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Volume 5, Issue 7

Not all are equal: strains from industrial sources possess uniquely large multireplicon genomes Open Access

Abstract

is a highly versatile, antibiotic-resistant Gram-negative bacterium known for causing opportunistic infections and contamination of industrial products. Despite extensive genomic analysis of clinical strains, no genomes exist for preservative-tolerant industrial strains. A unique collection of 69 industrial isolates was assembled and compared to clinical and environmental strains; 16 genetically distinct industrial strains were subjected to array tube genotyping, multilocus sequence typing and whole-genome sequencing. The industrial strains possessed high preservative tolerance and were dispersed widely across as a species, but recurrence of strains from the same lineage within specific industrial products and locations was identified. The industrial genomes (mean=7.0 Mb) were significantly larger than those of previously sequenced environmental (mean=6.5 Mb; =19) and clinical (mean=6.6 Mb; =66) strains. Complete sequencing of the industrial strain RW109, which encoded the largest genome (7.75 Mb), revealed a multireplicon structure including a megaplasmid (555 265 bp) and large plasmid (151 612 bp). The RW109 megaplasmid represented an emerging plasmid family conserved in seven industrial and two clinical strains, and associated with extremely stress-resilient phenotypes, including antimicrobial resistance and solvent tolerance. Here, by defining the detailed phylogenomics of industrial strains, we show that they uniquely possess multireplicon, megaplasmid-bearing genomes, and significantly greater genomic content worthy of further study.

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  • Accepted:
  • Published Online:
Keyword(s): contamination , industry microbiology , megaplasmids , phylogenomics and Pseudomonas aeruginosa
© 2019 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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2019-06-06
2024-04-19
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References

