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From pieces to patterns: evolutionary engineering in bacterial pathogens

Abstract

Evolutionary microbiology is a basic science that is increasingly forming the basis for new developments in public-health microbiology. Medical advances might depend on an understanding of the conditions that are required for the emergence and maintenance of human bacterial pathogens. An understanding of the evolutionary engineering rules that lead to virulence or drug resistance — specifically with bacteria in mind — are therefore important and are examined in this article.

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Figure 1: Pieces and patterns.
Figure 2: The core and peripheral genomes.
Figure 3: Genetic capitalism.

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Acknowledgements

The author is particularly indebted to T. M. Coque, and also to J.-C. Galán and R. Cantón, for endless discussions about the concepts, and for substantial help in selecting the best examples to be included in this review. Suggestions and criticisms of three referees were most welcome. The author acknowledges support of the Network 'Red Española de Investigación en Patología Infecciosa' (REIPI) of the Instituto Carlos III, Spanish Ministry of Health.

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DATABASES

Entrez

Enterococcus faecalis

Enterococcus faecium

Escherichia coli

Klebsiella pneumoniae

Lactococcus lactis

Listeria innocua

pT181

pUB110

Shigella flexneri

Staphylococcus aureus

Glossary

AMENSALISM

An interaction between two organisms in which the growth of one organism is suppressed by the other organism (for example, suppression of one bacterial organism through the production of toxins, such as bacteriocins, by another). Also known as antagonism.

CORREIA ELEMENTS

A family of repetitive DNA sequences. There are approximately 20 copies of this type of sequence in both Neisseria gonorrhoeae and Neisseria meningitidis

ENGINEERING

A random or causal process by which pieces come into contact with other pieces, resulting in stable interactions between them, eventually resulting in a function.

EXISTENCE CONDITIONS

The conditions that allow a particular genetic element (for example, a phage, plasmid or transposon) to become established and to be maintained in bacterial populations or communities.

METAGENOME

The collection of the genomes of the total microbiota found in a particular environment. For instance, libraries of total genomic DNA isolated directly from faeces or soil are termed metagenomic libraries.

OPERATIVE FUNCTION

A bacterial function that is related to housekeeping operations, or is involved in specific activities that are related to environmental adaptation, such as antibiotic resistance or virulence.

ORDER

A regular sequence of pieces that is maintained over time. The order itself promotes ordering of other pieces, because ordered pieces retain the ordering principles.

PATTERN

Any ordered structure resulting from stable interactions among pieces.

PIECE

Any type of biological unit (from a short DNA sequence to a whole organism or a supra-organismal structure) that is able to interact with another unit.

SUB-ORGANISMAL LEVEL

Any level in the hierarchy of pieces that is located below the individual organism (such as a bacterial cell); for example, molecules, short genetic sequences, genes, operons, plasmids and integrons.

SUPRA-ORGANISMAL LEVEL

Any level in the hierarchy of pieces that is located above the individual organism (such as a bacterial cell); for example, clones, species, demes, clades and communities. Selection at supra-organismal level is also known as 'higher-level selection'.

TRANS-HIERARCHICAL

A hierarchy is an asymmetrical organizational pattern of groups within groups; trans-hierarchical events are those occurring from bottom-to-top (upward causation) or top-to-bottom (downward causation) in the hierarchy.

VCR ELEMENT

A repetitive DNA sequence that is found in the chromosome of Vibrio cholerae.

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Baquero, F. From pieces to patterns: evolutionary engineering in bacterial pathogens. Nat Rev Microbiol 2, 510–518 (2004). https://doi.org/10.1038/nrmicro909

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