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Journal articles on the topic 'SXT/R391'

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Author: Grafiati

Published: 10 December 2022

Last updated: 28 January 2023

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1

Ceccarelli, Daniela, Aurélie Daccord, Mélissa René, and Vincent Burrus. "Identification of the Origin of Transfer (oriT) and a New Gene Required for Mobilization of the SXT/R391 Family of Integrating Conjugative Elements." Journal of Bacteriology 190, no. 15 (June 6, 2008): 5328–38. http://dx.doi.org/10.1128/jb.00150-08.

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ABSTRACT Integrating conjugative elements (ICEs) are self-transmissible, mobile elements that are widespread among bacteria. Following their excision from the chromosome, ICEs transfer by conjugation, a process initiated by a single-stranded DNA break at a specific locus called the origin of transfer (oriT). The SXT/R391 family of ICEs includes SXTMO10, R391, and more than 25 related ICEs found in gammaproteobacteria. A previous study mapped the oriT locus of SXTMO10 to a 550-bp intergenic region between traD and s043. We suspected that this was not the correct oriT locus, because the identical traD-s043 region in R391 and other SXT/R391 family ICEs was annotated as a gene of an unknown function. Here, we investigated the location and structure of the oriT locus in the ICEs of the SXT/R391 family and demonstrated that oriT SXT corresponds to a 299-bp sequence that contains multiple imperfect direct and inverted repeats and is located in the intergenic region between s003 and rumB′. The oriT SXT locus is well conserved among SXT/R391 ICEs, like R391, R997, and pMERPH, and cross-recognition of oriT SXT and oriT R391 by R391 and SXTMO10 was demonstrated. Furthermore, we identified a previously unannotated gene, mobI, located immediately downstream from oriT SXT, which proved to be essential for SXTMO10 transfer and SXTMO10-mediated chromosomal DNA mobilization. Deletion of mobI did not impair the SXTMO10-dependent transfer of the mobilizable plasmid CloDF13, suggesting that mobI has no role in the assembly of the SXTMO10 mating pair apparatus. Instead, mobI appears to be involved in the recognition of oriT SXT.

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2

Bioteau, Audrey, Romain Durand, and Vincent Burrus. "Redefinition and Unification of the SXT/R391 Family of Integrative and Conjugative Elements." Applied and Environmental Microbiology 84, no. 13 (April 13, 2018): e00485-18. http://dx.doi.org/10.1128/aem.00485-18.

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ABSTRACT Integrative and conjugative elements (ICEs) of the SXT/R391 family are key drivers of the spread of antibiotic resistance in Vibrio cholerae, the infectious agent of cholera, and other pathogenic bacteria. The SXT/R391 family of ICEs was defined based on the conservation of a core set of 52 genes and site-specific integration into the 5′ end of the chromosomal gene prfC. Hence, the integrase gene int has been intensively used as a marker to detect SXT/R391 ICEs in clinical isolates. ICEs sharing most core genes but differing by their integration site and integrase gene have been recently reported and excluded from the SXT/R391 family. Here we explored the prevalence and diversity of atypical ICEs in GenBank databases and their relationship with typical SXT/R391 ICEs. We found atypical ICEs in V. cholerae isolates that predate the emergence and expansion of typical SXT/R391 ICEs in the mid-1980s in seventh-pandemic toxigenic V. cholerae strains O1 and O139. Our analyses revealed that while atypical ICEs are not associated with antibiotic resistance genes, they often carry cation efflux pumps, suggesting heavy metal resistance. Atypical ICEs constitute a polyphyletic group likely because of occasional recombination events with typical ICEs. Furthermore, we show that the alternative integration and excision genes of atypical ICEs remain under the control of SetCD, the main activator of the conjugative functions of SXT/R391 ICEs. Together, these observations indicate that substitution of the integration/excision module and change of specificity of integration do not preclude atypical ICEs from inclusion into the SXT/R391 family. IMPORTANCE Vibrio cholerae is the causative agent of cholera, an acute intestinal infection that remains to this day a world public health threat. Integrative and conjugative elements (ICEs) of the SXT/R391 family have played a major role in spreading antimicrobial resistance in seventh-pandemic V. cholerae but also in several species of Enterobacteriaceae. Most epidemiological surveys use the integrase gene as a marker to screen for SXT/R391 ICEs in clinical or environmental strains. With the recent reports of closely related elements that carry an alternative integrase gene, it became urgent to investigate whether ICEs that have been left out of the family are a liability for the accuracy of such screenings. In this study, based on comparative genomics, we broaden the SXT/R391 family of ICEs to include atypical ICEs that are often associated with heavy metal resistance.

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3

Hochhut, Bianca, John W. Beaber, Roger Woodgate, and Matthew K. Waldor. "Formation of Chromosomal Tandem Arrays of the SXT Element and R391, Two Conjugative Chromosomally Integrating Elements That Share an Attachment Site." Journal of Bacteriology 183, no. 4 (February 15, 2001): 1124–32. http://dx.doi.org/10.1128/jb.183.4.1124-1132.2001.

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ABSTRACT The SXT element, a conjugative, self-transmissible, integrating element (a constin) originally derived from a Vibrio cholerae O139 isolate from India, and IncJ element R391, originally derived from a South African Providencia rettgeri isolate, were found to be genetically and functionally related. Both of these constins integrate site specifically into the Escherichia coli chromosome at an identical attachment site within the 5′ end of prfC. They encode nearly identical integrases, which are required for chromosomal integration, excision, and extrachromosomal circularization of these elements, and they have similar tra genes. Therefore, these closely related constins have virtually identical mechanisms for chromosomal integration and dissemination. The presence of either element in a recipient cell did not significantly reduce its ability to acquire the other element, indicating that R391 and SXT do not encode surface exclusion determinants. In cells harboring both elements, SXT and R391 were integrated in tandem fashion on the chromosome, and homologous recombination appeared to play little or no role in the formation of these arrays. Interference between R391 and SXT was detected by measuring the frequency of loss of an unselected resident element upon introduction of a second selected element. In these assays, R391 was found to have a stronger effect on SXT stability than vice versa. The level of expression and/or activity of the donor and recipient integrases may play a role in the interference between these two related constins.

