Identification and analysis of integrons and cassette arrays in bacterial genomes

Cury, Jean; Jové, Thomas; Touchon, Marie; Néron, Bertrand; Rocha, Eduardo P. C.

doi:10.1093/nar/gkw319

Cited by 241 publications

(240 citation statements)

References 75 publications

(97 reference statements)

Supporting

Mentioning

226

Contrasting

Unclassified

Order By: Relevance

“…On the other hand, the distance between attC sites provides an exact measure of cassette length but is affected by inaccuracies in the detection of attC sites (a missed attC can lead to the doubling of a cassette length). We performed these analyses for the 393 integrons identified by the IntegronFinder program (10) (Materials and Methods) and their respective replicons. CDSs in MIs and SCIs are significantly shorter than CDSs in replicons (median CDS lengths were 575, 362, and 818 bp, respectively [Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Cassette arrays represent a low-cost repository of valuable functions for the cell and most likely reflect a history of adaptive events. The number of cassettes in the array can be very large in SCIs (more than 200), while it rarely exceeds eight in MIs (9, 10). Interestingly, attC sites found in SCI cassette arrays generally show a high degree of sequence identity, which increases with the number of cassettes (10).…”

Section: Introductionmentioning

confidence: 99%

“…The number of cassettes in the array can be very large in SCIs (more than 200), while it rarely exceeds eight in MIs (9, 10). Interestingly, attC sites found in SCI cassette arrays generally show a high degree of sequence identity, which increases with the number of cassettes (10). In contrast, attC sites of MI cassette arrays differ in length and sequence (11).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance

Loot

Nivina

Cury

et al. 2017

mBio

Self Cite

View full text Add to dashboard Cite

Integrons ensure a rapid and “on demand” response to environmental stresses driving bacterial adaptation. They are able to capture, store, and reorder functional gene cassettes due to site-specific recombination catalyzed by their integrase. Integrons can be either sedentary and chromosomally located or mobile when they are associated with transposons and plasmids. They are respectively called sedentary chromosomal integrons (SCIs) and mobile integrons (MIs). MIs are key players in the dissemination of antibiotic resistance genes. Here, we used in silico and in vivo approaches to study cassette excision dynamics in MIs and SCIs. We show that the orientation of cassette arrays relative to replication influences attC site folding and cassette excision by placing the recombinogenic strands of attC sites on either the leading or lagging strand template. We also demonstrate that stability of attC sites and their propensity to form recombinogenic structures also regulate cassette excision. We observe that cassette excision dynamics driven by these factors differ between MIs and SCIs. Cassettes with high excision rates are more commonly found on MIs, which favors their dissemination relative to SCIs. This is especially true for SCIs carried in the Vibrio genus, where maintenance of large cassette arrays and vertical transmission are crucial to serve as a reservoir of adaptive functions. These results expand the repertoire of known processes regulating integron recombination that were previously established and demonstrate that, in terms of cassette dynamics, a subtle trade-off between evolvability and genetic capacitance has been established in bacteria.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance

Loot

Nivina

Cury

et al. 2017

mBio

Self Cite

View full text Add to dashboard Cite

show abstract

“…Although we were able to link resistance genes directly to replicon sequences in some cases (e.g., qnrD with Col3M), correlations between plasmid replicons and resistance genes could not be established in many cases, mainly because the current sequencing and de novo assembly methods are not able to assemble complete plasmid sequences (38); this does not necessarily mean that the resistance genes are unrelated to the plasmids carrying the detected replicons. We could not perform integron analysis using our draft genome sequences because complete integrons, In0 elements, and clusters of attC sites lacking integron-integrases (CALIN) cannot be accurately identified when contig breaks occur in these sequences (39).…”

Section: Ere(b) Erm(b) Mph(a) and Mph(b) In 23 Isolates The Ermentioning

confidence: 99%

Whole-Genome Analysis of Antimicrobial-Resistant and Extraintestinal Pathogenic Escherichia coli in River Water

