INTEGRALL: a database and search engine for integrons, integrases and gene cassettes

Moura, Alexandra; Soares, Mário J.; Pereira, Carolina; Leitão, Nuno; Henriques, Isabel; Correia, António

doi:10.1093/bioinformatics/btp105

Cited by 528 publications

(377 citation statements)

References 10 publications

Supporting

Mentioning

349

Contrasting

Order By: Relevance

“…In fact, the aadA gene cassettes are the most often reported cassettes in bacteria isolates and seem to persist in environments regardless of the limited use of such antibiotics at present [10,17]. Other gene cassettes involved in antibiotic resistance included aacA3C, aacA3, aacA4 0 -17, aacA7, aadB, drfA1, drfA12, drfA17, catB8, cmlA8, blaP1, bla OXA10a , and bla OXA-251 .…”

Section: Resultsmentioning

confidence: 99%

Novel Class 1 Integrons in Multi-drug Resistant Isolates from Eastern China

Sun

Shao

et al. 2013

Indian J Microbiol

View full text Add to dashboard Cite

Integrons are mobile genetic elements able to capture, express and excise resistance genes, playing an important role in the spread of bacterial resistance. The present study was to investigate the occurrence and diversity of integrons in 120 clinical multi-drug resistant Gram-negative isolates from eastern China. Screening of integrons was performed by PCR and gene cassettes were further characterized by PCR-RFLP and sequencing. Class 1 integrons were detected in 70.8 % of isolates and no class 2 and class 3 integrons were detected in any isolates. A total of 19 resistant gene cassettes were identified, four representative of novel gene cassettes: an aacA3 variant (aacA3c), an aacA4 variant (aacA4 0 -17), a bla OXA variant (bla OXA-251 ), and a catB8 gene cassette interrupted by an insertion sequence IS10 (catB8::IS10). In addition, 14 cassette arrays were detected, including three novel integrons:gcuD1-aacA4 0 -17-gcu38B-catB8::IS10 (In712), aacA3c-aadA13-bla OXA-251 (In713) and dfrA1-gcu37-aadA5 (In714). The presence of novel integron structures in clinical isolates suggests hospital environments may favor the formation of novel combination of gene cassettes. Moreover, the high prevalence of integrons in multi-drug resistant isolates highlights the urgent need to employ effective means to avoid dissemination of drug-resistant bacteria.

show abstract

Section: Resultsmentioning

confidence: 99%

Novel Class 1 Integrons in Multi-drug Resistant Isolates from Eastern China

Sun

Shao

et al. 2013

Indian J Microbiol

View full text Add to dashboard Cite

show abstract

“…Consequently, a number of dedicated databases have been established for annotation and curation of integrons and their gene cassettes (101,102). Software for identifying cassettes in DNA sequences has been developed (39).…”

Section: Gene Cassette Diversity and Functionmentioning

confidence: 99%

Integrons: Past, Present, and Future

Gillings

2014

Microbiol Mol Biol Rev

561

472

View full text Add to dashboard Cite

SUMMARY Integrons are versatile gene acquisition systems commonly found in bacterial genomes. They are ancient elements that are a hot spot for genomic complexity, generating phenotypic diversity and shaping adaptive responses. In recent times, they have had a major role in the acquisition, expression, and dissemination of antibiotic resistance genes. Assessing the ongoing threats posed by integrons requires an understanding of their origins and evolutionary history. This review examines the functions and activities of integrons before the antibiotic era. It shows how antibiotic use selected particular integrons from among the environmental pool of these elements, such that integrons carrying resistance genes are now present in the majority of Gram-negative pathogens. Finally, it examines the potential consequences of widespread pollution with the novel integrons that have been assembled via the agency of human antibiotic use and speculates on the potential uses of integrons as platforms for biotechnology.

show abstract

“…Open reading frames and pseudogenes were predicted using RAST 2.0 [33] combined with BLASTP/BLASTN searches [34] against the UniProtKB/Swiss-Prot database [35] and the RefSeq database [36]. Annotation of resistance genes, mobile elements, and other features was carried out using the online databases including CARD [37], ResFinder [38], BacMet [39], ISfinder [40], INTEGRALL [41], and the Tn Number Registry [42]. Multiple and pairwise sequence comparisons were performed using MUSCLE 3.8.31 [43] and BLASTN, respectively.…”

Section: Sequencing and Annotationmentioning

confidence: 99%

WITHDRAWN: Structure genomics of two chimera plasmids p675920-1 and p675920-2 coexisting in a multi-drug resistant Klebsiella pneumoniae isolate

Feng¹,

Yin²,

Zhan³

et al. 2018

Oncotarget

View full text Add to dashboard Cite

This study dealt with detailed genomic characterization of two multidrug resistant (MDR) plasmids p675920-1 and p675920-2 from a single clinical Klebsiella pneumoniae isolate 675920. p675920-1 was essentially a hybrid of the IncFII plasmid pHN7A8 and the IncR plasmid pKPC-LK30, and functioned as an IncFII plasmid with inactivation of the IncR replication gene. The backbone of p675920-2 was a hybrid of a novel replicon, three maintenance regions (22.0-, 2.7-, 2.6-kb in length, respectively) as found in pKPYL2, p10164-3 and pK1HV, respectively, and the entire 25.9-kb conjugal transfer region of pKPYL2. p675920-1 and p675920-2 carried a large number of resistance genes, which contributed to resistance to at least seven classes of antibiotics (β-lactams, quinolones, aminoglycosides, fosfomycins, sulphonamides, trimethoprims, and tetracyclines) and one kind of heavy mental (mercury). All of these resistance genes are associated with mobile elements such as insertion sequences, insertion sequence-based transposition units, and transposons, which constituted a total of three novel MDR regions, two in p675920-1 and another in p675920-2. Coexistence of two MDR plasmids p675920-1 and p675920-2 made K. pneumoniae 675920 tend to become extensively drug-resistant.

show abstract

INTEGRALL: a database and search engine for integrons, integrases and gene cassettes

Cited by 528 publications

References 10 publications

Novel Class 1 Integrons in Multi-drug Resistant Isolates from Eastern China

Novel Class 1 Integrons in Multi-drug Resistant Isolates from Eastern China

Integrons: Past, Present, and Future

WITHDRAWN: Structure genomics of two chimera plasmids p675920-1 and p675920-2 coexisting in a multi-drug resistant Klebsiella pneumoniae isolate

Contact Info

Product

Resources

About