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4

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, and 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, no. 6 (March 10, 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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5

Burrus, Vincent, and Matthew K. Waldor. "Formation of SXT Tandem Arrays and SXT-R391 Hybrids." Journal of Bacteriology 186, no. 9 (May 1, 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.

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6

Poulin-Laprade, Dominic, and Vincent Burrus. "A λ Cro-Like Repressor Is Essential for the Induction of Conjugative Transfer of SXT/R391 Elements in Response to DNA Damage." Journal of Bacteriology 197, no. 24 (October 5, 2015): 3822–33. http://dx.doi.org/10.1128/jb.00638-15.

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ABSTRACTIntegrative and conjugative elements (ICEs) of the SXT/R391 family are the main contributors to acquired multidrug resistance in the seventh pandemic lineage ofVibrio cholerae, the etiological agent of the diarrheal disease cholera. Conjugative transfer of SXT/R391 ICEs is triggered by antibiotics and agents promoting DNA damage through RecA-dependent autoproteolysis of SetR, an ICE-encoded λ CI-like repressor. Here, we describe the role of CroS, a distant λ Cro homolog, as a key component contributing to the regulation of expression of the activator SetCD that orchestrates the expression of the conjugative transfer genes. We show that deletion ofcroSabolishes the SOS response-dependent induction of SXT despite the presence of a functionalsetRgene. Using quantitative reverse transcription-PCR andlacZreporter assays, we also show that CroS repressessetRandsetCDexpression by binding to operator sites shared with SetR. Furthermore, we provide evidence of an additional operator site bound by SetR and CroS. Finally, we show that SetCD expression generates a positive feedback loop due to SXT excision and replication in a fraction of the cell population. Together, these results refine our understanding of the genetic regulation governing the propagation of major vectors of multidrug resistance.IMPORTANCEHealthcare systems worldwide are challenged by an alarming drug resistance crisis caused by the massive and rapid propagation of antibiotic resistance genes and the associated emergence of multidrug-resistant pathogenic bacteria. SXT/R391 ICEs contribute to this phenomenon not only in clinical and environmental vibrios but also in several members of the familyEnterobacteriaceae. We have identified and characterized here the regulator CroS as a key factor in the stimulation of conjugative transfer of these ICEs in response to DNA-damaging agents. We have also untangled conflicting evidence regarding autoactivation of transfer by the master activator of SXT/R391 ICEs, SetCD. Discovery of CroS provides a clearer and more complete understanding of the regulatory network that governs the dissemination of SXT/R391 ICEs in bacterial populations.

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7

Harada, Sohei, Yoshikazu Ishii, Tomoo Saga, Kazuhiro Tateda, and Keizo Yamaguchi. "Chromosomally Encoded blaCMY-2 Located on a Novel SXT/R391-Related Integrating Conjugative Element in a Proteus mirabilis Clinical Isolate." Antimicrobial Agents and Chemotherapy 54, no. 9 (June 21, 2010): 3545–50. http://dx.doi.org/10.1128/aac.00111-10.

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ABSTRACT Integrating conjugative elements (ICEs) are mobile genetic elements that can transfer from the chromosome of a host to the chromosome of a new host through the process of excision, conjugation, and integration. Although SXT/R391-related ICEs, originally demonstrated in Vibrio cholerae O139 isolates, have become prevalent among V. cholerae isolates in Asia, the prevalence of the ICEs among Gram-negative bacteria other than Vibrio spp. remains unknown. In addition, SXT/R391-related ICEs carrying genes conferring resistance to extended-spectrum cephalosporins have never been described. Here we carried out a genetic analysis of a cefoxitin-resistant Proteus mirabilis clinical isolate, TUM4660, which revealed the presence of a novel SXT/R391-related ICE, ICEPmiJpn1. ICEPmiJpn1 had a core genetic structure showing high similarity to that of R391 and carried xis and int genes completely identical to those of R391, while an IS10-mediated composite transposon carrying bla CMY-2 was integrated into the ICE. A nucleotide sequence identical to the 3′ part of ISEcp1 was located upstream of the bla CMY-2 gene, and other genes observed around bla CMY-2 in earlier studies were also present. Furthermore, the nucleotide sequences of hot spot 2 and hot spot 4 in ICEPmiJpn1 showed high similarity to that of hot spot 2 in SXTMO10 and with a part of the nucleotide sequence found in P. mirabilis ATCC 29906, respectively. ICEPmiJpn1 was successfully transferred to Escherichia coli, Klebsiella pneumoniae, Salmonella enterica serovar Typhimurium, and Citrobacter koseri in conjugation experiments. These observations suggest that ICEs may contribute to the dissemination of antimicrobial resistance genes among clinically relevant Enterobacteriaceae, which warrants careful observation of the prevalence of ICEs, including SXT/R391-related ICEs.

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8

Lei, Chang-Wei, An-Yun Zhang, Hong-Ning Wang, Bi-Hui Liu, Li-Qin Yang, and 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, no. 3 (January 11, 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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9

Marrero, Joeli, and Matthew K. Waldor. "Determinants of Entry Exclusion within Eex and TraG Are Cytoplasmic." Journal of Bacteriology 189, no. 17 (June 15, 2007): 6469–73. http://dx.doi.org/10.1128/jb.00522-07.

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ABSTRACT We report here functional and topological analyses of TraG and Eex, the donor and recipient cell inner membrane proteins that mediate entry exclusion in the SXT/R391 family of integrative conjugative elements. We found that the exclusion-determining regions of the Eex variants EexS (SXT) and EexR (R391) are located in distinct yet overlapping regions of the proteins. Unexpectedly, the carboxyl-terminal regions of TraG and Eex, which contain the residues essential for exclusion activity and specificity, were found to localize in the cell cytoplasm. These observations suggest that complex topological rearrangements of conjugative proteins must occur during mating to enable these domains to interact.

