The Novel Pseudomonas Putida Plasmid p12969-2 Harbors an In127-Carrying Multidrug-Resistant Region

References

• Fernandez M , PorcelM, De La TorreJet al. Analysis of the pathogenic potential of nosocomial Pseudomonas putida strains. Front. Microbiol. 6, 871 (2015).
   PubMed Web of Science ®Google Scholar
• Carpenter RJ , HartzellJD, ForsbergJA, BabelBS, GanesanA. Pseudomonas putida war wound infection in a US Marine: a case report and review of the literature.J. Infect.56 (4), 234–240 (2008).
   PubMed Web of Science ®Google Scholar
• Yoshino Y , KitazawaT, KamimuraM, TatsunoK, OtaY, YotsuyanagiH. Pseudomonas putida bacteremia in adult patients: five case reports and a review of the literature.J. Infect. Chemother.17 (2), 278–282 (2011).
   PubMed Web of Science ®Google Scholar
• Fass RJ , BarnishanJ, SolomonMC, AyersLW. In vitro activities of quinolones, β-lactams, tobramycin, and trimethoprim-sulfamethoxazole against nonfermentative gram-negative bacilli.Antimicrob. Agents Chemother.40 (6), 1412–1418 (1996).
   PubMed Web of Science ®Google Scholar
• Bhattacharya D , DeyS, KadamSet al. Isolation of NDM-1-producing multidrug-resistant Pseudomonas putida from a paediatric case of acute gastroenteritis, India. New Microbes New Infect. 5, 5–9 (2015).
   PubMedGoogle Scholar
• Bogaerts P , HuangTD, Rodriguez-VillalobosHet al. Nosocomial infections caused by multidrug-resistant Pseudomonas putida isolates producing VIM-2 and VIM-4 metallo-beta-lactamases. J. Antimicrob. Chemother. 61 (3), 749–751 (2008).
   PubMed Web of Science ®Google Scholar
• Lombardi G , LuzzaroF, DocquierJDet al. Nosocomial infections caused by multidrug-resistant isolates of Pseudomonas putida producing VIM-1 metallo-β-lactamase. J. Clin. Microbiol. 40 (11), 4051–4055 (2002).
   PubMed Web of Science ®Google Scholar
• Juan C , ZamoranoL, MenaA, AlbertiS, PerezJL, OliverA. Metallo-β-lactamase-producing Pseudomonas putida as a reservoir of multidrug resistance elements that can be transferred to successful Pseudomonas aeruginosa clones.J. Antimicrob. Chemother.65 (3), 474–478 (2010).
   PubMed Web of Science ®Google Scholar
• Molina L , UdaondoZ, DuqueEet al. Antibiotic resistance determinants in a Pseudomonas putida strain isolated from a hospital. PLoS ONE 9 (1), e81604 (2014).
   PubMed Web of Science ®Google Scholar
• Sun F , ZhouD, WangQet al. Genetic characterization of a novel blaDIM-2-carrying megaplasmid p12969-DIM from clinical Pseudomonas putida . J. Antimicrob. Chemother. 71 (4), 909–912 (2016).
   PubMed Web of Science ®Google Scholar
• Molina L , DuqueE, GomezMJet al. The pGRT1 plasmid of Pseudomonas putida DOT-T1E encodes functions relevant for survival under harsh conditions in the environment. Environ. Microbiol. 13 (8), 2315–2327 (2011).
   PubMed Web of Science ®Google Scholar
• Frank JA , ReichCI, SharmaS, WeisbaumJS, WilsonBA, OlsenGJ. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes.Appl. Environ. Microbiol.74 (8), 2461–2470 (2008).
   PubMed Web of Science ®Google Scholar
• Xiao X , ZhangJ, ZhangYet al. Two methods for extraction of high-purity genomic DNA from mucoid Gram-negative bacteria. Afric. J. Microbiol. Res. 5 (23), 4013–4018 (2011).
   Web of Science ®Google Scholar
• GeneMark . http://topaz.gatech.edu/GeneMark.
   Google Scholar
• Rapid Annotation Using Subsystem Technology (RAST) Server . http://rast.nmpdr.org/.
