Pseudomonas aeruginosa Genomic Structure and Diversity

Klockgether, Jens; Cramer, Nina; Wiehlmann, Lutz; Davenport, Colin; Tümmler, Burkhard

doi:10.3389/fmicb.2011.00150

Cited by 254 publications

(281 citation statements)

References 60 publications

(119 reference statements)

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“…ICEs are still remarkably poorly understood considering their wide distribution in bacterial genomes and importance among conjugative systems (7). The system we study here, ICEclc, is an example of an abundant ICE family in a wide variety of γ-and β-proteobacteria (14,17), among which are several P. aeruginosa isolates (10,11,41). Our results enable us to draw a number of conclusions about the basic steps in the behavior of the ICEclc family.…”

Section: Discussionmentioning

confidence: 85%

“…It has been estimated that conjugative systems of ICEs are more abundant among bacteria than those of plasmids (7), yet we know far less about ICE behavior because they are difficult to follow and isolate. ICEs have attracted interest because they can transmit antibiotic resistance genes (8) and suspected virulence factors (9)(10)(11), but also genes for toxic compound degradation (12,13) and heavy metal resistance (14). Several evolutionary distinct families of ICEs have been described, which have a mechanistically similar lifestyle (4,6,15).…”

mentioning

confidence: 99%

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Highly variable individual donor cell fates characterize robust horizontal gene transfer of an integrative and conjugative element

Delavat

Mitri

Pelet

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

106

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Horizontal gene transfer is an important evolutionary mechanism for bacterial adaptation. However, given the typical low transfer frequencies in a bacterial population, little is known about the fate and interplay of donor cells and the mobilized DNA during transfer. Here we study transfer of an integrative and conjugative element (ICE) among individual live bacterial cells. ICEs are widely distributed mobile DNA elements that are different than plasmids because they reside silent in the host chromosome and are maintained through vertical descent. Occasionally, ICEs become active, excise, and transmit their DNA to a new recipient, where it is reintegrated. We develop a fluorescent tool to differentiate excision, transfer, and reintegration of a model ICE named ICEclc (for carrying the clc genes for chlorocatechol metabolism) among single Pseudomonas cells by using timelapse microscopy. We find that ICEclc activation is initiated in stationary phase cells, but excision and transfer predominantly occur only when such cells have been presented with new nutrients. Donors with activated ICE develop a number of different states, characterized by reduced cell division rates or growth arrest, persistence, or lysis, concomitant with ICE excision, and likely, ICE loss or replication. The donor cell state transitions can be described by using a stochastic model, which predicts that ICE fitness is optimal at low initiation rates in stationary phase. Despite highly variable donor cell fates, ICE transfer is remarkably robust overall, with 75% success after excision. Our results help to better understand ICE behavior and shed a new light on bacterial cellular differentiation during horizontal gene transfer.

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Section: Discussionmentioning

confidence: 85%

mentioning

confidence: 99%

Highly variable individual donor cell fates characterize robust horizontal gene transfer of an integrative and conjugative element

Delavat

Mitri

Pelet

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

106

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“…First, it is observed that the %GC range of the core genes (1.78%) is more than 3 times greater than that of the next most diverse species, Pseudomonas aeruginosa (0.52%), which has an average genome size approximately four times that of G. vaginalis and is known to take up DNA from many other species (39). Next, it is observed that G. vaginalis possesses the smallest core genome, calculated by three different criteria, of any of the two dozen bacterial species for which there are eight or more high-quality draft or complete genomes available for comparative analyses.…”

Section: Discussionmentioning

confidence: 99%

Comparative Genomic Analyses of 17 Clinical Isolates of Gardnerella vaginalis Provide Evidence of Multiple Genetically Isolated Clades Consistent with Subspeciation into Genovars

et al. 2012

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Gardnerella vaginalis is associated with a spectrum of clinical conditions, suggesting high degrees of genetic heterogeneity among stains. Seventeen G. vaginalis isolates were subjected to a battery of comparative genomic analyses to determine their level of relatedness. For each measure, the degree of difference among the G. vaginalis strains was the highest observed among 23 pathogenic bacterial species for which at least eight genomes are available. Genome sizes ranged from 1.491 to 1.716 Mb; GC contents ranged from 41.18% to 43.40%; and the core genome, consisting of only 746 genes, makes up only 51.6% of each strain's genome on average and accounts for only 27% of the species supragenome. Neighbor-grouping analyses, using both distributed gene possession data and core gene allelic data, each identified two major sets of strains, each of which is composed of two groups. Each of the four groups has its own characteristic genome size, GC ratio, and greatly expanded core gene content, making the genomic diversity of each group within the range for other bacterial species. To test whether these 4 groups corresponded to genetically isolated clades, we inferred the phylogeny of each distributed gene that was present in at least two strains and absent in at least two strains; this analysis identified frequent homologous recombination within groups but not between groups or sets. G. vaginalis appears to include four nonrecombining groups/clades of organisms with distinct gene pools and genomic properties, which may confer distinct ecological properties. Consequently, it may be appropriate to treat these four groups as separate species.

