MOBscan: Automated Annotation of MOB Relaxases

Garcillán-Barcia, M. Pilar; Redondo-Salvo, Santiago; Vielva, Luis; Cruz, Fernando de la

doi:10.1007/978-1-4939-9877-7_21

Cited by 104 publications

(96 citation statements)

References 36 publications

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“…The RefSeq protein files from the CEG-bearing genomes identified by diamond were extracted. We used the hmmsearch function of the HMMER3 software package v3.3 (http://hmmer.org/) [24] to search the proteomes against the standalone version of MOBfamDB, a curated hidden Markov models (HMM) relaxase database (https://castillo.dicom.unican.es/mobscan_about/) [25]. We also used this function to search the pfam v33.0 database for tyrosine or serine recombinase accessions numbers (Pfam IDs PF00589 and PF07508).…”

Section: Methodsmentioning

confidence: 99%

Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically relevant bacteria

et al. 2020

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Carbapenemases inactivate most β-lactam antibiotics, including carbapenems, and have frequently been reported among Enterobacteriaceae , Acinetobacter spp. and Pseudomonas spp. Traditionally, the horizontal gene transfer of carbapenemase-encoding genes (CEGs) has been linked to plasmids. However, given that integrative and conjugative elements (ICEs) are possibly the most abundant conjugative elements among prokaryotes, we conducted an in silico analysis to ascertain the likely role of ICEs in the spread of CEGs among all bacterial genomes (n=182 663). We detected 17 520 CEGs, of which 66 were located within putative ICEs among several bacterial species (including clinically relevant bacteria, such as Pseudomonas aeruginosa , Klebsiella pneumoniae and Escherichia coli ). Most CEGs detected within ICEs belong to the IMP, NDM and SPM metallo-beta-lactamase families, and the serine beta-lactamase KPC and GES families. Different mechanisms were likely responsible for acquisition of these genes. The majority of CEG-bearing ICEs belong to the MPFG, MPFT and MPFF classes and often encode resistance to other antibiotics (e.g. aminoglycosides and fluoroquinolones). This study provides a snapshot of the different CEGs associated with ICEs among available bacterial genomes and sheds light on the underappreciated contribution of ICEs to the spread of carbapenem resistance globally.

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Section: Methodsmentioning

confidence: 99%

Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically relevant bacteria

et al. 2020

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“…We searched for ARGs on extracted ICEs using amrfinder v3.6.7 and default parameters (50% minimum coverage of the reference protein and 90% minimum identity) (https://github.com/ncbi/amr/wiki/AMRFinder-database) [28]. Positive ICE hits for crpP-encoding genes were further characterized; we used fastANI v1.3 (https://github.com/ParBLiSS/ FastANI) [29] to compute whole-genome average nucleotide identity (ANI) of non-P. aeruginosa crpP-positive hits, antismash online tool (https://antismash.secondarymetabolites.org/#!/start) [30] to look for secondary metabolite biosynthesis gene clusters, BAGEL (http://bagel4.molgenrug.nl/) [31] to trace bacteriocins, macsyfinder v1.0.5 (https://github.com/gem-pasteur/macsyfinder) [32,33] to assess the MPF family, MOBscan standalone version (https://castillo.dicom.unican.es/mobscan_about/) [34] to check relaxase (MOB) families and the CRISPRCasFinder online tool (https://crisprcas.i2bc.paris-saclay. fr/) [35] to detect clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas).…”

Section: Mining Ices In Complete Genomesmentioning

confidence: 99%

ICEs Are the Main Reservoirs of the Ciprofloxacin-Modifying crpP Gene in Pseudomonas aeruginosa

Botelho

Grosso

Peixe

2020

Genes

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The ciprofloxacin-modifying crpP gene was recently identified in a plasmid isolated from a Pseudomonas aeruginosa clinical isolate. Homologues of this gene were also identified in Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii. We set out to explore the mobile elements involved in the acquisition and spread of this gene in publicly available and complete genomes of Pseudomonas spp. All Pseudomonas complete genomes were downloaded from NCBI’s Refseq library and were inspected for the presence of the crpP gene. The mobile elements carrying this gene were further characterized. The crpP gene was identified only in P. aeruginosa, in more than half of the complete chromosomes (61.9%, n = 133/215) belonging to 52 sequence types, of which the high-risk clone ST111 was the most frequent. We identified 136 crpP-harboring integrative and conjugative elements (ICEs), with 93.4% belonging to the mating-pair formation G (MPFG) family. The ICEs were integrated at the end of a tRNALys gene and were all flanked by highly conserved 45-bp direct repeats. The crpP-carrying ICEs contain 26 core genes (2.2% of all 1193 genes found in all the ICEs together), which are present in 99% or more of the crpP-harboring ICEs. The most frequently encoded traits on these ICEs include replication, transcription, intracellular trafficking and cell motility. Our work suggests that ICEs are the main vectors promoting the dissemination of the ciprofloxacin-modifying crpP gene in P. aeruginosa.

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“…It encodes a relaxase, a coupling protein (CP) and a "type IV secretion system" (T4SS) [8,9], including VirB4, a conserved ATPase providing energy [10]. Three distinct superfamilies of relaxases have been identified thus far in ICEs from Firmicutes: the MobP, MobC and MobT [2,11,12]. The relaxase recognizes and cleaves one of the DNA strands of the circular element, specifically at the oriT site [13][14][15].…”

Section: Introductionmentioning

confidence: 99%

Abundance, Diversity and Role of ICEs and IMEs in the Adaptation of Streptococcus salivarius to the Environment

Lao

Guédon

Lacroix

et al. 2020

Genes

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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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MOBscan: Automated Annotation of MOB Relaxases

Cited by 104 publications

References 36 publications

Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically relevant bacteria

Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically relevant bacteria

ICEs Are the Main Reservoirs of the Ciprofloxacin-Modifying crpP Gene in Pseudomonas aeruginosa

Abundance, Diversity and Role of ICEs and IMEs in the Adaptation of Streptococcus salivarius to the Environment

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