Gomi

Matsuda

Matsumura

et al. 2017

Appl Environ Microbiol

View full text Add to dashboard Cite

Contamination of surface waters by antimicrobial-resistant bacteria and pathogenic bacteria is a great concern. In this study, 531 Escherichia coli isolates obtained from the Yamato River in Japan were evaluated phenotypically for resistance to 25 antimicrobials. Seventy-six isolates (14.3%) were multidrug resistant (MDR), 66 (12.4%) were nonsusceptible to one or two classes of agents, and 389 (73.3%) were susceptible. We performed whole-genome sequencing of selected strains by using Illumina technology. In total, the genome sequences of 155 strains were analyzed for antibiotic resistance determinants and phylogenetic characteristics. More than 50 different resistance determinants, including acquired resistance genes and chromosomal resistance mutations, were detected. Among the sequenced MDR strains (n ϭ 66), sequence type 155 (ST155) complex (n ϭ 9), ST10 complex (n ϭ 9), and ST69 complex (n ϭ 7) were prevalent. Among extraintestinal pathogenic E. coli (ExPEC) strains (n ϭ 58), clinically important clonal groups, namely, ST95 complex (n ϭ 18), ST127 complex (n ϭ 8), ST12 complex (n ϭ 6), ST14 complex (n ϭ 6), and ST131 complex (n ϭ 6), were prevalent, demonstrating the clonal distribution of environmental ExPEC strains. Typing of the fimH (type 1 fimbrial adhesin) gene revealed that ST131 complex strains carried fimH22 or fimH41, and no strains belonging to the fimH30 subgroup were detected. Fine-scale phylogenetic analysis and virulence gene content analysis of strains belonging to the ST95 complex (one of the major clonal ExPEC groups causing community-onset infections) revealed no significant differences between environmental and clinical strains. The results indicate contamination of surface waters by E. coli strains belonging to clinically important clonal groups.IMPORTANCE The prevalence of antimicrobial-resistant and pathogenic E. coli strains in surface waters is a concern because surface waters are used as sources for drinking water, irrigation, and recreational purposes. In this study, MDR and ExPEC strains in river water were characterized by genomic sequencing and analysis. We detected more than 50 resistance determinants and identified clonal groups specific to MDR and ExPEC strains. This study showed contamination of surface waters by E. coli strains belonging to clinically important clonal groups. Overall, this study advances our understanding of environmental MDR and ExPEC strains.KEYWORDS antimicrobial resistance, Escherichia coli, ExPEC, whole-genome sequencing E scherichia coli is a commensal member of the gastrointestinal tract of humans and other warm-blooded animals. Consequently, E. coli, as well as Enterococcus spp., has long been used as an indicator of fecal contamination to assess the microbial quality of surface waters. Although most E. coli strains are harmless, some strains are pathogenic

show abstract

“…Previous data confirmed that this class had a lower prevalence. [15][16][17] In addition, the class I and II integrons were detected in 26 females and 6 male patients (32%) and 18 females and 3 male patients (21%), respectively. There were significant relationships between resistance to trimethoprimsulfamethoxazole (P < 0.001), ciprofloxacin (P < 0.01), and tetracycline (P < 0.005), and the class I integron.…”

Section: Discussionmentioning

confidence: 99%

The Relationship Between Class I and II Integrons and Antibiotic Resistance Among Escherichia coli Isolates From Urinary Tract Infections

Nojoomi¹,

Vafaee²,

Rajabi-vardanjani³

2018

Int J Enteric Pathog

View full text Add to dashboard Cite

Identification and analysis of integrons and cassette arrays in bacterial genomes

Cited by 241 publications

References 75 publications

Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance

Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance

Whole-Genome Analysis of Antimicrobial-Resistant and Extraintestinal Pathogenic Escherichia coli in River Water

The Relationship Between Class I and II Integrons and Antibiotic Resistance Among Escherichia coli Isolates From Urinary Tract Infections

Contact Info

Product

Resources

About