The Accessory Genome of
            <i>Pseudomonas aeruginosa</i>

Kung, Vanderlene L.; Ozer, Egon A.; Hauser, Alan R.

doi:10.1128/mmbr.00027-10

Cited by 276 publications

(340 citation statements)

References 236 publications

(237 reference statements)

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“…Gene contents in the low-GC-content regions implied the occurrence of horizontal gene transfer via prophage and transposases. The major features of typical phage islands were the presence of phage integrase, which performs integration of the phage elements, phage transcriptional regulators, helicase activity-possessing primase, and genes related to genome packaging, followed by many genes with unknown functions (21,22). In accordance with previous reports, some of the low-GC-content genomic regions were associated with phage-related sequences.…”

Section: Resultssupporting

confidence: 73%

Comparative Genomic and Transcriptomic Analyses Reveal Habitat Differentiation and Different Transcriptional Responses during Pectin Metabolism in Alishewanella Species

Jung

Park

2013

Appl Environ Microbiol

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Alishewanella species are expected to have high adaptability to diverse environments because they are isolated from different natural habitats. To investigate how the evolutionary history of Alishewanella species is reflected in their genomes, we performed comparative genomic and transcriptomic analyses of A. jeotgali, A. aestuarii, and A. agri, which were isolated from fermented seafood, tidal flat sediment, and soil, respectively. Genomic islands with variable GC contents indicated that invasion of prophage and transposition events occurred in A. jeotgali and A. agri but not in A. aestuarii. Habitat differentiation of A. agri from a marine environment to a terrestrial environment was proposed because the species-specific genes of A. agri were similar to those of soil bacteria, whereas those of A. jeotgali and A. aestuarii were more closely related to marine bacteria. Comparative transcriptomic analysis with pectin as a sole carbon source revealed different transcriptional responses in Alishewanella species, especially in oxidative stress-, methylglyoxal detoxification-, membrane maintenance-, and protease/chaperone activity-related genes. Transcriptomic and experimental data demonstrated that A. agri had a higher pectin degradation rate and more resistance to oxidative stress under pectin-amended conditions than the other 2 Alishewanella species. However, expression patterns of genes in the pectin metabolic pathway and of glyoxylate bypass genes were similar among all 3 Alishewanella species. Our comparative genomic and transcriptomic data revealed that Alishewanella species have evolved through horizontal gene transfer and habitat differentiation and that pectin degradation pathways in Alishewanella species are highly conserved, although stress responses of each Alishewanella species differed under pectin culture conditions.

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Section: Resultssupporting

confidence: 73%

Comparative Genomic and Transcriptomic Analyses Reveal Habitat Differentiation and Different Transcriptional Responses during Pectin Metabolism in Alishewanella Species

Jung

Park

2013

Appl Environ Microbiol

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“…GIs represent important components of the accessory genome of P. aeruginosa, mainly encoding catabolic pathways, virulence factors, and possibly also resistance determinants (21). However, few GIs associated with resistance genes have been described (18,(22)(23)(24), and only two of them have been fully sequenced (22,24).…”

Section: Geneticmentioning

confidence: 99%

Tn 6249 , a New Tn 6162 Transposon Derivative Carrying a Double-Integron Platform and Involved with Acquisition of the bla _VIM-1 Metallo-β-Lactamase Gene in Pseudomonas aeruginosa

