encoded onLegionella pneumophilaICE-βox. Deletion of this gene, which we namecsrT, had no observed effect under laboratory conditions. However, ectopic expression ofcsrTabrogated the protection to hydrogen peroxide and macrophage degradation that ICE-βox confers toL. pneumophila. When ectopically expressed,csrTalso repressedL. pneumophilaflagellin production and motility, a function similar to the core genome's canonicalcsrA. Moreover,csrTrestored the repression of motility tocsrAmutants ofBacillus subtilis, a finding consistent with the predicted function of CsrT as an mRNA binding protein. Since all known ICEs of legionellae encode coinheritedcsrA-type IV secretion system pairs, we postulate that CsrA superfamily proteins regulate ICE activity to increase their horizontal spread, thereby expandingL. pneumophilaversatility.IMPORTANCEICEs are mobile DNA elements whose type IV secretion machineries mediate spread among bacterial populations. All surveyed ICEs within theLegionellagenus also carry paralogs of the essential life cycle regulatorcsrA. It is striking that thecsrAloci could be classified into distinct families based on either their sequence or the subtype of the adjacent type IV secretion system locus. To investigate whether ICE-encodedcsrAparalogs are bona fide regulators, we analyzed ICE-βox as a model system. When expressed ectopically, itscsrAparalog inhibited multiple ICE-βox phenotypes, as well as the motility of not onlyLegionellabut alsoBacillus subtilis. Accordingly, we predict that CsrA regulators equip legionellae ICEs to promote their spread via dedicated type IV secretion systems.

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Pradervand, N., F. Delavat, S. Sulser, R. Miyazaki e J. R. van der Meer. "The TetR-Type MfsR Protein of the Integrative and Conjugative Element (ICE) ICEclc Controls both a Putative Efflux System and Initiation of ICE Transfer". Journal of Bacteriology 196, n. 22 (2 settembre 2014): 3971–79. http://dx.doi.org/10.1128/jb.02129-14.

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Lin, Tzu-Lung, Cha-Ze Lee, Pei-Fang Hsieh, Shih-Feng Tsai e Jin-Town Wang. "Characterization of Integrative and Conjugative Element ICEKp1-Associated Genomic Heterogeneity in a Klebsiella pneumoniae Strain Isolated from a Primary Liver Abscess". Journal of Bacteriology 190, n. 2 (2 novembre 2007): 515–26. http://dx.doi.org/10.1128/jb.01219-07.

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ABSTRACT Genomic heterogeneity has been shown to be associated with Klebsiella pneumoniae strains causing pyogenic liver abscesses (PLA) and metastatic infections. In order to explore the mechanism responsible for genomic heterogeneity in K. pneumoniae, we compared the complete genomic sequences of strains NTUH-K2044 and MGH78578. An ∼76-kbp DNA fragment located adjacent to an asparagine (asn) tRNA gene was present in NTUH-K2044 but not in MGH78578. This fragment could be divided into three regions with different functions, and structurally it resembled a functional integrative and conjugative element (ICE), ICEEc1, in Escherichia coli. The 5′ region of this fragment contained genes similar to a high-pathogenicity island (HPI) of Yersinia pestis and Yersinia pseudotuberculosis. The middle region was similar to part of a large plasmid in K. pneumoniae, and the 3′ region contained genes responsible for DNA conjugative transfer. Therefore, this DNA fragment was designated ICEKp1. Precise excision and extrachromosomal circularization of ICEKp1 were detected in K. pneumoniae wild-type strain NTUH-K2044. ICEKp1 could integrate into the asn tRNA loci of the chromosome of another K. pneumoniae isolate. The prevalence of ICEKp1 was higher in PLA strains (38 of 42 strains) than in non-tissue-invasive strains (5 of 32 strains). Therefore, ICEKp1 may contribute to the transmission of the HPI and result in K. pneumoniae PLA infection-associated genomic heterogeneity.

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Lao, Julie, Gérard Guédon, Thomas Lacroix, Florence Charron-Bourgoin, Virginie Libante, Valentin Loux, Hélène Chiapello, Sophie Payot e Nathalie Leblond-Bourget. "Abundance, Diversity and Role of ICEs and IMEs in the Adaptation of Streptococcus salivarius to the Environment". Genes 11, n. 9 (26 agosto 2020): 999. http://dx.doi.org/10.3390/genes11090999.

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Streptococcus salivarius is a significant contributor to the human oral, pharyngeal and gut microbiomes that contribute to the maintenance of health. The high genomic diversity observed in this species is mainly caused by horizontal gene transfer. This work aimed to evaluate the contribution of integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs) in S. salivarius genome diversity. For this purpose, we performed an in-depth analysis of 75 genomes of S. salivarius and searched for signature genes of conjugative and mobilizable elements. This analysis led to the retrieval of 69 ICEs, 165 IMEs and many decayed elements showing their high prevalence in S. salivarius genomes. The identification of almost all ICE and IME boundaries allowed the identification of the genes in which these elements are inserted. Furthermore, the exhaustive analysis of the adaptation genes carried by these elements showed that they encode numerous functions such as resistance to stress, to antibiotics or to toxic compounds, and numerous enzymes involved in diverse cellular metabolic pathways. These data support the idea that not only ICEs but also IMEs and decayed elements play an important role in S. salivarius adaptation to the environment.