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10

He, Dandan, Liangliang Wang, Shiyu Zhao, Lanping Liu, Jianhua Liu, Gongzheng Hu, and 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, no. 5 (February 4, 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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Zakharova, I. B., S. Yu Vodyanitskaya, M. V. Podshivalova, V. D. Kruglikov, I. V. Arkhangelskaya, and D. V. Viktorov. "Molecular genetic characterization of Vibrio cholerae non-01/non-0139 strains isolated from ship ballast and port surface water in rostov region." Epidemiology and Infectious Diseases 20, no. 3 (June 15, 2015): 47–50. http://dx.doi.org/10.17816/eid40889.

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In the given paper there are presented the results of analysis for presence in genomes of Vibrio cholerae non-O1/non-O139 strains isolated from ships' ballast water and the coastal zone of Taganrog Gulf class 1 integrons (In1) and SXT/R391 integrative conjugative elements. The intact sequence of In13'-conservative segment (qacEdelta1-sul) was detected in 3 strains (no. 33, 59, 182), whereas in strains V. cholerae no. 28 and 52 there were revealed the probable changes of target sequence (duplication and deletion, respectively). The fragment of SXT/R391 integrase IntSXT gene was detected in 7 of 10 strains tested. Group of strains no. 27, 36, 38, 117 and 59, 182 belong to 2 most common identified genotypes, while the rest isolates are characterized by unique genotypes that indicates to different source of their origins.

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Böltner, Dietmar, Claire MacMahon, J. Tony Pembroke, Peter Strike, and A. Mark Osborn. "R391: a Conjugative Integrating Mosaic Comprised of Phage, Plasmid, and Transposon Elements." Journal of Bacteriology 184, no. 18 (September 15, 2002): 5158–69. http://dx.doi.org/10.1128/jb.184.18.5158-5169.2002.

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ABSTRACT The conjugative, chromosomally integrating element R391 is the archetype of the IncJ class of mobile genetic elements. Originally found in a South African Providencia rettgeri strain, R391 carries antibiotic and mercury resistance traits, as well as genes involved in mutagenic DNA repair. While initially described as a plasmid, R391 has subsequently been shown to be integrated into the bacterial chromosome, employing a phage-like integration mechanism closely related to that of the SXT element from Vibrio cholerae O139. Analysis of the complete 89-kb nucleotide sequence of R391 has revealed a mosaic structure consisting of elements originating in bacteriophages and plasmids and of transposable elements. A total of 96 open reading frames were identified; of these, 30 could not be assigned a function. Sequence similarity suggests a relationship of large sections of R391 to sequences from Salmonella, in particular those corresponding to the putative conjugative transfer proteins, which are related to the IncHI1 plasmid R27. A composite transposon carrying the kanamycin resistance gene and a novel insertion element were identified. Challenging the previous assumption that IncJ elements are plasmids, no plasmid replicon was identified on R391, suggesting that they cannot replicate autonomously.

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Sugimoto, Yuta, Fumito Maruyama, and Satoru Suzuki. "Draft Genome Sequence of a Shewanella halifaxensis Strain Isolated from the Intestine of Marine Red Seabream (Pagrus major), Which Includes an Integrative Conjugative Element with Macrolide Resistance Genes." Genome Announcements 6, no. 16 (April 19, 2018): e00297-18. http://dx.doi.org/10.1128/genomea.00297-18.

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ABSTRACT Shewanella halifaxensis strain 6JANF4-E-4 was isolated from the intestine of a red seabream (Pagrus major). Here, we report the draft genome sequence of this bacterium, which includes an integrative conjugative element of the SXT/R391 family, where the macrolide resistance determinants mef(C) and mph(G) exist.

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Rodríguez-Blanco, Arturo, Manuel L. Lemos, and Carlos R. Osorio. "Integrating Conjugative Elements as Vectors of Antibiotic, Mercury, and Quaternary Ammonium Compound Resistance in Marine Aquaculture Environments." Antimicrobial Agents and Chemotherapy 56, no. 5 (February 6, 2012): 2619–26. http://dx.doi.org/10.1128/aac.05997-11.

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ABSTRACTThe presence of SXT/R391-related integrating conjugative elements (ICEs) in bacterial strains isolated from fish obtained from marine aquaculture environments in 2001 to 2010 in the northwestern Iberian Peninsula was studied. ICEs were detected in 12 strains taxonomically related toVibrio scophthalmi(3 strains),Vibrio splendidus(5 strains),Vibrio alginolyticus(1 strain),Shewanella haliotis(1 strain), andEnterovibrio nigricans(2 strains), broadening the known host range able to harbor SXT/R391-like ICEs. Variable DNA regions, which confer element-specific properties to ICEs of this family, were characterized. One of the ICEs encoded antibiotic resistance functions in variable region III, consisting of a tetracycline resistance locus. Interestingly, hot spot 4 included genes providing resistance to rifampin (ICEVspPor2 and ICEValPor1) and quaternary ammonium compounds (QACs) (ICEEniSpa1), and variable region IV included a mercury resistance operon (ICEVspSpa1 and ICEEniSpa1). The S exclusion group was more represented than the R exclusion group, accounting for two-thirds of the total ICEs. Mating experiments allowed ICE mobilization toEscherichia colistrains, showing the corresponding transconjugants' rifampin, mercury, and QAC resistance. These results show the first evidence of ICEs providing rifampin and QAC resistances, suggesting that these mobile genetic elements contribute to the dissemination of antimicrobial, heavy metal, and QAC resistance determinants in aquaculture environments.

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Roman, Véronica L., Christophe Merlin, Marko P. J. Virta, and Xavier Bellanger. "EpicPCR 2.0: Technical and Methodological Improvement of a Cutting-Edge Single-Cell Genomic Approach." Microorganisms 9, no. 8 (August 2, 2021): 1649. http://dx.doi.org/10.3390/microorganisms9081649.