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“…Depending on the sampling site, the P. aeruginosa clone ST309 displayed different but related pulsotypes, suggesting intraclonal genomic rearrangements. Comparative genomics of P. aeruginosa presents a picture of a mosaic genome with strain-specific segments that interrupt the core genome (24,46). As for other bacteria, genome composition and plasticity appear to be related to niche adaptation (24).…”

Section: Discussionmentioning

confidence: 99%

Pseudomonas aeruginosa and Achromobacter sp. Clonal Selection Leads to Successive Waves of Contamination of Water in Dental Care Units

Abdouchakour

Dupont

Grau

et al. 2015

Appl Environ Microbiol

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Dental care unit waterlines (DCUWs) consist of complex networks of thin tubes that facilitate the formation of microbial biofilms. Due to the predilection toward a wet environment, strong adhesion, biofilm formation, and resistance to biocides, Pseudomonas aeruginosa, a major human opportunistic pathogen, is adapted to DCUW colonization. Other nonfermentative Gramnegative bacilli, such as members of the genus Achromobacter, are emerging pathogens found in water networks. We reported the 6.5-year dynamics of bacterial contamination of waterlines in a dental health care center with 61 dental care units (DCUs) connected to the same water supply system. The conditions allowed the selection and the emergence of clones of Achromobacter sp. and P. aeruginosa characterized by multilocus sequence typing, multiplex repetitive elements-based PCR, and restriction fragment length polymorphism in pulsed-field gel electrophoresis, biofilm formation, and antimicrobial susceptibility. One clone of P. aeruginosa and 2 clones of Achromobacter sp. colonized successively all of the DCUWs: the last colonization by P. aeruginosa ST309 led to the closing of the dental care center. Successive dominance of species and clones was linked to biocide treatments. Achromobacter strains were weak biofilm producers compared to P. aeruginosa ST309, but the coculture of P. aeruginosa and Achromobacter enhanced P. aeruginosa ST309 biofilm formation. Intraclonal genomic microevolution was observed in the isolates of P. aeruginosa ST309 collected chronologically and in Achromobacter sp. clone A. The contamination control was achieved by a complete reorganization of the dental health care center by removing the connecting tubes between DCUs. D ental instruments on dental care units (DCUs), such as ultrasonic scalers, air scalers, and high-speed turbine dental handpieces, are cooled by DCU-supplied water, which also irrigates and cools the tooth surface during dental treatment (1). Water is also supplied to the DCU cup filler outlet used by patients for oral rinsing and to the bowl rinse outlet rinsing the DCU spittoon. Therefore, DCU waterlines (DCUWs) consist of a complex network formed by meters of narrow-bore plastic tubing of mostly 2-to 3-mm internal diameter. In narrow-bore tubes, a thin immobile layer of fluid, called the hydrodynamic boundary layer, exists at the interface of the lumen wall and the moving water (2). This hydrodynamic phenomenon is associated with water stagnation when the DCU is not used, and heating of water to at least 20°C enhances the development of microbial biofilm in the tubes (3).The DCUWs appear to be a technological niche in which complex interactions occur among members of the microbial community (4-6). Regarding bacteria, DCUWs have been shown to promote the formation of biofilm, predominantly seeded from environmental bacteria in the water supply (4-6). More rarely, human bacteria such as staphylococci or oral bacteria have been detected, indicating a retraction of oral fluids from the surgical devices to the wate...

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Pseudomonas aeruginosa Genomic Structure and Diversity

Cited by 254 publications

References 60 publications

Highly variable individual donor cell fates characterize robust horizontal gene transfer of an integrative and conjugative element

Highly variable individual donor cell fates characterize robust horizontal gene transfer of an integrative and conjugative element

Comparative Genomic Analyses of 17 Clinical Isolates of Gardnerella vaginalis Provide Evidence of Multiple Genetically Isolated Clades Consistent with Subspeciation into Genovars

Pseudomonas aeruginosa and Achromobacter sp. Clonal Selection Leads to Successive Waves of Contamination of Water in Dental Care Units

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