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Baranowski, Eric, Emilie Dordet-Frisoni, Eveline Sagné, Marie-Claude Hygonenq, Gabriela Pretre, Stéphane Claverol, Laura Fernandez, Laurent Xavier Nouvel e Christine Citti. "The Integrative Conjugative Element (ICE) ofMycoplasma agalactiae: Key Elements Involved in Horizontal Dissemination and Influence of Coresident ICEs". mBio 9, n. 4 (3 luglio 2018). http://dx.doi.org/10.1128/mbio.00873-18.

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ABSTRACTThe discovery of integrative conjugative elements (ICEs) in wall-less mycoplasmas and the demonstration of their role in massive gene flows within and across species have shed new light on the evolution of these minimal bacteria. Of these, the ICE of the ruminant pathogenMycoplasma agalactiae(ICEA) represents a prototype and belongs to a new clade of the Mutator-like superfamily that has no preferential insertion site and often occurs as multiple chromosomal copies. Here, functional genomics and mating experiments were combined to address ICEA functions and define the minimal ICEA chassis conferring conjugative properties toM. agalactiae. Data further indicated a complex interaction among coresident ICEAs, since the minimal ICEA structure was influenced by the occurrence of additional ICEA copies that cantrans-complement conjugation-deficient ICEAs. However, this cooperative behavior was limited to the CDS14 surface lipoprotein, which is constitutively expressed by coresident ICEAs, and did not extend to other ICEA proteins, including thecis-acting DDE recombinase and components of the mating channel whose expression was detected only sporadically. Remarkably, conjugation-deficient mutants containing a single ICEA copy knocked out incds14can be complemented by neighboring cells expressing CDS14. This result, together with those revealing the conservation of CDS14 functions in closely related species, may suggest a way for mycoplasma ICEs to extend their interaction outside their chromosomal environment. Overall, this report provides a first model of conjugative transfer in mycoplasmas and offers valuable insights into understanding horizontal gene transfer in this highly adaptive and diverse group of minimal bacteria.IMPORTANCEIntegrative conjugative elements (ICEs) are self-transmissible mobile genetic elements that are key mediators of horizontal gene flow in bacteria. Recently, a new category of ICEs was identified that confer conjugative properties to mycoplasmas, a highly adaptive and diverse group of wall-less bacteria with reduced genomes. Unlike classical ICEs, these mobile elements have no preferential insertion specificity, and multiple mycoplasma ICE copies can be found randomly integrated into the host chromosome. Here, the prototype ICE ofMycoplasma agalactiaewas used to define the minimal conjugative machinery and to propose the first model of ICE transfer in mycoplasmas. This model unveils the complex interactions taking place among coresident ICEs and suggests a way for these elements to extend their influence outside their chromosomal environment. These data pave the way for future studies aiming at deciphering chromosomal transfer, an unconventional mechanism of DNA swapping that has been recently associated with mycoplasma ICEs.

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Colombi, Elena, Benjamin J. Perry, John T. Sullivan, Amanuel A. Bekuma, Jason J. Terpolilli, Clive W. Ronson e Joshua P. Ramsay. "Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium". Microbial Genomics 7, n. 10 (4 ottobre 2021). http://dx.doi.org/10.1099/mgen.0.000657.

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Members of the Mesorhizobium genus are soil bacteria that often form nitrogen-fixing symbioses with legumes. Most characterised Mesorhizobium spp. genomes are ~8 Mb in size and harbour extensive pangenomes including large integrative and conjugative elements (ICEs) carrying genes required for symbiosis (ICESyms). Here, we document and compare the conjugative mobilome of 41 complete Mesorhizobium genomes. We delineated 56 ICEs and 24 integrative and mobilizable elements (IMEs) collectively occupying 16 distinct integration sites, along with 24 plasmids. We also demonstrated horizontal transfer of the largest (853,775 bp) documented ICE, the tripartite ICEMspSymAA22. The conjugation systems of all identified ICEs and several plasmids were related to those of the paradigm ICESym ICEMlSymR7A, with each carrying conserved genes for conjugative pilus formation (trb), excision (rdfS), DNA transfer (rlxS) and regulation (fseA). ICESyms have likely evolved from a common ancestor, despite occupying a variety of distinct integration sites and specifying symbiosis with diverse legumes. We found extensive evidence for recombination between ICEs and particularly ICESyms, which all uniquely lack the conjugation entry-exclusion factor gene trbK. Frequent duplication, replacement and pseudogenization of genes for quorum-sensing-mediated activation and antiactivation of ICE transfer suggests ICE transfer regulation is constantly evolving. Pangenome-wide association analysis of the ICE identified genes potentially involved in symbiosis, rhizosphere colonisation and/or adaptation to distinct legume hosts. In summary, the Mesorhizobium genus has accumulated a large and dynamic pangenome that evolves through ongoing horizontal gene transfer of large conjugative elements related to ICEMlSymR7A.

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