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Genome Biol Evol DOI:10.1093/gbe/evu225

The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences.

Publication TypeJournal Article
Year of Publication2014
AuthorsTouchon, M, Cury, J, Yoon, E-J, Krizova, L, Cerqueira, GC, Murphy, C, Feldgarden, M, Wortman, J, Clermont, D, Lambert, T, Grillot-Courvalin, C, Nemec, A, Courvalin, P, Rocha, EPC
JournalGenome Biol Evol
Volume6
Issue10
Pages2866-82
Date Published2014 Oct 13
ISSN1759-6653
KeywordsAcinetobacter, Clustered Regularly Interspaced Short Palindromic Repeats, Genome, Bacterial, Genomics, Interspersed Repetitive Sequences, Phylogeny
Abstract

Bacterial genomics has greatly expanded our understanding of microdiversification patterns within a species, but analyses at higher taxonomical levels are necessary to understand and predict the independent rise of pathogens in a genus. We have sampled, sequenced, and assessed the diversity of genomes of validly named and tentative species of the Acinetobacter genus, a clade including major nosocomial pathogens and biotechnologically important species. We inferred a robust global phylogeny and delimited several new putative species. The genus is very ancient and extremely diverse: Genomes of highly divergent species share more orthologs than certain strains within a species. We systematically characterized elements and mechanisms driving genome diversification, such as conjugative elements, insertion sequences, and natural transformation. We found many error-prone polymerases that may play a role in resistance to toxins, antibiotics, and in the generation of genetic variation. Surprisingly, temperate phages, poorly studied in Acinetobacter, were found to account for a significant fraction of most genomes. Accordingly, many genomes encode clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems with some of the largest CRISPR-arrays found so far in bacteria. Integrons are strongly overrepresented in Acinetobacter baumannii, which correlates with its frequent resistance to antibiotics. Our data suggest that A. baumannii arose from an ancient population bottleneck followed by population expansion under strong purifying selection. The outstanding diversification of the species occurred largely by horizontal transfer, including some allelic recombination, at specific hotspots preferentially located close to the replication terminus. Our work sets a quantitative basis to understand the diversification of Acinetobacter into emerging resistant and versatile pathogens.

URLhttp://gbe.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=25313016
DOI10.1093/gbe/evu225
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/25313016?dopt=Abstract

Alternate JournalGenome Biol Evol
PubMed ID25313016
PubMed Central IDPMC4224351
Grant ListHHSN272200900018C / AI / NIAID NIH HHS / United States
U19 AI110818 / AI / NIAID NIH HHS / United States
HHSN272200900018C / / PHS HHS / United States