Genome organization of epidemic Acinetobacter baumannii strains

Nocera, Pier Paolo Di; Rocco, Francesco; Giannouli, Maria; Triassi, Maria; Zarrilli, Raffaele

doi:10.1186/1471-2180-11-224

Cited by 84 publications

(96 citation statements)

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“…The majority of mutations in the dinB::Km strain were transversions (7 out of 10), as were the majority of mutations in the dinB ϩ strain (21 out of 32). Analysis of the total sequences of the dinB ϩ and dinB::Km strains combined revealed the majority (67%; 28 out of 42) of base-pair substitutions to be transversions (Table 3), a signature of DNA Pol V in E. coli, and all but one listed substitution (A-to-G transition) are also known to be DNA Pol V generated (45). …”

Section: Resultsmentioning

confidence: 99%

“…baumannii is notorious for readily incorporating foreign DNA, such as transposons, insertion sequence elements, and antibiotic resistance-encoding islands, into its genome (1,2,45). Therefore, it has the ability to acquire antibiotic resistances possibly from a wide range of bacteria.…”

Section: Discussionmentioning

confidence: 99%

“…The error-prone DNA Pol V is known to bypass UV-induced DNA lesions, and it is responsible for most UV-induced mutagenesis; because of this, umuD and umuC are highly regulated in E. coli to minimize the intracellular concentration of active DNA Pol V (17). A. baumannii is capable of UVinduced mutagenesis, and it has also been observed that it carries multiple umuD and umuC genes (45,46). It has been assumed that these genes are responsible for the mutagenesis.…”

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confidence: 99%

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Antibiotic Resistance Acquired through a DNA Damage-Inducible Response in Acinetobacter baumannii

Norton

Spilkia

Godoy

2013

Journal of Bacteriology

112

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Acinetobacter baumannii is an emerging nosocomial, opportunistic pathogen that survives desiccation and quickly acquires resistance to multiple antibiotics. Escherichia coli gains antibiotic resistances by expressing genes involved in a global response to DNA damage. Therefore, we asked whether A. baumannii does the same through a yet undetermined DNA damage response akin to the E. coli paradigm. We found that recA and all of the multiple error-prone DNA polymerase V (Pol V) genes, those organized as umuDC operons and unlinked, are induced upon DNA damage in a RecA-mediated fashion. Consequently, we found that the frequency of rifampin-resistant (Rif r ) mutants is dramatically increased upon UV treatment, alkylation damage, and desiccation, also in a RecA-mediated manner. However, in the recA insertion knockout strain, in which we could measure the recA transcript, we found that recA was induced by DNA damage, while uvrA and one of the unlinked umuC genes were somewhat derepressed in the absence of DNA damage. Thus, the mechanism regulating the A. baumannii DNA damage response is likely different from that in E. coli. Notably, it appears that the number of DNA Pol V genes may directly contribute to desiccation-induced mutagenesis. Sequences of the rpoB gene from desiccation-induced Rif r mutants showed a signature that was consistent with E. coli DNA polymerase V-generated base-pair substitutions and that matched that of sequenced A. baumannii clinical Rif r isolates. These data strongly support an A. baumannii DNA damage-inducible response that directly contributes to antibiotic resistance acquisition, particularly in hospitals where A. baumannii desiccates and tenaciously survives on equipment and surfaces.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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confidence: 99%

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Antibiotic Resistance Acquired through a DNA Damage-Inducible Response in Acinetobacter baumannii

Norton

Spilkia

Godoy

2013

Journal of Bacteriology

112

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“…Internationally, there are several epidemic clonal complexes of A. baumannii (e.g., the international clones I, II, and III) spreading across different health care facilities, and each clonal complex contains a subset of diversified strains (14)(15)(16). Compar-ative genomic analysis revealed that A. baumannii outbreaks at hospitals might be polyclonal and provided evidence for gene transfer and genome reorganization among different frequent genotypes (17)(18)(19)(20)(21). Understanding the genome diversification within a subset of closely related strains from the same clonal complex and their population dynamics during colonization provides insight for evolution and adaptation of bacterial pathogens (22,23).…”