   Google Scholar
• Prodigal . http://prodigal.ornl.gov/.
   Google Scholar
• ExPASy – SIB Bioinformatics Resource Portal . UniProtKB/Swiss-Prot.http://web.expasy.org/docs/swiss-prot_guideline.html.
   Google Scholar
• MOTIF: Searching Protein Sequence Motifs . www.genome.jp/tools/motif/.
   Google Scholar
• INTERPROScan . Query page.http://129.175.105.74/genomics/lbmgeiprscan.html.
   Google Scholar
• The Comprehensive Antibiotic Resistance Database . http://arpcard.mcmaster.ca.
   Google Scholar
• Center for Genomic Epidemiology . ResFinder 2.1.https://cge.cbs.dtu.dk/services/ResFinder/.
   Google Scholar
• NCBI . How to submit β-Lactamse data.www.ncbi.nlm.nih.gov/pathogens/submit_beta_lactamase.
   Google Scholar
• BacMet: Antibacterial Biocide and Metal Resistance Genes Database . http://bacmet.biomedicine.gu.se/.
   Google Scholar
• ISfinder . https://www-is.biotoul.fr/.
   Google Scholar
• INTERGRALL – The Integron Database . http://integrall.bio.ua.pt/?.
   Google Scholar
• UCL – Eastman Dental Institute . Tn Number Registry.www.ucl.ac.uk/eastman/research/departments/microbial-diseases/tn.
   Google Scholar
• Group II Introns Database . http://webapps2.ucalgary.ca/∼groupii/blast.html.
   Google Scholar
• Inkscape . https://inkscape.org.
   Google Scholar
• Kholodii GY , YurievaOV, GorlenkoZet al. Tn5041: a chimeric mercury resistance transposon closely related to the toluene degradative transposon Tn4651. Microbiology 143 (Pt 8), 2549–2556 (1997).
   PubMedGoogle Scholar
• Hallet B , ArciszewskaLK, SherrattDJ. Reciprocal control of catalysis by the tyrosine recombinases XerC and XerD: an enzymatic switch in site-specific recombination.Mol. Cell4 (6), 949–959 (1999).
   PubMed Web of Science ®Google Scholar
• Gerdes K , Moller-JensenJ, Bugge JensenR. Plasmid and chromosome partitioning: surprises from phylogeny.Mol. Microbiol.37 (3), 455–466 (2000).
   PubMed Web of Science ®Google Scholar
• Mruk I , KobayashiI. To be or not to be: regulation of restriction–modification systems and other toxin-antitoxin systems.Nucleic Acids Res.42 (1), 70–86 (2014).
   PubMed Web of Science ®Google Scholar
• Van Melderen L , Saavedra De BastM. Bacterial toxin-antitoxin systems: more than selfish entities?PLoS Genet.5 (3), e1000437 (2009).
   PubMed Web of Science ®Google Scholar
• Fineran PC , BlowerTR, FouldsIJ, HumphreysDP, LilleyKS, SalmondGP. The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair.Proc. Natl Acad. Sci. USA106 (3), 894–899 (2009).
   PubMed Web of Science ®Google Scholar
• Zielenkiewicz U , CeglowskiP. The toxin-antitoxin system of the streptococcal plasmid pSM19035.J. Bacteriol.187 (17), 6094–6105 (2005).
   PubMed Web of Science ®Google Scholar
• Palmer BR , MarinusMG. The dam and dcm strains of Escherichia coli–a review.Gene143 (1), 1–12 (1994).
   PubMed Web of Science ®Google Scholar
• Li GM . Mechanisms and functions of DNA mismatch repair.Cell Res.18 (1), 85–98 (2008).
   PubMed Web of Science ®Google Scholar
• Goldsmith M , Sarov-BlatL, LivnehZ. Plasmid-encoded MucB protein is a DNA polymerase (pol RI) specialized for lesion bypass in the presence of MucA’, RecA, and SSB.Proc. Natl Acad. Sci. USA97 (21), 11227–11231 (2000).
   PubMed Web of Science ®Google Scholar
• Zhu H , ShumanS. A primer-dependent polymerase function of Pseudomonas aeruginosa ATP-dependent DNA ligase (LigD).J. Biol. Chem.280 (1), 418–427 (2005).