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EpicPCR (Emulsion, Paired Isolation and Concatenation PCR) is a recent single-cell genomic method based on a fusion-PCR allowing us to link a functional sequence of interest to a 16S rRNA gene fragment and use the mass sequencing of the resulting amplicons for taxonomic assignment of the functional sequence-carrying bacteria. Although it is interesting because it presents the highest efficiency for assigning a bacterial host to a marker, epicPCR remains a complex multistage procedure with technical difficulties that may easily impair the approach depth and quality. Here, we described how to adapt epicPCR to new gene targets and environmental matrices while identifying the natural host range of SXT/R391 integrative and conjugative elements in water microbial communities from the Meurthe River (France). We notably show that adding a supplementary PCR step allowed us to increase the amplicon yield and thus the number of reads obtained after sequencing. A comparison of operational taxonomic unit (OTU) identification approaches when using biological and technical replicates demonstrated that, although OTUs can be validated when obtained from three out of three technical replicates, up to now, results obtained from two or three biological replicates give a similar and even a better confidence level in OTU identification, while allowing us to detect poorly represented SXT/R391 hosts in microbial communities.

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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, no. 2 (December 7, 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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Marrero, Joeli, and Matthew K. Waldor. "The SXT/R391 Family of Integrative Conjugative Elements Is Composed of Two Exclusion Groups." Journal of Bacteriology 189, no. 8 (February 16, 2007): 3302–5. http://dx.doi.org/10.1128/jb.01902-06.

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ABSTRACT Conjugative elements often encode entry exclusion systems that convert host cells into poor recipients for identical or similar elements. The diversity of exclusion systems within families of conjugative elements has received little attention. We report here the most comprehensive study to date of the diversity of exclusion determinants within a single family of conjugative elements. Unexpectedly, our analyses indicate that there are only two exclusion groups among the diverse members of the SXT/R391 family of integrative conjugative elements.

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Ryan, Michael P., Shannon Slattery, and J. Tony Pembroke. "A Novel Arsenate-Resistant Determinant Associated with ICEpMERPH, a Member of the SXT/R391 Group of Mobile Genetic Elements." Genes 10, no. 12 (December 16, 2019): 1048. http://dx.doi.org/10.3390/genes10121048.

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ICEpMERPH, the first integrative conjugative element (ICE) of the SXT/R391 family isolated in the United Kingdom and Europe, was analyzed to determine the nature of its adaptive functions, its genetic structure, and its homology to related elements normally found in pathogenic Vibrio or Proteus species. Whole genome sequencing of Escherichia coli (E. coli) isolate K802 (which contains the ICEpMERPH) was carried out using Illumina sequencing technology. ICEpMERPH has a size of 110 Kb and 112 putative open reading frames (ORFs). The “hotspot regions” of the element were found to contain putative restriction digestion systems, insertion sequences, and heavy metal resistance genes that encoded resistance to mercury, as previously reported, but also surprisingly to arsenate. A novel arsenate resistance system was identified in hotspot 4 of the element, unrelated to other SXT/R391 elements. This arsenate resistance system was potentially linked to two genes: orf69, encoding an organoarsenical efflux major facilitator superfamily (MFS) transporter-like protein related to ArsJ, and orf70, encoding nicotinamide adenine dinucleotide (NAD)-dependent glyceraldehyde-3-phosphate dehydrogenase. Phenotypic analysis using isogenic strains of Escherichia coli strain AB1157 with and without the ICEpMERPH revealed resistance to low levels of arsenate in the range of 1–5 mM. This novel, low-level resistance may have an important adaptive function in polluted environments, which often contain low levels of arsenate contamination. A bioinformatic analysis on the novel determinant and the phylogeny of ICEpMERPH was presented.

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Zakharova, Irina B., Yu A. Kuzyutina, M. V. Podshivalova, A. A. Zamarin, A. V. Toporkov, and D. V. Viktorov. "Detection and analysis of integrative conjugative elements in Vibrio spp. strains, isolated in the Volgograd region." Epidemiology and Infectious Diseases 21, no. 6 (December 15, 2016): 347–51. http://dx.doi.org/10.17816/eid40944.

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The presence of integrative conjugative elements (ICEs) of SXT/R391 family in different Vibrio species isolated from natural water sources in the Volgograd region in 2003 - 2014 was established. Trimethoprim (dfr18), streptomycin (strB) and sulfametoxazol (sulII) resistance genes were detected in ICEs pattern of in V. choleraenon-O1/non-O139 strains. In Vibrio spp. ICEs strains not referred to V. cholerae type there was detected another variant of dihydrofolate reductase gene - dfrA1 localized outside the main resistance cluster. The obtained results indicate to that aqueous Vibrio spp. strains may be potential reservoir of resistance genes.

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Rodríguez-Blanco, Arturo, Manuel L. Lemos, and Carlos R. Osorio. "Unveiling the pan-genome of the SXT/R391 family of ICEs: molecular characterisation of new variable regions of SXT/R391-like ICEs detected in Pseudoalteromonas sp. and Vibrio scophthalmi." Antonie van Leeuwenhoek 109, no. 8 (May 26, 2016): 1141–52. http://dx.doi.org/10.1007/s10482-016-0716-3.

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Poulin-Laprade, Dominic, Dominick Matteau, Pierre-Étienne Jacques, Sébastien Rodrigue, and Vincent Burrus. "Transfer activation of SXT/R391 integrative and conjugative elements: unraveling the SetCD regulon." Nucleic Acids Research 43, no. 4 (February 6, 2015): 2045–56. http://dx.doi.org/10.1093/nar/gkv071.

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Böltner, Dietmar, and A. Mark Osborn. "Structural comparison of the integrative and conjugative elements R391, pMERPH, R997, and SXT." Plasmid 51, no. 1 (January 2004): 12–23. http://dx.doi.org/10.1016/j.plasmid.2003.10.003.

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Roman, Veronica L., Christophe Merlin, Sandrine Baron, Emeline Larvor, Laetitia Le Devendec, Marko P. J. Virta, and Xavier Bellanger. "Abundance and environmental host range of the SXT/R391 ICEs in aquatic environmental communities." Environmental Pollution 288 (November 2021): 117673. http://dx.doi.org/10.1016/j.envpol.2021.117673.

