Co-diversification of Enterococcus faecium Core Genomes and PBP5: Evidences of pbp5 Horizontal Transfer

Novais, Carla; Tedim, Ana P.; Lanza, Val F.; Freitas, Ana R.; Silveira, Eduarda; Escada, Ricardo; Roberts, Adam P.; Al‐Haroni, Mohammed; Baquero, Fernando; Peixe, Luı́sa; Coque, Teresa M.

doi:10.3389/fmicb.2016.01581

Cited by 35 publications

(32 citation statements)

References 79 publications

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“…Transfer of large regions of the chromosome has also been observed in E. faecium, although the mechanism is different from what has been observed in E. faecalis because it is not mediated by PRPs (231)(232)(233). Interestingly, the pbp5 gene has been shown to be transferable as part of large chromosomal regions, and pbp5 horizontal gene transfer might be relevant in the acquisition of ␤-lactam resistance in clinical strains (233,234). Two of the most prevalent plasmid types are the Inc18 group and the pRUM family (227).…”

Section: Conjugative Transposable Elementsmentioning

confidence: 98%

The Enterococcus: a Model of Adaptability to Its Environment

2019

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SUMMARYThe genusEnterococcuscomprises a ubiquitous group of Gram-positive bacteria that are of great relevance to human health for their role as major causative agents of health care-associated infections. The enterococci are resilient and versatile species able to survive under harsh conditions, making them well adapted to the health care environment. Two species cause the majority of enterococcal infections:Enterococcus faecalisandEnterococcus faecium. Both species demonstrate intrinsic resistance to common antibiotics, such as virtually all cephalosporins, aminoglycosides, clindamycin, and trimethoprim-sulfamethoxazole. Additionally, a remarkably plastic genome allows these two species to readily acquire resistance to further antibiotics, such as high-level aminoglycoside resistance, high-level ampicillin resistance, and vancomycin resistance, either through mutation or by horizontal transfer of genetic elements conferring resistance determinants.

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Section: Conjugative Transposable Elementsmentioning

confidence: 98%

The Enterococcus: a Model of Adaptability to Its Environment

2019

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“…This is in part because transfer can occur across vast phylogenetic distances in the prokaryotes (109) but also because transfer is usually limited to a small stretch of DNA (47), ranging from several thousand bases in genetic transformation (110) to several hundred thousand in conjugation (111,112). The short lengths transferred provide that a recipient can acquire a small adaptive set of genes from a donor without also acquiring a huge number of genes ("genetic baggage") that would be maladaptive for the recipient (110).…”

Section: The Genetic Basis Of Early Diversificationmentioning

confidence: 99%

Transmission in the Origins of Bacterial Diversity, From Ecotypes to Phyla

Cohan

2017

Microbiol Spectr

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Any two lineages, no matter how distant they are now, began their divergence as one population splitting into two lineages that could coexist indefinitely. The rate of origin of higher-level taxa is therefore the product of the rate of speciation times the probability that two new species coexist long enough to reach a particular level of divergence. Here I have explored these two parameters of disparification in bacteria. Owing to low recombination rates, sexual isolation is not a necessary milestone of bacterial speciation. Rather, irreversible and indefinite divergence begins with ecological diversification, that is, transmission of a bacterial lineage to a new ecological niche, possibly to a new microhabitat but at least to new resources. Several algorithms use sequence data from a taxon of focus to identify phylogenetic groups likely to bear the dynamic properties of species. Identifying these newly divergent lineages allows us to characterize the genetic bases of speciation, as well as the ecological dimensions upon which new species diverge. Speciation appears to be least frequent when a given lineage has few new resources it can adopt, as exemplified by photoautotrophs, C1 heterotrophs, and obligately intracellular pathogens; speciation is likely most rapid for generalist heterotrophs. The genetic basis of ecological divergence may determine whether ecological divergence is irreversible and whether lineages will diverge indefinitely into the future. Long-term coexistence is most likely when newly divergent lineages utilize at least some resources not shared with the other and when the resources themselves will coexist into the remote future.

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“…Note that K. pneumoniae has intrinsic (plasmid-independent) resistance to AbA. Although it was not analyzed in this study (but is included in the model), a clone of E. faecium resistant to AbA might transfer this resistance to a susceptible clone at a rate of 10 −4 (62).…”

Section: Methodsmentioning

confidence: 99%

Simulating the Influence of Conjugative Plasmids Kinetic Values on the Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model

Campos

San-Milán

Sempere

et al. 2020

Preprint

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20Plasmids harboring antibiotic resistance genes differ in their kinetic values as plasmid 21 conjugation rate, segregation rate by incompatibility with related plasmids, rate of 22 stochastic loss during replication, cost reducing the host-cell fitness, and frequency of 23 compensatory mutations to reduce plasmid cost, depending on the cell mutation 24 frequency. How variation in these values influence the success of a plasmid and their 25 resistance genes in complex ecosystems, as the microbiota? Genes are located in 26 plasmids, plasmids in cells, cells in populations. These populations are embedded in 27 ensembles of species in different human hosts, are able to exchange between them 28 bacterial ensembles during cross-infection and are located in the hospital or the 29 community setting, under various levels of antibiotic exposure. Simulations using new 30 membrane computing methods help predict the influence of plasmid kinetic values on 31 such multilevel complex system. In our simulation, conjugation frequency needed to be 32 at least 10 -3 to clearly influence the dominance of a strain with a resistant plasmid. Host 33 strains able to stably maintain two copies of similar plasmids harboring different 34 resistances, coexistence of these resistances can occur in the population. Plasmid loss 35 rates of 10 -4 or 10 -5 or plasmid fitness costs ≥0.06 favor the plasmids located in the most 36 abundant species. The beneficial effect of compensatory mutations for plasmid fitness 37 cost is proportional to this cost, only at high mutation frequencies (10 -3 -10 -5 ). 38Membrane computing helps set a multilevel landscape to study the effect of changes in 39 plasmid kinetic values on the success of resistant organisms in complex ecosystems. 40 41 42 43 44 Plasmid kinetics are widely assumed to necessarily influence the spread of antibiotic 45 resistance genes in bacterial populations and ecosystems (1-10). The main parameters 46 that affect plasmid kinetics are: a) the rate of plasmid conjugation/transfer (the rate at 47 which a bacterial cell harboring a conjugative plasmid [donor] transfers this plasmid to 48 a recipient cell; b) the segregation rate due to plasmid incompatibility (considering the 49 number of plasmid genome copies that are stably maintained in a bacterial cell); c) the 50 rate of plasmid cost (the reduction imposed by the presence [and transfer] of a plasmid 51 in the growth rate of the host bacterial cell); d) the rate of plasmid cost compensation 52 (measuring the effect of mutations reducing plasmid cost); e) the frequency of 53 mutational events in the plasmid or bacterial genome; and f) the rate of plasmid loss (the 54 rate at which plasmids are lost during the bacterial replication process). 55 However, the effects of these changes on the kinetics of plasmid resistance genes among 56 bacterial populations are necessarily influenced by numerous other factors acting in 57 actual biological ecosystems, such as the intestinal microbiota. Of these factors, our 58 previously published studies...

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Co-diversification of Enterococcus faecium Core Genomes and PBP5: Evidences of pbp5 Horizontal Transfer

Cited by 35 publications

References 79 publications

The Enterococcus: a Model of Adaptability to Its Environment

The Enterococcus: a Model of Adaptability to Its Environment

Transmission in the Origins of Bacterial Diversity, From Ecotypes to Phyla

Simulating the Influence of Conjugative Plasmids Kinetic Values on the Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model

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