Pilato

Pollini

Rossolini

2015

Antimicrob Agents Chemother

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cThe In70.2 integron platform appears to be a conserved structure involved in the dissemination of the bla VIM-1 metallo-␤-lactamase gene in Pseudomonas aeruginosa. The genetic context of the In70.2 integron platform from P. aeruginosa VR-143/97, the VIM-1-producing index strain isolated in Italy in 1997, was fully characterized by a next-generation sequencing approach refined by conventional sequencing. The In70.2 integron platform from VR-143/97 was found to be associated with a defective Tn402-like transposon inserted into the urf2 gene of a Tn3 family transposon of an original structure, named Tn6249, which also carried a partially deleted mer operon and an In90 integron platform in a tail-to-tail orientation. Tn6249 was inserted into a PACS171b-like genomic island, which was in turn inserted into the endA gene of the Pseudomonas chromosomal backbone. Tn6249 showed a similar structure and a conserved location with respect to that of Tn6060, a Tn3 family transposon associated with In70.2 and carrying a double-integron platform, which was detected in a VIM-1-producing P. aeruginosa strain isolated in Australia in 2008. Both Tn6249 and Tn6060 are apparently derived from Tn6162, a mercury resistance transposon carrying an integron platform, which was found in P. aeruginosa isolates from different geographic locations. The conservation of the genetic context of Tn6249 and Tn6060 suggests an in situ evolution of these elements after the insertion of a Tn6162-like ancestor into the PACS171b-like genomic island (GI) present in the genome of a successful widespread P. aeruginosa clonal lineage. Metallo-␤-lactamases (MBLs) have emerged as a major threat to antimicrobial chemotherapy due to their extended-spectrum activity against most ␤-lactams, including carbapenems, and their resistance to ␤-lactamase inhibitors, such as clavulanate, sulbactam, tazobactam, and avibactam (1). Among the several acquired MBLs reported in Gram-negative pathogens, the VIM-type enzymes have been detected worldwide in a large number of species, including Pseudomonas aeruginosa, other Gram-negative nonfermenters (GNNFs), and Enterobacteriaceae, and together with the IMP and NDM types, they are currently the MBLs with the greatest epidemiological and clinical impact (1-3). In P. aeruginosa, VIM-type enzymes are overall the most widespread and prevalent acquired MBLs (1, 4-7).Genes encoding VIM-type MBLs are usually carried on mobile gene cassettes associated with class 1 integron platforms (8), and integron-mediated cassette mobility has contributed to their dissemination, as indicated by the finding of bla VIM gene cassettes as part of different cassette arrays (9, 10). On the other hand, class 1 integron platforms are associated with functional or defective Tn402-like transposons, which preferentially target the res sites of plasmids and transposons of the Tn3 family (11-13), thus establishing genetic linkages that may further contribute to the mobility of the integron platforms (8).In P. aeruginosa VR-143/97, the bla VIM-1 index strain is...

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“…However, integrons accomplish mobility only when they are associated with a specific mobile genetic element, such as a transposon, conjugative plasmid, or genomic island (10). The genomic islands in P. aeruginosa are mostly integrative and conjugative elements (ICEs) and are named according to their characteristics, i.e., P. aeruginosa pathogenicity island or the name of their host, i.e., Liverpool epidemic strain genomic islands or, more broadly, i.e., P. aeruginosa genomic island (PAGI) (11). Thus far, 14 PAGIs have been identified (12).…”

mentioning

confidence: 99%

Clonal Dissemination of Pseudomonas aeruginosa Sequence Type 235 Isolates Carrying bla _IMP-6 and Emergence of bla _GES-24 and bla _IMP-10 on Novel Genomic Islands PAGI-15 and -16 in South Korea