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Wozniak, Rachel A. F., Derrick E. Fouts, Matteo Spagnoletti, Mauro M. Colombo, Daniela Ceccarelli, Geneviève Garriss, Christine Déry, Vincent Burrus, and Matthew K. Waldor. "Comparative ICE Genomics: Insights into the Evolution of the SXT/R391 Family of ICEs." PLoS Genetics 5, no. 12 (December 24, 2009): e1000786. http://dx.doi.org/10.1371/journal.pgen.1000786.

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Rybal’chenko, D. A., E. Yu Shchelkanova, Yu V. Lozovsky, A. V. Fedorov, and N. I. Smirnova. "Prevalence of Different Types of Integrative Conjugative Element SXT/R391 Encoding Multiple Antibiotic Resistance Among Clinical Strains of Cholera Agent." Problems of Particularly Dangerous Infections, no. 1 (April 20, 2022): 137–47. http://dx.doi.org/10.21055/0370-1069-2022-1-137-147.

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The aim of the work was to study the prevalence of different types of SXT element with different composition of antibiotic resistance genes among clinical strains of the El Tor cholera pathogen isolated in Russia, Ukraine and cholera-endemic countries in Asia and Africa.Materials and methods. The subject of the study was 27 strains and nucleotide sequences of 77 strains of Vibrio cholerae El Tor available from the NCBI GenBank. The structure of the SXT element and its type were determined using the Mauve and BLAST v.2.9.0 programs. Phylogenetic relations of strains with different types of SXT were identified using Snippy v.4.6.0 and MrBayes v.3.2.7 software. Assessment of strain sensitivity to antibiotics was carried out in accordance with Methodological Regulations 4.2.2495-09.Results and discussion. Two types of SXT element (ICEVchInd5 and ICEVchBan9) have been identified among the studied strains from Russia and Ukraine, which have different composition of antibiotic resistance genes: floR, strAB, sul2, dfrA1 and floR, tetAR, strAB, sul2, dfrA1, respectively. At the same time, the studied strains from Asia and Africa contain five types of SXT: ICEVchInd5, ICEVchBan9, ICEVchBan5, SXTTET, ICEVchInd5ΔVRIII, which differ in size and/or composition of resistance genes. Of these, the last three have not been found in Russia and Ukraine. Due to the high level of genomic diversity of SXT in the population of V. cholerae in endemic regions, there is a risk of importation of cholera pathogen strains with altered resistance to antibiotics into Russia. Phylogenetic relations of 76 strains with different SXT types and different alleles of the ctxB gene encoding the B subunit of cholera toxin have been assessed based on SNP analysis. A close phylogenetic relation between strains with the same type of SXT isolated in Russia and Asian countries has been demonstrated, which confirms the importation of the causative agent of cholera with multiple resistance to antibiotics from this region and the need for constant monitoring of the sensitivity of V. cholerae to antimicrobial drugs.

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Mata, Caterina, Ferran Navarro, Elisenda Miró, Timothy R. Walsh, Beatriz Mirelis, and Mark Toleman. "Prevalence of SXT/R391-like integrative and conjugative elements carrying blaCMY-2 in Proteus mirabilis." Journal of Antimicrobial Chemotherapy 66, no. 10 (July 13, 2011): 2266–70. http://dx.doi.org/10.1093/jac/dkr286.

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Roy, David, Kevin T. Huguet, Frédéric Grenier, and Vincent Burrus. "IncC conjugative plasmids and SXT/R391 elements repair double-strand breaks caused by CRISPR–Cas during conjugation." Nucleic Acids Research 48, no. 16 (June 18, 2020): 8815–27. http://dx.doi.org/10.1093/nar/gkaa518.

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Abstract Bacteria have evolved defence mechanisms against bacteriophages. Restriction-modification systems provide innate immunity by degrading invading DNAs that lack proper methylation. CRISPR–Cas systems provide adaptive immunity by sampling the genome of past invaders and cutting the DNA of closely related DNA molecules. These barriers also restrict horizontal gene transfer mediated by conjugative plasmids. IncC conjugative plasmids are important contributors to the global dissemination of multidrug resistance among pathogenic bacteria infecting animals and humans. Here, we show that IncC conjugative plasmids are highly resilient to host defence systems during entry into a new host by conjugation. Using a TnSeq strategy, we uncover a conserved operon containing five genes (vcrx089–vcrx093) that confer a novel host defence evasion (hde) phenotype. We show that vcrx089–vcrx090 promote resistance against type I restriction-modification, whereas vcrx091–vcxr093 promote CRISPR–Cas evasion by repairing double-strand DNA breaks via recombination between short sequence repeats. vcrx091, vcrx092 and vcrx093 encode a single-strand binding protein, and a single-strand annealing recombinase and double-strand exonuclease related to Redβ and λExo of bacteriophage λ, respectively. Homologous genes of the integrative and conjugative element R391 also provide CRISPR–Cas evasion. Hence, the conserved hde operon considerably broadens the host range of large families of mobile elements spreading multidrug resistance.

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

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Pembroke, J. Tony, and Anna V. Piterina. "A novel ICE in the genome ofShewanella putrefaciensW3-18-1: comparison with the SXT/R391 ICE-like elements." FEMS Microbiology Letters 264, no. 1 (November 2006): 80–88. http://dx.doi.org/10.1111/j.1574-6968.2006.00452.x.

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Garriss, G., D. Poulin-Laprade, and V. Burrus. "DNA-Damaging Agents Induce the RecA-Independent Homologous Recombination Functions of Integrating Conjugative Elements of the SXT/R391 Family." Journal of Bacteriology 195, no. 9 (February 22, 2013): 1991–2003. http://dx.doi.org/10.1128/jb.02090-12.

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Balado, Miguel, Manuel L. Lemos, and Carlos R. Osorio. "Integrating conjugative elements of the SXT/R391 family from fish-isolatedVibriosencode restriction-modification systems that confer resistance to bacteriophages." FEMS Microbiology Ecology 83, no. 2 (October 10, 2012): 457–67. http://dx.doi.org/10.1111/1574-6941.12007.

