Diversity and Horizontal Transfer of Antarctic Pseudomonas spp. Plasmids

Romaniuk, Krzysztof; Styczyński, Michał; Decewicz, Przemysław; Buraczewska, Oliwia; Uhrynowski, Witold; Fondi, Marco; Wolosiewicz, Marcin; Szuplewska, Magdalena; Dziewit, Łukasz

doi:10.3390/genes10110850

Cited by 8 publications

(7 citation statements)

References 96 publications

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“…Based on an analysis of their replication systems, the plasmids were classified into the IncQ-3 subgroup. Interestingly, in all 16 strains various sets of plasmids accompanying IncQ-3 replicons were observed, which may exemplify HGT events among bacteria inhabiting the analyzed wastewater treatment plant, as observed previously for other environments [34][35][36]. Based on their genetic structure and gene load, the identified plasmids were divided into three groups: (i) p5.4_c4 and p115_p2, (ii) p458_p3 and p426_p3, (iii) p435_c4 ( Figure 1, Table 1).…”

Section: Structural and Functional Genomics Of Five Novel Incq Plasmidssupporting

confidence: 66%

Molecular Characterization and Comparative Genomics of IncQ-3 Plasmids Conferring Resistance to Various Antibiotics Isolated from a Wastewater Treatment Plant in Warsaw (Poland)

et al. 2020

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As small, mobilizable replicons with a broad host range, IncQ plasmids are widely distributed among clinical and environmental bacteria. They carry antibiotic resistance genes, and it has been shown that they confer resistance to β-lactams, fluoroquinolones, aminoglycosides, trimethoprim, sulphonamides, and tetracycline. The previously proposed classification system divides the plasmid group into four subgroups, i.e., IncQ-1, IncQ-2, IncQ-3, and IncQ-4. The last two subgroups have been poorly described so far. The aim of this study was to analyze five newly identified IncQ-3 plasmids isolated from a wastewater treatment plant in Poland and to compare them with all known plasmids belonging to the IncQ-3 subgroup whose sequences were retrieved from the NCBI database. The complete nucleotide sequences of the novel plasmids were annotated and bioinformatic analyses were performed, including identification of core genes and auxiliary genetic load. Furthermore, functional experiments testing plasmid mobility were carried out. Phylogenetic analysis based on three core genes (repA, mobA/repB, and mobC) revealed the presence of three main clusters of IncQ-3 replicons. Apart from having a highly conserved core, the analyzed IncQ-3 plasmids were vectors of antibiotic resistance genes, including (I) the qnrS2 gene that encodes fluoroquinolone resistance and (II) β-lactam, trimethoprim, and aminoglycoside resistance genes within integron cassettes.

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Section: Structural and Functional Genomics Of Five Novel Incq Plasmidssupporting

confidence: 66%

Molecular Characterization and Comparative Genomics of IncQ-3 Plasmids Conferring Resistance to Various Antibiotics Isolated from a Wastewater Treatment Plant in Warsaw (Poland)

et al. 2020

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“…In order to obtain a standard range, the length of the sequence was taken into account by the Romaniuk et al, 2019 article (18). We obtained 26 Pseudomonas aeruginosa plasmid sequences from the aforementioned screening, which are further considered for the AMR prediction.…”

Section: Methodsmentioning

confidence: 99%

Web-based Tool Validation for Antimicrobial Resistance Prediction: An Empirical Comparative Analysis

Routray

Sahoo

Nayak

et al. 2022

Preprint

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Global public health is seriously threatened by Antimicrobial Resistance (AMR), and there is an urgent need for quick and precise AMR diagnostic tools. The prevalence of novel Antibiotic Resistance Genes (ARGs) has increased substantially during the last decade, owing to the recent burden of microbial sequencing. The major problem is extracting vital information from the massive amounts of generated data. Even though there are many tools available to predict AMR, very few of them are accurate and can keep up with the unstoppable growth of data in the present. Here, we briefly examine a variety of AMR prediction tools that are available. We highlighted three potential tools from the perspective of the user experience that is preferable web-based AMR prediction analysis, as a web-based tool offers users accessibility across devices, device customization, system integration, eliminating the maintenance hassles, and provides enhanced flexibility and scalability. By using the Pseudomonas aeruginosa Complete Plasmid Sequence (CPS), we conducted a case study in which we identified the strengths and shortcomings of the system and empirically discussed its prediction efficacy of AMR sequences, ARGs, amount of information produced and visualisation. We discovered that ResFinder delivers a great amount of information regarding the ARGS along with improved visualisation. KmerResistance is useful for identifying resistance plasmids, obtaining information about related species and the template gene, as well as predicting ARGs. ResFinderFG does not provide any information about ARGs, but it predicts AMR determinants and has a better visualisation than KmerResistance.

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“…Different studies have shown that Pseudomonas spp. is the dominant genus among Arctic and Antarctic cultivable bacteria [23], owing to its metabolic versatility, low nutritional requirements, and ability to resist extreme environmental conditions [9] y [20]. These characteristics allow the species of this genus to colonize different ecological niches, as they have an r-strategy that allows them to grow rapidly on enriched media and successfully compete in h eterotro phic conditions [24].…”

Section: B Isolation Of Bacteria Producing Cold-active Enzymesmentioning

confidence: 99%

Pseudomonas strains from the Livingston Island, Antarctica: a source of cold-active hydrolytic enzymes

Rubiano-Labrador¹,

Acevedo-Barrios²,

Lazaro³

et al. 2022

Proceedings of the 20th LACCEI International Multi-Conference for Engineering, Education and Technology: “Education, Research A

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Pseudomonas spp. is considered one of the most successful bacterial genera due to its plasticity and meta bo lic ve rsatility, which has allowed it to colonize different ecosystems, including Antarctica. The ability of Pseudomonas to adapt a n d survive in the hostile conditions of the Antarctic makes them a re se rvoir of enzymes that can be used in different biotechnological applications; however, research on this genus in Antarctica is still in its infancy. Therefore, the aim of this study was to isolate and characterise cold-adapted Pseudomonas from Livingston Island, Antarctica, and expl ore t h eir a bi l it y to produce cold-active hydrolytic enzymes. In the present study, we isolated seven cold-adapted bacteria related to the genus Pseudomonas. The isolated strains have the ability to produce hydrolytic enzymes. These results demonstrate that cold-adapted Pseudomonas from Antarctica are a promising source of coldactive enzymes with biotechnological potential.

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Diversity and Horizontal Transfer of Antarctic Pseudomonas spp. Plasmids

Cited by 8 publications

References 96 publications

Molecular Characterization and Comparative Genomics of IncQ-3 Plasmids Conferring Resistance to Various Antibiotics Isolated from a Wastewater Treatment Plant in Warsaw (Poland)

Molecular Characterization and Comparative Genomics of IncQ-3 Plasmids Conferring Resistance to Various Antibiotics Isolated from a Wastewater Treatment Plant in Warsaw (Poland)

Web-based Tool Validation for Antimicrobial Resistance Prediction: An Empirical Comparative Analysis

Pseudomonas strains from the Livingston Island, Antarctica: a source of cold-active hydrolytic enzymes

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