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confidence: 99%

Population Dynamics of an Acinetobacter baumannii Clonal Complex during Colonization of Patients

et al. 2014

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Acinetobacter baumannii has emerged as one of the leading pathogens causing hospital-acquired infection. The success of A. baumannii as a pathogen has to a large extent been attributed to its capacity to remodel its genome. Several major epidemic clonal complexes of A. baumannii spread across different health care facilities around the world, each of which contains a subset of diversified strains. However, little is known about the population dynamics during colonization of A. baumannii within hosts. Here, whole-genome sequencing was used to analyze population dynamics of A. baumannii strains isolated from a group of patients at different time points as well as from different sites of a particular patient. Seven out of nine of the sampled A. baumannii strains belonged to the international clone II (CC92 clonal complex). While the A. baumannii strains were found to be stable in three patients, there was a change of A. baumannii strains in one patient. Comparative genomic analysis revealed that the accessory genome of these strains contained a large set of virulence-encoding genes and these virulence factors might play a role in determining population dynamics. Microscale genome modification has been revealed by analysis of single nucleotide polymorphisms (SNPs) between A. baumannii strains isolated from the same patient. Parallel evolutionary traits have been observed during genome diversification when A. baumannii colonize in different patients. Our study suggested that both antibiotic usage and host environment might impose selective forces that drive the rapid adaptive evolution in colonizing A. baumannii.

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“…Strains display striking variability in accessory gene content (5,8), including antibiotic resistance genes (9), even among related isolates of a single outbreak (10). This genomic variability presumably reflects the actions of transmissible plasmids, insertion elements, phage, integrons, natural transformation, and recombination (11)(12)(13)(14)(15)(16)(17)(18).…”

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Resources for Genetic and Genomic Analysis of Emerging Pathogen Acinetobacter baumannii

et al. 2015

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Acinetobacter baumannii is a Gram-negative bacterial pathogen notorious for causing serious nosocomial infections that resist antibiotic therapy. Research to identify factors responsible for the pathogen's success has been limited by the resources available for genome-scale experimental studies. This report describes the development of several such resources for A. baumannii strain AB5075, a recently characterized wound isolate that is multidrug resistant and displays robust virulence in animal models. We report the completion and annotation of the genome sequence, the construction of a comprehensive ordered transposon mutant library, the extension of high-coverage transposon mutant pool sequencing (Tn-seq) to the strain, and the identification of the genes essential for growth on nutrient-rich agar. These resources should facilitate large-scale genetic analysis of virulence, resistance, and other clinically relevant traits that make A. baumannii a formidable public health threat. IMPORTANCEAcinetobacter baumannii is one of six bacterial pathogens primarily responsible for antibiotic-resistant infections that have become the scourge of health care facilities worldwide. Eliminating such infections requires a deeper understanding of the factors that enable the pathogen to persist in hospital environments, establish infections, and resist antibiotics. We present a set of resources that should accelerate genome-scale genetic characterization of these traits for a reference isolate of A. baumannii that is highly virulent and representative of current outbreak strains.A cinetobacter baumannii is a Gram-negative opportunistic pathogen that causes infections with serious morbidity and mortality and is one of a group of six pathogens responsible for most multidrug-resistant (MDR) nosocomial infections (the ESKAPE pathogens, i.e., Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) (1, 2). The pathogen is infamous for its ability to persist in hospital settings, a feature that reflects its capacity for long-term survival on abiotic surfaces through resistance to desiccation and disinfectants (3).Genomic and molecular epidemiological studies of A. baumannii isolates have helped define the pathogen's global population structure, its antibiotic resistance gene repertoire, the size and content of its pangenome, and phylogenetic relationships among outbreak strains (3-6). Three primary clonal lineages (GC1 to GC3) appear responsible for the majority of hospital outbreaks globally (7). Although these lineages display restricted genetic diversity among core genes (7), the species' genome is actually quite dynamic. Strains display striking variability in accessory gene content (5, 8), including antibiotic resistance genes (9), even among related isolates of a single outbreak (10). This genomic variability presumably reflects the actions of transmissible plasmids, insertion elements, phage, integrons, natural transformation, and reco...

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Genome organization of epidemic Acinetobacter baumannii strains

Cited by 84 publications

References 65 publications

Antibiotic Resistance Acquired through a DNA Damage-Inducible Response in Acinetobacter baumannii

Antibiotic Resistance Acquired through a DNA Damage-Inducible Response in Acinetobacter baumannii

Population Dynamics of an Acinetobacter baumannii Clonal Complex during Colonization of Patients

Resources for Genetic and Genomic Analysis of Emerging Pathogen Acinetobacter baumannii

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