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Sato, Juliana Lumi, Douglas Lyra de Holanda Fonseca, and Rodrigo S. Galhardo. "rumAB genes from SXT/R391 ICEs confer UV-induced mutability to Proteus mirabilis hosts and improve conjugation after UV irradiation." DNA Repair 112 (April 2022): 103297. http://dx.doi.org/10.1016/j.dnarep.2022.103297.

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Beaber, J. W., V. Burrus, B. Hochhut, and M. K. Waldor. "Comparison of SXT and R391, two conjugative integrating elements: definition of a genetic backbone for the mobilization of resistance determinants." Cellular and Molecular Life Sciences (CMLS) 59, no. 12 (December 1, 2002): 2065–70. http://dx.doi.org/10.1007/s000180200006.

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Bie, Luyao, Hao Wu, Xin-Hua Wang, Mingyu Wang, and Hai Xu. "Identification and characterization of new members of the SXT/R391 family of integrative and conjugative elements (ICEs) in Proteus mirabilis." International Journal of Antimicrobial Agents 50, no. 2 (August 2017): 242–46. http://dx.doi.org/10.1016/j.ijantimicag.2017.01.045.

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Kiiru, John N., Suleiman M. Saidi, Bruno M. Goddeeris, Njeri C. Wamae, Patrick Butaye, and Samuel M. Kariuki. "Molecular characterisation of Vibrio cholerae O1 strains carrying an SXT/R391-like element from cholera outbreaks in Kenya: 1994-2007." BMC Microbiology 9, no. 1 (2009): 275. http://dx.doi.org/10.1186/1471-2180-9-275.

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Daccord, A., M. Mursell, D. Poulin-Laprade, and V. Burrus. "Dynamics of the SetCD-Regulated Integration and Excision of Genomic Islands Mobilized by Integrating Conjugative Elements of the SXT/R391 Family." Journal of Bacteriology 194, no. 21 (August 24, 2012): 5794–802. http://dx.doi.org/10.1128/jb.01093-12.

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37

HU, QIONGXIA, and LANMING CHEN. "Virulence and Antibiotic and Heavy Metal Resistance of Vibrio parahaemolyticus Isolated from Crustaceans and Shellfish in Shanghai, China." Journal of Food Protection 79, no. 8 (August 1, 2016): 1371–77. http://dx.doi.org/10.4315/0362-028x.jfp-16-031.

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ABSTRACT Vibrio parahaemolyticus can cause serious human seafoodborne gastroenteritis and even death. In this study, we isolated and characterized 208 V. parahaemolyticus strains from 10 species of commonly consumed crustaceans and shellfish available in fish markets in Shanghai, People's Republic of China, in 2014. Most of these aquatic species had not been detected previously. The results revealed an extremely low occurrence of pathogenic V. parahaemolyticus carrying the toxin gene trh (1.9%). However, a high level of resistance to the antibiotics ampicillin (94.2%), rifampin (93.3%), and streptomycin (77.9%) was found. Approximately 74.5% of the isolates had multidrug-resistant phenotypes. Tolerance to the heavy metals Cu2+, Pb2+, and Cd2+ was detected in the majority of antibiotic resistant isolates. The resistance patterns differed depending on the tested samples. The crustaceans Penaeus monodon and Marsupenaeus japonicus harbored more antibiotic-resistant bacteria, whereas the isolates from the crustacean Litopenaeus vannamei and the shellfish Busycon canaliculatus had high tolerance to eight heavy metals tested. In contrast to the wide distribution of multidrug resistance and tolerance to heavy metals, lower percentages of plasmid DNA (22.6%) and SXT/R391-like integrative and conjugative elements (4.8%) were detected in the isolates, suggesting that V. parahaemolyticus in these aquatic species may have adopted some other molecular mechanisms that mediated the high prevalence of resistance determinants. The results of this study support the need for food safety risk assessment of aquatic products.

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Daccord, Aurélie, Daniela Ceccarelli, and Vincent Burrus. "Integrating conjugative elements of the SXT/R391 family trigger the excision and drive the mobilization of a new class of Vibrio genomic islands." Molecular Microbiology 78, no. 3 (September 28, 2010): 576–88. http://dx.doi.org/10.1111/j.1365-2958.2010.07364.x.

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He, Juan, Changwei Lei, Cui Li, Xuechun Wang, Pengfei Cui, and Hongning Wang. "Identification of a novel genomic resistance island PmGRI1-STP3 and an SXT/R391 integrative conjugative element in Proteus mirabilis of swine origin in China." Journal of Global Antimicrobial Resistance 25 (June 2021): 77–81. http://dx.doi.org/10.1016/j.jgar.2021.02.018.

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40

Bordeleau, Eric, Eric Brouillette, Nathaniel Robichaud, and Vincent Burrus. "Beyond antibiotic resistance: integrating conjugative elements of the SXT/R391 family that encode novel diguanylate cyclases participate to c-di-GMP signalling inVibrio cholerae." Environmental Microbiology 12, no. 2 (February 2010): 510–23. http://dx.doi.org/10.1111/j.1462-2920.2009.02094.x.

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41

Carraro, Nicolas, Dominique Poulin, and Vincent Burrus. "Replication and Active Partition of Integrative and Conjugative Elements (ICEs) of the SXT/R391 Family: The Line between ICEs and Conjugative Plasmids Is Getting Thinner." PLOS Genetics 11, no. 6 (June 10, 2015): e1005298. http://dx.doi.org/10.1371/journal.pgen.1005298.

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Lei, Chang-Wei, Tian-Ge Yao, Jia Yan, Bo-Yang Li, Xue-Chun Wang, Yu Zhang, Yu-Feng Gao, and Hong-Ning Wang. "Identification of Proteus genomic island 2 variants in two clonal Proteus mirabilis isolates with coexistence of a novel genomic resistance island PmGRI1." Journal of Antimicrobial Chemotherapy 75, no. 9 (June 9, 2020): 2503–7. http://dx.doi.org/10.1093/jac/dkaa215.

