Diversity and Evolution of the Tn
            <i>5801-tet</i>
            (M)-Like Integrative and Conjugative Elements among Enterococcus, Streptococcus, and Staphylococcus

León‐Sampedro, Ricardo; Novais, Carla; Peixe, Luı́sa; Baquero, Fernando; Coque, Teresa M.

doi:10.1128/aac.01864-15

Cited by 44 publications

(51 citation statements)

References 56 publications

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“…The trimethoprim-resistant gene dfrG and two more genes with unknown function were located within this insertion. A similar insertion has been reported previously in some ST17 and ST18 E. faecium strains [16] which is thought to result in defective protection against tetracyclines [17]. Lastly, all strains had a homologue of the E. faecalis IsaA gene which confers resistance to quinipristin-dalfopristin.…”

Section: Resultssupporting

confidence: 76%

“…It is notable that all isolates had 2 loose matches for the tetracycline resistance gene tetM . By further examining the region where these tetM -like sequences are located, we found that the 5 genomes had a Tn5801-like transposon (full-length or fragment) containing a sequence similar to Staphylococcus aureus Mu50 tetM gene [16], but with a 3,229 bp insertion. The trimethoprim-resistant gene dfrG and two more genes with unknown function were located within this insertion.…”

Section: Resultsmentioning

confidence: 99%

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Emergence of an Australian-like pstS-null vancomycin resistant Enterococcus faecium clone in Scotland

Lemonidis

Salih

Dancer

et al. 2017

Preprint

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Multi-locus sequencing typing (MLST) is widely used to monitor the phylogeny of microbial outbreaks. However, several strains of vancomycin-resistant Enterococcus faecium (VREfm) with a missing MLST locus (pstS) have recently emerged in Australia, with a few cases also reported in England. Here, we identified similarly distinct strains circulating in two closely located hospitals in Scotland. Whole genome sequencing of five VREfm strains isolated from these hospitals identified four pstS-null strains across both hospitals, while the fifth was of a multi-locus sequence type (ST) 262, which is the first documented in the UK. All five Scottish isolates had an insertion in the tetM gene, which is associated with increased susceptibility to tetracyclines, providing no other tetracycline-resistant gene is present. Such an insertion, which encompasses a dfrG gene and two currently uncharacterised genes, was additionally identified in all tested VanA-type pstS-null VREfm strains (5 English and 18 Australian). Phylogenetic comparison with other VREfm genomes indicates that the four pstS-null Scottish isolates sequenced in this study are more closely related to pstS-null strains from Australia rather than the English pstS-null isolates. Given how rapidly such pstS-null strains have expanded in Australia, the emergence of this clone in Scotland raises concerns for a potential outbreak.

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Section: Resultssupporting

confidence: 76%

Section: Resultsmentioning

confidence: 99%

Emergence of an Australian-like pstS-null vancomycin resistant Enterococcus faecium clone in Scotland

Lemonidis

Salih

Dancer

et al. 2017

Preprint

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“…The presence of the same IMESag- rpsI type in strains belonging to different CCs suggests that this integrative element has been transmitted both vertically and horizontally, as has been shown for GBS strains harbouring Tn 5801 [51]. Although the mechanisms that induce ICE/IME excision from the chromosome are not fully understood, our results showed that the IMESag- rpsI from the HRC isolate was able to excise as circular intermediates when compared with other reference strains (figure 5).…”

Section: Discussionmentioning

confidence: 91%

Streptococcal group B integrative and mobilizable element IMESag-rpsIencodes a functional relaxase involved in its transfer

