Not all Pseudomonas aeruginosa are equal: strains from industrial sources possess uniquely large multireplicon genomes

Weiser, Rebecca; Green, Angharad E; Bull, Matthew; Cunningham-Oakes, Edward; Jolley, Keith A.; Maiden, Martin C. J.; Hall, Amanda; Winstanley, Craig; Weightman, Andrew J.; Donoghue, Denise; Amézquita, Aléjandro; Connor, Thomas R.; Mahenthiralingam, Eshwar

doi:10.1099/mgen.0.000276

Cited by 31 publications

(46 citation statements)

References 63 publications

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“…Our findings indicated that members of the megaplasmid family are widely distributed geographically and have been isolated from various sources, both environmental (including sewage, sludge, high-arsenic soil, lake water, plant material and phenol treatment bioreactors) and clinical (including sputum, pneumonia, urine, faeces, blood, keratitis, cerebrospinal fluid and burn samples). Recent characterisation of P. aeruginosa industrial isolates carrying related megaplasmids further supports our observations on the wide distribution of the pBT2436-like family 36 . We were able to detect plasmid sequences highly similar to pBT2436 in genomes from at least six different Pseudomonas species.…”

Section: Discussionsupporting

confidence: 86%

A megaplasmid family driving dissemination of multidrug resistance in Pseudomonas

et al. 2020

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Multidrug resistance (MDR) represents a global threat to health. Here, we used whole genome sequencing to characterise Pseudomonas aeruginosa MDR clinical isolates from a hospital in Thailand. Using long-read sequence data we obtained complete sequences of two closely related megaplasmids (>420 kb) carrying large arrays of antibiotic resistance genes located in discrete, complex and dynamic resistance regions, and revealing evidence of extensive duplication and recombination events. A comprehensive pangenomic and phylogenomic analysis indicates that: 1) these large plasmids comprise an emerging family present in different members of the Pseudomonas genus, and associated with multiple sources (geographical, clinical or environmental); 2) the megaplasmids encode diverse niche-adaptive accessory traits, including multidrug resistance; 3) the accessory genome of the megaplasmid family is highly flexible and diverse. The history of the megaplasmid family, inferred from our analysis of the available database, suggests that members carrying multiple resistance genes date back to at least the 1970s.

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Section: Discussionsupporting

confidence: 86%

A megaplasmid family driving dissemination of multidrug resistance in Pseudomonas

et al. 2020

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“…Other pan-genome analysis in P. aeruginosa also found clusters than could be identi ed by the ST pro le (51,52).…”

Section: Discussionmentioning

confidence: 82%

“…While multiple comparative genomic analyses (many using a pan-genome approach) have been reported for P. aeruginosa (39,51,60,(52)(53)(54)(55)(56)(57)(58)(59), most of them include incomplete, fragmented or draft genomes, or sequences of few genes. In 2015, complete genomes were used in a similar approach, but only 17 genomes were available (NCBI), which only three corresponded to high-risk clones (57).…”

Section: Discussionmentioning

confidence: 99%

From Pan-genome to the Genomic Context of the Two Integrons of ST-111 Pseudomonas Aeruginosa AG1: A VIM-2-carrying Old-acquaintance and a Novel Imp-18-carrying Integron

Molina-Mora

Batán

García

2020

Preprint

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Background Pseudomonas aeruginosa is an opportunist and versatile organism responsible for infections among immunocompromised hosts. This pathogen has high intrinsic resistance to most antimicrobials, including critical strains due to resistance to carbapenems, a last-resort antibiotic. P. aeruginosa AG1 (PaeAG1) is a Costa Rican high-risk ST-111 strain with resistance to multiple antibiotics, including carbapenems due to the activity of both VIM-2 and IMP-18 metallo-β-lactamases (MBLs). These genes are harbored in two class 1 integrons, belonging to one out of the 57 PaeAG1 genomic islands. However, the genomic context related to these determinants in PaeAG1 and other P. aeruginosa strains is unclear. Thus, we implemented a comparative genomic approach to define and up-date the phylogenetic relationship among complete P. aeruginosa genomes using a pan-genome analysis. We also studied the PaeAG1 genomic islands content in other strains and the architecture of genomic regions around the VIM-2- and IMP-18-carrying integrons. Results With 211 strains, the up-dated P. aeruginosa pan-genome revealed that complete genome sequences are able to separate clones by MLST profile (ST), including a clear ST-111 cluster with PaeAG1. The PaeAG1 genomic islands were found to define a diverse presence/absence pattern among related genomes, but content was related to phylogenetic relationships. Finally, landscape reconstruction of specific genomic regions showed that VIM-2-carrying integron (In59-like) is an old-acquaintance element harbored in a known genomic region completely found in other two ST-111 strains. In addition, PaeAG1 has an exclusive genomic region containing a novel IMP-18-carrying integron (registered as In1666), with an arrangement never reported before. Conclusions We provide new insights about the genomic determinants associated with the resistance to carbapenems in the high-risk PaeAG1 using comparative genomics. With the pan-genome analysis and the comparison of PaeAG1 genomic islands in other strains, it was possible to describe the genomic landscape of the two MBLs-carrying integrons, including an old-acquaintance element carrying VIM-2 and a new IMP-18-carrying integron.