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Abstract Objectives To characterize the MDR genomic islands (GIs) in Proteus mirabilis isolates. Methods Two P. mirabilis strains (C55 and C74) of chicken origin were subjected to WGS (HiSeq and PacBio) and the MDR GIs were determined. Results P. mirabilis strains C55 and C74 are clonal strains and harbour different Proteus genomic island 2 (PGI2) variants (PGI2-C55 and PGI2-C74). The MDR region of PGI2-C55 is composed of two class 1 integrons, separated by a region containing seven copies of IS26 and eight resistance genes, including blaCTX-M-3 and fosA3. The region in PGI2-C74 is a complete In4-type class 1 integron, harbouring five gene cassettes (dfrA16, blaCARB-2, aadA2, cmlA1 and aadA1). In addition, C55 and C74 carry an SXT/R391 integrative and conjugative element (ICEPmiJpn1), harbouring blaCMY-2, and a novel 50.46 kb genomic resistance island named PmGRI1-C55. PmGRI1-C55 harbours a tyrosine-type recombinase/integrase that might be responsible for the integration of PmGRI1-C55 at the 3′ end of tRNA-Sec. It carries an MDR region derived from Tn2670 that harbours a Tn21 region and carries six resistance genes (catA1, blaTEM-1b, aphA1a, sul2, strA and strB). Blast analysis showed diverse PmGRI1 variants in P. mirabilis and Escherichia coli strains. Conclusions The finding of the two new PGI2 variants highlights that the homologous recombination between shared components of class 1 integrons and transposition by IS26 promote the diversity of MDR regions in PGI2. PmGRI1 is a new GI that carries various resistance genes identified in P. mirabilis and E. coli.

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Wang, Hailiang, Bochao Sun, Guosi Xie, Xiaoyuan Wan, Jie Huang, and Xiaoling Song. "Spotlight on a novel bactericidal mechanism and a novel SXT/R391-like integrative and conjugative element, carrying multiple antibiotic resistance genes, in Pseudoalteromonas flavipulchra strain CDM8." Microbiological Research 242 (January 2021): 126598. http://dx.doi.org/10.1016/j.micres.2020.126598.

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Song, Yuze, Pan Yu, Bailin Li, Yingjie Pan, Xiaojun Zhang, Jian Cong, Yinying Zhao, Hua Wang, and Lanming Chen. "The mosaic accessory gene structures of the SXT/R391-like integrative and conjugative elements derived from Vibrio spp. isolated from aquatic products and environment in the Yangtze River estuary, China." BMC Microbiology 13, no. 1 (2013): 214. http://dx.doi.org/10.1186/1471-2180-13-214.

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45

Song, Zhou, Lei Zuo, Cui Li, Yiming Tian, and Hongning Wang. "Copper Ions Facilitate the Conjugative Transfer of SXT/R391 Integrative and Conjugative Element Across Bacterial Genera." Frontiers in Microbiology 11 (February 2, 2021). http://dx.doi.org/10.3389/fmicb.2020.616792.

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Copper can persist stably in the environment for prolonged periods. Except for inducing antibiotic resistance in bacteria, copper ions (Cu2+) can facilitate the horizontal transfer of plasmid DNA. However, whether and how Cu2+ can accelerate the conjugative transfer of SXT/R391 integrative and conjugative element (ICE) is still largely unknown. In this study, Proteus mirabilis ChSC1905, harboring an SXT/R391 ICE that carried 21 antibiotic resistance genes (ARGs), was used as a donor, and Escherichia coli EC600 was used as a recipient. Cu2+, at subinhibitory and environmentally relevant concentrations (1–10 μmol/L), significantly accelerated the conjugative transfer of SXT/R391 ICE across bacterial genera (from P. mirabilis to E. coli) (p < 0.05). The combined analyses of phenotypic tests and genome-wide sequencing indicated that reactive oxygen species (ROS) production and cell membrane permeability were critical in the enhanced conjugative transfer of SXT/R391 ICE. Furthermore, the expression of genes related to cell adhesion and ATP synthesis was also significantly upregulated on exposure to Cu2+ at a concentration of 5 μmol/L. This study clarified the potential mechanisms of Cu2+ to promote the conjugative transfer of SXT/R391 ICE, revealing the potential risk imposed by Cu2+ on the horizontal transfer of SXT/R391 ICE-mediated ARGs.

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Ryan, Michael P., Shannon Slattery, and J. Tony Pembroke. "Identification and characterisation of a Novel SXT/R391 ICE mobile genetic element isolated from an Irish wastewater environment." Access Microbiology 4, no. 5 (May 27, 2022). http://dx.doi.org/10.1099/acmi.ac2021.po0367.

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Human and animal pathogenic bacteria are constantly being released into the environment through human activity. Many of these organisms can harbour genes such as virulence genes, antibiotic resistance and heavy metal resistance genes that are inserted into plasmids, transposons and Integrating Conjugating elements (ICEs), leading to potential spread. Such spread can be detected among water and soil communities and in particular in wastewater treatment plants. This makes wastewater and treatment plants a potential reservoir for mobile genetic elements including SXT/R391 ICEs, commonly detected amongst enterobacterial genera. Many plasmid and ICE genomes have been detected serendipitously from clinical sources but few have been identified without selection. Here we examined a domestic wastewater treatment plant to identify, isolate and characterize SXT/R391 ICE’s without selection. Standard microbial replica plating in conjunction with ICE specific (conserved integrase gene) PCR techniques were employed to identify an SXT/R391 ICE MGE using a range of enterobactial selective media. A Novel SXT/R391 ICE MGE was identified from a wastewater Proteus mirabilisstrain. Whole genome sequencing using Ilumina sequencing technology revealed a novel 81 kb element which on annotation contained 75 open reading frames. The “hotspot regions”, which contain adaptive genes, encoded a novel bacteriophage defence mechanisms but lacked other selectable determinants. With the continuous arms race between bacteria and phage, bacteria have developed novel resistance mechanism systems that protect the bacteria from phage. Such systems may be key adaptive mechanisms harboured by ICEs particularly in wastewater systems which will contain large phage populations.