et al. 2016

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Streptococcus agalactiae or Group B Streptococcus (GBS) are opportunistic bacteria that can cause lethal sepsis in children and immuno-compromised patients. Their genome is a reservoir of mobile genetic elements that can be horizontally transferred. Among them, integrative and conjugative elements (ICEs) and the smaller integrative and mobilizable elements (IMEs) primarily reside in the bacterial chromosome, yet have the ability to be transferred between cells by conjugation. ICEs and IMEs are therefore a source of genetic variability that participates in the spread of antibiotic resistance. Although IMEs seem to be the most prevalent class of elements transferable by conjugation, they are poorly known. Here, we have studied a GBS-IME, termed IMESag-rpsI, which is widely distributed in GBS despite not carrying any apparent virulence trait. Analyses of 240 whole genomes showed that IMESag-rpsI is present in approximately 47% of the genomes, has a roughly constant size (approx. 9 kb) and is always integrated at a single location, the 3′-end of the gene encoding the ribosomal protein S9 (rpsI). Based on their genetic variation, several IMESag-rpsI types were defined (A–J) and classified in clonal complexes (CCs). CC1 was the most populated by IMESag-rpsI (more than 95%), mostly of type-A (71%). One CC1 strain (S. agalactiae HRC) was deep-sequenced to understand the rationale underlying type-A IMESag-rpsI enrichment in GBS. Thirteen open reading frames were identified, one of them encoding a protein (MobSag) belonging to the broadly distributed family of relaxases MOBV1. Protein MobSag was purified and, by a newly developed method, shown to cleave DNA at a specific dinucleotide. The S. agalactiae HRC-IMESag-rpsI is able to excise from the chromosome, as shown by the presence of circular intermediates, and it harbours a fully functional mobilization module. Further, the mobSag gene encoded by this mobile element is able to promote plasmid transfer among pneumococcal strains, suggesting that MobSag facilitates the spread of IMESag-rpsI and that this spread would explain the presence of the same IMESag-rpsI type in GBS strains belonging to different CCs.

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“…These adaptations include the presence of CRISPR-Cas in the chromosome (Palmer and Gilmore, 2010;Price et al, 2016), restriction-modification (RM) and anti-RM systems, which would act against certain plasmids (e.g. pCF10); or lineagespecific bacteriocins carried by pheromone-responsive plasmids (Kurushima et al, 2016) or conjugative transposons (Tn916-like elements) that might influence the transfer of genetic material within and between lineages (Manson et al, 2010;Laverde Gomez et al, 2011;León-Sampedro et al, 2016;Price et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

Phylogenomics of Enterococcus faecalis from wild birds: new insights into host‐associated differences in core and accessory genomes of the species

León‐Sampedro

Campo

Rodríguez-Baños

et al. 2019

Environmental Microbiology

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Summary Wild birds have been suggested to be reservoirs of antimicrobial resistant and/or pathogenic Enterococcus faecalis (Efs) strains, but the scarcity of studies and available sequences limit our understanding of the population structure of the species in these hosts. Here, we analysed the clonal and plasmid diversity of 97 Efs isolates from wild migratory birds. We found a high diversity, with most sequence types (STs) being firstly described here, while others were found in other hosts including some predominant in poultry. We found that pheromone‐responsive plasmids predominate in wild bird Efs while 35% of the isolates entirely lack plasmids. Then, to better understand the ecology of the species, the whole genome of fivestrains with known STs (ST82, ST170, ST16 and ST55) were sequenced and compared with all the Efs genomes available in public databases. Using several methods to analyse core and accessory genomes (AccNET, PLACNET, hierBAPS and PANINI), we detected differences in the accessory genome of some lineages (e.g. ST82) demonstrating specific associations with birds. Conversely, the genomes of other Efs lineages exhibited divergence in core and accessory genomes, reflecting different adaptive trajectories in various hosts. This pangenome divergence, horizontal gene transfer events and occasional epidemic peaks could explain the population structure of the species.

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Diversity and Evolution of the Tn 5801-tet (M)-Like Integrative and Conjugative Elements among Enterococcus, Streptococcus, and Staphylococcus

Cited by 44 publications

References 56 publications

Emergence of an Australian-like pstS-null vancomycin resistant Enterococcus faecium clone in Scotland

Emergence of an Australian-like pstS-null vancomycin resistant Enterococcus faecium clone in Scotland

Streptococcal group B integrative and mobilizable element IMESag-rpsIencodes a functional relaxase involved in its transfer

Phylogenomics of Enterococcus faecalis from wild birds: new insights into host‐associated differences in core and accessory genomes of the species

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