Phenotypic and genomic characterization of <i>Pseudomonas aeruginosa</i> isolates recovered from catheter-associated urinary tract infections in an Egyptian hospital.

"the present study shows how phenotypic analysis alongside genomic analysis may help us understand the amr and virulence profiles of p aeruginosa contributing to cautis in egypt multilocus sequence typing antimicrobial resistance biofilm formation virulence factors megaplasmid openaccessembargo 0 the draft genome sequences included in the study are available under bioproject prjna913392 .; table 2 pbt2436-like megaplasmid reference sequences included in this study plasmid species and strain size (bp) no of predicted genes * country source genbank accession reference(s) pbt2436 p aeruginosa 2436 422 811 537 thailand respiratory infection cp039989 [ ] pbt2101 p aeruginosa 2101 439 744 556 thailand respiratory infection cp039991 [ ] unnamed2 p aeruginosa ar_0356 438 531 557 unknown unknown cp027170 [ ] unnamed2 p aeruginosa ar439 437 392 549 unknown unknown cp029096 [ ] unnamed3 p aeruginosa ar441 438 529 560 unknown unknown cp029094 [ ] pjb37 p aeruginosa ffup_ps_37 464 804 597 portugal respiratory infection ky494864 [ ] pbm413 p aeruginosa pa121617 423 017 537 pr china respiratory infection cp016215 [ ] poz176 p aeruginosa pa96 500 839 621 pr china respiratory infection kc543497 [ ] p12939-oxa p aeruginosa (unknown) 496 436 607 pr china unknown mf344569 [ ] p727-imp p aeruginosa (unknown) 430 173 534 pr china unknown mf344568 [ ] pa681-imp p aeruginosa (unknown) 397 519 486 pr china unknown mf344570 [ ] pr31014-imp p aeruginosa (unknown) 374 000 456 pr china unknown mf344571 [ ] prbl16 p citronellolis sjte-3 370 338 486 pr china wastewater sludge cp015879 [ ] p1 p koreensis p19e3 467 568 598 switzerland origanum majorana cp027478 [ ] psy153-mdr p putida sy153 468 170 579 pr china urinary tract infection ky883660 [ ] *predicted in this study using bakta. supplementary data and material associated with this article are available from figshare at https://figshare com/projects/phenotypic_and_genomic_characterization_of_pseudomonas_aeruginosa_isolates_recovered_from_catheter-associated_urinary_tract_infections_in_an_egyptian_hospital/156639 .; the bakta-annotated whole-genome sequence data are available from figshare in genbank format.; the bakta-annotated plasmid sequence data are available from figshare in genbank format.; the bespoke r script associated with processing of the sequence data along with all output files are provided as supplementary material on figshare. table 2 ) blastn searches (supplementary material: blastn _hits_plasmids xlsx"

"fastani v1 33 [ ] was used to determine how similar the sequences of the newly identified megaplasmids were to those of pbt2436 and other reference genomes ( table 2 ); visualization of the conserved regions between pairs of plasmid sequences was achieved using the --visualize option of fastani and the r script available at https://github com/parbliss/fastani .; the bespoke r script associated with processing of the sequence data along with all output files are provided as supplementary material on figshare. the bespoke r script associated with processing of the sequence data along with all output files are provided as supplementary material on figshare."

"Conflicts of interest The authors declare that there are no conflicts of interest."

"Funding information This work was funded by The Egyptian Ministry of Higher Education and Scientific Research represented by The Egyptian Bureau for Cultural and Educational Affairs in London. Computing resources used in this study were funded through the Research Contingency Fund of Nottingham Trent University."