Hong

Yoon

Lee

et al. 2016

Antimicrob Agents Chemother

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bA total of 431 Pseudomonas aeruginosa clinical isolates were collected from 29 general hospitals in South Korea in 2015. Antimicrobial susceptibility was tested by the disk diffusion method, and MICs of carbapenems were determined by the agar dilution method. Carbapenemase genes were amplified by PCR and sequenced, and the structures of class 1 integrons surrounding the carbapenemase gene cassettes were analyzed by PCR mapping. Multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were performed for strain typing. Whole-genome sequencing was carried out to analyze P. aeruginosa genomic islands (PAGIs) carrying the bla IMP-6 , bla IMP-10 , and bla GES-24 genes. The rates of carbapenem-nonsusceptible and carbapenemase-producing P. aeruginosa isolates were 34.3% (148/431) and 9.5% (41/431), respectively. IMP-6 was the most prevalent carbapenemase type, followed by VIM-2, IMP-10, and GES-24. All carbapenemase genes were located on class 1 integrons of 6 different types on the chromosome. All isolates harboring carbapenemase genes exhibited genetic relatedness by PFGE (similarity > 80%); moreover, all isolates were identified as sequence type 235 (ST235), with the exception of two ST244 isolates by MLST. The bla IMP-6 , bla IMP-10 , and bla GES-24 genes were found to be located on two novel PAGIs, designated PAGI-15 and PAGI-16. Our data support the clonal spread of an IMP-6-producing P. aeruginosa ST235 strain, and the emergence of IMP-10 and GES-24 demonstrates the diversification of carbapenemases in P. aeruginosa in Korea. Pseudomonas aeruginosa is an opportunistic pathogen that causes various nosocomial infections, including sepsis, pneumonia, and urinary tract infections (1). Treatment of P. aeruginosa infections is often difficult because of the intrinsic drug resistance of P. aeruginosa and the ability of this pathogen to acquire genes for antimicrobial resistance determinants (2). Carbapenems are used as last-resort drugs for the treatment of infections caused by multidrug-resistant P. aeruginosa, due to their high affinity for penicillin-binding proteins, stability to various ␤-lactamases, and ability to easily pass through the bacterial outer membrane. However, the increasing use of carbapenems has resulted in the emerging phenomenon of carbapenem resistance (3).P. aeruginosa can become resistant to carbapenems by reduced permeability of the outer membrane due to loss of substrate-specific outer membrane porin OprD, frequently accompanied by AmpC hyperproduction and overexpression of efflux systems (4), along with acquisition of genes encoding carbapenemases (5). While the molecular mechanism of carbapenem resistance is geographically variable, diverse classes of carbapenemase have been increasingly identified in P. aeruginosa, including class A (KPC and GES variants), class B (IMP, VIM, and NDM metallo-␤-lactamases [MBLs]), and class D (OXA variants) (6). The MBLs, in particular IMP and VIM enzymes, are the most widespread carbapenemases in P. aeruginosa (7), with IMP-6 exclusivel...

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The Accessory Genome of Pseudomonas aeruginosa

Cited by 276 publications

References 236 publications

Comparative Genomic and Transcriptomic Analyses Reveal Habitat Differentiation and Different Transcriptional Responses during Pectin Metabolism in Alishewanella Species

Comparative Genomic and Transcriptomic Analyses Reveal Habitat Differentiation and Different Transcriptional Responses during Pectin Metabolism in Alishewanella Species

Tn 6249 , a New Tn 6162 Transposon Derivative Carrying a Double-Integron Platform and Involved with Acquisition of the bla _VIM-1 Metallo-β-Lactamase Gene in Pseudomonas aeruginosa

Clonal Dissemination of Pseudomonas aeruginosa Sequence Type 235 Isolates Carrying bla _IMP-6 and Emergence of bla _GES-24 and bla _IMP-10 on Novel Genomic Islands PAGI-15 and -16 in South Korea

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The Accessory Genome of Pseudomonas aeruginosa

Cited by 276 publications

References 236 publications

Comparative Genomic and Transcriptomic Analyses Reveal Habitat Differentiation and Different Transcriptional Responses during Pectin Metabolism in Alishewanella Species

Comparative Genomic and Transcriptomic Analyses Reveal Habitat Differentiation and Different Transcriptional Responses during Pectin Metabolism in Alishewanella Species

Tn 6249 , a New Tn 6162 Transposon Derivative Carrying a Double-Integron Platform and Involved with Acquisition of the bla VIM-1 Metallo-β-Lactamase Gene in Pseudomonas aeruginosa

Clonal Dissemination of Pseudomonas aeruginosa Sequence Type 235 Isolates Carrying bla IMP-6 and Emergence of bla GES-24 and bla IMP-10 on Novel Genomic Islands PAGI-15 and -16 in South Korea

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Tn 6249 , a New Tn 6162 Transposon Derivative Carrying a Double-Integron Platform and Involved with Acquisition of the bla _VIM-1 Metallo-β-Lactamase Gene in Pseudomonas aeruginosa

Clonal Dissemination of Pseudomonas aeruginosa Sequence Type 235 Isolates Carrying bla _IMP-6 and Emergence of bla _GES-24 and bla _IMP-10 on Novel Genomic Islands PAGI-15 and -16 in South Korea