   PubMed Web of Science ®Google Scholar
• Gong C , MartinsA, BongiornoP, GlickmanM, ShumanS. Biochemical and genetic analysis of the four DNA ligases of mycobacteria.J. Biol. Chem.279 (20), 20594–20606 (2004).
   PubMed Web of Science ®Google Scholar
• Garcillan-Barcia MP , FranciaMV, De La CruzF. The diversity of conjugative relaxases and its application in plasmid classification.FEMS Microbiol. Rev.33 (3), 657–687 (2009).
   PubMed Web of Science ®Google Scholar
• Sexton JA , VogelJP. Type IVB secretion by intracellular pathogens.Traffic3 (3), 178–185 (2002).
   PubMed Web of Science ®Google Scholar
• Tsuda M , MinegishiK, IinoT. Toluene transposons Tn4651 and Tn4653 are class II transposons.J. Bacteriol.171 (3), 1386–1393 (1989).
   PubMed Web of Science ®Google Scholar
• Ilves H , HorakR, KivisaarM. Involvement of sigma(S) in starvation-induced transposition of Pseudomonas putida transposon Tn4652.J. Bacteriol.183 (18), 5445–5448 (2001).
   PubMed Web of Science ®Google Scholar
• Yano H , GenkaH, OhtsuboY, NagataY, TopEM, TsudaM. Cointegrate-resolution of toluene-catabolic transposon Tn4651: determination of crossover site and the segment required for full resolution activity.Plasmid69 (1), 24–35 (2013).
   PubMed Web of Science ®Google Scholar
• Maeda K , NojiriH, ShintaniM, YoshidaT, HabeH, OmoriT. Complete nucleotide sequence of carbazole/dioxin-degrading plasmid pCAR1 in Pseudomonas resinovorans strain CA10 indicates its mosaicity and the presence of large catabolic transposon Tn4676.J. Mol. Biol.326 (1), 21–33 (2003).
   PubMed Web of Science ®Google Scholar
• Delihas N . Impact of small repeat sequences on bacterial genome evolution.Genome Biol. Evol.3, 959–973 (2011).
   PubMed Web of Science ®Google Scholar
• Kholodii G , GorlenkoZ, MindlinS, HobmanJ, NikiforovV. Tn5041-like transposons: molecular diversity, evolutionary relationships and distribution of distinct variants in environmental bacteria.Microbiology148 (Pt 11), 3569–3582 (2002).
   PubMedGoogle Scholar
• RNAfold Software . http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi.
   Google Scholar
• Petrova M , GorlenkoZ, MindlinS. Tn5045, a novel integron-containing antibiotic and chromate resistance transposon isolated from a permafrost bacterium.Res. Microbiol.162 (3), 337–345 (2011).
   PubMed Web of Science ®Google Scholar
• Gillings MR . Integrons: past, present, and future.Microbiol. Mol. Biol. Rev.78 (2), 257–277 (2014).
   PubMed Web of Science ®Google Scholar
• Gillings M , BoucherY, LabbateMet al. The evolution of class 1 integrons and the rise of antibiotic resistance. J. Bacteriol. 190 (14), 5095–5100 (2008).
   PubMed Web of Science ®Google Scholar
• Branco R , ChungAP, JohnstonT, GurelV, MoraisP, ZhitkovichA. The chromate-inducible chrBACF operon from the transposable element TnOtChr confers resistance to chromium(VI) and superoxide.J. Bacteriol.190 (21), 6996–7003 (2008).
   PubMed Web of Science ®Google Scholar
• Zong Z . The complex genetic context of blaPER-1 flanked by miniature inverted-repeat transposable elements in Acinetobacter johnsonii .PLoS ONE9 (2), e90046 (2014).
   PubMed Web of Science ®Google Scholar
• Domingues S , TolemanMA, NielsenKM, Da SilvaGJ. Identical miniature inverted repeat transposable elements flank class 1 integrons in clinical isolates of Acinetobacter spp.J. Clin. Microbiol.51 (7), 2382–2384 (2013).
   PubMed Web of Science ®Google Scholar