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“…However, due to the highly adaptive divergence within the GIs regions, the P. aeruginosa pan-genome is continuously extended. Nearly half of the new environmental and industrial isolates had new genotypes, indicating the wide geographically dispersing of the distinct clones [ 40 , 41 ].…”

Section: Resultsmentioning

confidence: 99%

“…Although P. aeruginosa PAEM, similar to the strains DSM 50071 T , PAO1, and LESB58, is included into the most represented P. aeruginosa phylogenetic group based on the whole-genome analysis [ 39 , 40 ], the comparable part of its genome (35 contigs) distinguishes from the DSM 50071 T and PAO1 genomes by 10 GIs, containing 122 and 151 CDSs, respectively ( Figure 4 ). Meanwhile, it distinguishes from LESB58 by 11 GIs, containing 160 CDSs, with the longest GI of 34497 bp, according to the analysis by IslandViewer 4 [ 38 ].…”

Section: Resultsmentioning

confidence: 99%

Genomic Features of a Food-Derived Pseudomonas aeruginosa Strain PAEM and Biofilm-Associated Gene Expression under a Marine Bacterial α-Galactosidase

Balabanova

Shkryl

Slepchenko

et al. 2020

IJMS

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The biofilm-producing strains of P. aeruginosa colonize various surfaces, including food products and industry equipment that can cause serious human and animal health problems. The biofilms enable microorganisms to evolve the resistance to antibiotics and disinfectants. Analysis of the P. aeruginosa strain (serotype O6, sequence type 2502), isolated from an environment of meat processing (PAEM) during a ready-to-cook product storage (−20 °C), showed both the mosaic similarity and differences between free-living and clinical strains by their coding DNA sequences. Therefore, a cold shock protein (CspA) has been suggested for consideration of the evolution probability of the cold-adapted P. aeruginosa strains. In addition, the study of the action of cold-active enzymes from marine bacteria against the food-derived pathogen could contribute to the methods for controlling P. aeruginosa biofilms. The genes responsible for bacterial biofilm regulation are predominantly controlled by quorum sensing, and they directly or indirectly participate in the synthesis of extracellular polysaccharides, which are the main element of the intercellular matrix. The levels of expression for 14 biofilm-associated genes of the food-derived P. aeruginosa strain PAEM in the presence of different concentrations of the glycoside hydrolase of family 36, α-galactosidase α-PsGal, from the marine bacterium Pseudoalteromonas sp. KMM 701 were determined. The real-time PCR data clustered these genes into five groups according to the pattern of positive or negative regulation of their expression in response to the action of α-galactosidase. The results revealed a dose-dependent mechanism of the enzymatic effect on the PAEM biofilm synthesis and dispersal genes.

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Not all Pseudomonas aeruginosa are equal: strains from industrial sources possess uniquely large multireplicon genomes

Cited by 31 publications

References 63 publications

A megaplasmid family driving dissemination of multidrug resistance in Pseudomonas

A megaplasmid family driving dissemination of multidrug resistance in Pseudomonas

From Pan-genome to the Genomic Context of the Two Integrons of ST-111 Pseudomonas Aeruginosa AG1: A VIM-2-carrying Old-acquaintance and a Novel Imp-18-carrying Integron

Genomic Features of a Food-Derived Pseudomonas aeruginosa Strain PAEM and Biofilm-Associated Gene Expression under a Marine Bacterial α-Galactosidase

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