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Spagnoletti, Matteo, Daniela Ceccarelli, Adrien Rieux, Marco Fondi, Elisa Taviani, Renato Fani, Mauro M. Colombo, Rita R. Colwell, and François Balloux. "Acquisition and Evolution of SXT-R391 Integrative Conjugative Elements in the Seventh-Pandemic Vibrio cholerae Lineage." mBio 5, no. 4 (August 19, 2014). http://dx.doi.org/10.1128/mbio.01356-14.

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ABSTRACT SXT-R391 Integrative conjugative elements (ICEs) are self-transmissible mobile genetic elements able to confer multidrug resistance and other adaptive features to bacterial hosts, including Vibrio cholerae, the causative agent of cholera. ICEs are arranged in a mosaic genetic structure composed of a conserved backbone interspersed with variable DNA clusters located in conserved hot spots. In this study, we investigated ICE acquisition and subsequent microevolution in pandemic V. cholerae. Ninety-six ICEs were retrieved from publicly available sequence databases from V. cholerae clinical strains and were compared to a set of reference ICEs. Comparative genomics highlighted the existence of five main ICE groups with a distinct genetic makeup, exemplified by ICEVchInd5, ICEVchMoz10, SXT, ICEVchInd6, and ICEVchBan11. ICEVchInd5 (the most frequent element, represented by 70 of 96 elements analyzed) displayed no sequence rearrangements and was characterized by 46 single nucleotide polymorphisms (SNPs). SNP analysis revealed that recent inter-ICE homologous recombination between ICEVchInd5 and other ICEs circulating in gammaproteobacteria generated ICEVchMoz10, ICEVchInd6, and ICEVchBan11. Bayesian phylogenetic analyses indicated that ICEVchInd5 and SXT were independently acquired by the current pandemic V. cholerae O1 and O139 lineages, respectively, within a period of only a few years. IMPORTANCE SXT-R391 ICEs have been recognized as key vectors of antibiotic resistance in the seventh-pandemic lineage of V. cholerae, which remains a major cause of mortality and morbidity on a global scale. ICEs were acquired only recently in this clade and are acknowledged to be major contributors to horizontal gene transfer and the acquisition of new traits in bacterial species. We have reconstructed the temporal dynamics of SXT-R391 ICE acquisition and spread and have identified subsequent recombination events generating significant diversity in ICEs currently circulating among V. cholerae clinical strains. Our results showed that acquisition of SXT-R391 ICEs provided the V. cholerae seventh-pandemic lineage not only with a multidrug resistance phenotype but also with a powerful molecular tool for rapidly accessing the pan-genome of a large number of gammaproteobacteria.

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Lei, Chang-Wei, Yan-Peng Chen, Zhuang-Zhuang Kang, Ling-Han Kong, and Hong-Ning Wang. "Characterization of a Novel SXT/R391 Integrative and Conjugative Element Carrying cfr, blaCTX-M-65, fosA3, and aac(6′)-Ib-cr in Proteus mirabilis." Antimicrobial Agents and Chemotherapy 62, no. 9 (July 2, 2018). http://dx.doi.org/10.1128/aac.00849-18.

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ABSTRACT A novel 139,487-bp SXT/R391 integrative and conjugative element, ICEPmiChnBCP11, was characterized in Proteus mirabilis of swine origin in China. ICEPmiChnBCP11 harbors 20 different antimicrobial resistance genes, including the clinically important rRNA methyltransferase gene cfr, the extended-spectrum β-lactamase gene blaCTX-M-65, fosfomycin resistance gene fosA3, and fluoroquinolone resistance gene aac(6′)-Ib-cr. An ISPpu12-mediated composite transposon containing various resistance genes and 10 copies of IS26 is inserted in hot spot 4. ICEPmiChnBCP11 was successfully transferred to Escherichia coli.

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Zhang, Fengwei, Xianwei Ye, Zhiqiu Yin, Mingda Hu, Boqian Wang, Wenting Liu, Beiping Li, Hongguang Ren, Yuan Jin, and Junjie Yue. "Comparative genomics reveals new insights into the evolution of the IncA and IncC family of plasmids." Frontiers in Microbiology 13 (November 16, 2022). http://dx.doi.org/10.3389/fmicb.2022.1045314.

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Incompatibility groups IncA and IncC plasmids are of great concern due to their ability to disseminate antibiotic resistance in bacteria via conjugative transfer. A deep understanding of their genomic structures and evolutionary characteristics is of great significance for improving our knowledge about its multidrug-resistance evolution and dissemination. However, current knowledge of their backbone structure, features of core functional modules and the characteristics of variable regions is based on a few plasmids, which highlights the need for a comprehensive systematic study. The present study thoroughly compared and analysed 678 IncA and IncC plasmid genomes. We found that their core functional genes were occasionally deficient and sometimes existed as multiple functional copies/multiple families, which resulted in much diversity. The phylogeny of 13 core functional genes corresponded well to the plasmid subtypes. The conjugative transfer system gained diverse complexity and exhibited many previously unnoticed types with multiple combinations. The insertion of mobile genetic elements (MGEs) in plasmids varied between types and was present in 4 insertion spots in different types of plasmids with certain types of transposons, integrons and insertion sequences. The impact of gene duplication, deletion, the insertion of MGEs, genome rearrangement and recombination resulted in the complex dynamic variable backbone of IncA and IncC plasmids. And IncA and IncC plasmids were more complex than their closest relative SXT/R391 integrative conjugative elements (ICEs), which included nearly all of the diversity of SXT/R391 in key systems. Our work demonstrated a global and systematic view of the IncA and IncC plasmids and provides many new insights into their genome evolution.

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Sato, Juliana L., Marina R. B. Fonseca, Louise T. Cerdeira, Maria C. B. Tognim, Thais C. M. Sincero, Mario C. Noronha do Amaral, Nilton Lincopan, and Rodrigo S. Galhardo. "Genomic Analysis of SXT/R391 Integrative Conjugative Elements From Proteus mirabilis Isolated in Brazil." Frontiers in Microbiology 11 (October 20, 2020). http://dx.doi.org/10.3389/fmicb.2020.571472.

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