  1. Pendleton JN, Gorman SP, Gilmore BF. Clinical relevance of the ESKAPE pathogens. Expert Rev Anti Infect Ther 2013; 11:297–308 [View Article]
     [Google Scholar]
  2. Lipuma JJ. The changing microbial epidemiology in cystic fibrosis. Clin Microbiol Rev 2010; 23:299–323 [View Article]
     [Google Scholar]
  3. Pirnay JP, Bilocq F, Pot B, Cornelis P, Zizi M et al. Pseudomonas aeruginosa population structure revisited. PLoS One 2009; 4:e7740 [View Article]
     [Google Scholar]
  4. Jimenez L. Microbial diversity in pharmaceutical product recalls and environments. PDA J Pharma Sci Technol 2007; 61:383–399
     [Google Scholar]
  5. White J, Gilbert J, Hill G, Hill E, Huse SM et al. Culture-independent analysis of bacterial fuel contamination provides insight into the level of concordance with the standard industry practice of aerobic cultivation. Appl Environ Microbiol 2011; 77:4527–4538 [View Article]
     [Google Scholar]
  6. Lundov MD, Moesby L, Zachariae C, Johansen JD. Contamination versus preservation of cosmetics: a review on legislation, usage, infections, and contact allergy. Contact Derm 2009; 60:70–78 [View Article]
     [Google Scholar]
  7. Stephenson JR, Heard SR, Richards MA, Tabaqchali S. Outbreak of septicaemia due to contaminated mouthwash. Br Med J 1984; 289:1584–1584 [View Article]
     [Google Scholar]
  8. Becks VE, Lorenzoni NM. Pseudomonas aeruginosa outbreak in a neonatal intensive care unit: a possible link to contaminated hand lotion. Am J Infect Control 1995; 23:396–398 [View Article]
     [Google Scholar]
  9. Reid FR, Wood TO. Pseudomonas corneal ulcer. the causative role of contaminated eye cosmetics. Arch Ophthalmol 1979; 97:1640–1641
     [Google Scholar]
  10. Steinberg DC. Regulatory review: 2010 frequency of preservative use. Cosmetics and Toiletries 2010; 125:46–51
     [Google Scholar]
  11. Neza E, Centini M. Microbiologically Contaminated and Over-Preserved Cosmetic Products According Rapex 2008–2014. Cosmetics 2016; 3:3 [View Article]
     [Google Scholar]
  12. Weiser R, Donoghue D, Weightman A, Mahenthiralingam E. Evaluation of five selective media for the detection of Pseudomonas aeruginosa using a strain panel from clinical, environmental and industrial sources. J Microbiol Methods 2014; 99:8–14 [View Article]
     [Google Scholar]
  13. De Soyza A, Hall AJ, Mahenthiralingam E, Drevinek P, Kaca W et al. Developing an international Pseudomonas aeruginosa reference panel. Microbiologyopen 2013; 2:1010–1023 [View Article]
     [Google Scholar]
  14. Cullen L, Weiser R, Olszak T, Maldonado RF, Moreira AS et al. Phenotypic characterization of an international Pseudomonas aeruginosa reference panel: strains of cystic fibrosis (CF) origin show less in vivo virulence than non-CF strains. Microbiology 2015; 161:1961–1977 [View Article]
     [Google Scholar]
  15. Winsor GL, Van Rossum T, Lo R, Khaira B, Whiteside MD et al. Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes. Nucleic Acids Res 2009; 37:D483–D488 [View Article]
     [Google Scholar]
  16. Mahenthiralingam E, Campbell ME, Foster J, Lam JS, Speert DP. Random amplified polymorphic DNA typing of Pseudomonas aeruginosa isolates recovered from patients with cystic fibrosis. J Clin Microbiol 1996; 34:1129–1135
     [Google Scholar]
  17. Wiehlmann L, Cramer N, Tümmler B. Habitat-associated skew of clone abundance in the Pseudomonas aeruginosa population. Environ Microbiol Rep 2015; 7:955–960 [View Article]
     [Google Scholar]
  18. Jolley KA, Maiden MCJ. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 2010; 11:595 [View Article]
     [Google Scholar]
  19. Rushton L, Sass A, Baldwin A, Dowson CG, Donoghue D et al. Key role for efflux in the preservative susceptibility and adaptive resistance of Burkholderia cepacia complex bacteria. Antimicrob. Agents Chemother. 2013; 57:2972–2980 [View Article]
     [Google Scholar]
  20. O'Toole GA. Microtiter dish biofilm formation assay. J Vis Exp 2011; 47: [View Article]
     [Google Scholar]
  21. Wiehlmann L, Wagner G, Cramer N, Siebert B, Gudowius P et al. Population structure of Pseudomonas aeruginosa . Proc Natl Acad Sci U S A 2007; 104:8101–8106 [View Article]
     [Google Scholar]
  22. Feil EJ, Li BC, Aanensen DM, Hanage WP, Spratt BG. eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J Bacteriol 2004; 186:1518–1530 [View Article]
     [Google Scholar]
  23. Song L, Jenner M, Masschelein J, Jones C, Bull MJ et al. Discovery and biosynthesis of gladiolin: A Burkholderia gladioli antibiotic with promising activity against Mycobacterium tuberculosis . J Am Chem Soc 2017; 139:7974–7981 [View Article]
     [Google Scholar]
  24. Curran B, Jonas D, Grundmann H, Pitt T, Dowson CG. Development of a multilocus sequence typing scheme for the opportunistic pathogen Pseudomonas aeruginosa . J Clin Microbiol 2004; 42:5644–5649 [View Article]
     [Google Scholar]
  25. Connor TR, Loman NJ, Thompson S, Smith A, Southgate J et al. CLIMB (the cloud Infrastructure for microbial bioinformatics): an online resource for the medical microbiology community. Microb Genom 2016; 2:e000086 [View Article]
     [Google Scholar]
  26. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article]
     [Google Scholar]
  27. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000; 28:33–36 [View Article]
     [Google Scholar]
  28. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007; 35:W182–W185 [View Article]
     [Google Scholar]
  29. Arndt D, Grant JR, Marcu A, Sajed T, Pon A et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016; 44:W16–W21 [View Article]
     [Google Scholar]
  30. Bertelli C, Laird MR, Williams KP, Lau BY, Hoad G et al. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res 2017; 45:W30–W35 [View Article]
     [Google Scholar]
  31. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article]
     [Google Scholar]
  32. Stothard P, Wishart DS. Circular genome visualization and exploration using CGView. Bioinformatics 2005; 21:537–539 [View Article]
     [Google Scholar]
  33. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: Rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article]
     [Google Scholar]
  34. Löytynoja A. Phylogeny-aware alignment with PRANK. Multiple sequence alignment methods 2014155–170
     [Google Scholar]
  35. Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 2009; 26:1641–1650 [View Article]
     [Google Scholar]
  36. McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA et al. The comprehensive antibiotic resistance database. Antimicrob. Agents Chemother. 2013; 57:3348–3357 [View Article]
     [Google Scholar]
  37. Letunic I, Bork P. Interactive tree of life (iTOL) V3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 2016; 44:W242–W245 [View Article]
     [Google Scholar]
  38. Stothard P, Grant JR, Van Domselaar G. Visualizing and comparing circular genomes using the CGView family of tools. Brief Bioinform 2017; 7: [View Article]
     [Google Scholar]
  39. Thomas CM, Haines AS, Koshleva IA, Boronin A. Pseudomonas plasmids. In Rehm BHA. editor Pseudomonas Model Organism, Pathogen, Cell Factory Weinheim, Germany: Wiley-VCH GmbH & Co; 2008 pp 293–330
     [Google Scholar]
  40. Li PE, Lo CC, Anderson JJ, Davenport KW, Bishop-Lilly KA et al. Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform. Nucleic Acids Res 2017; 45:67–80 [View Article]
     [Google Scholar]
  41. Rose H, Baldwin A, Dowson CG, Mahenthiralingam E. Biocide susceptibility of the Burkholderia cepacia complex. J Antimicrob Chemother 2009; 63:502–510 [View Article]
     [Google Scholar]
  42. Cramer N, Wiehlmann L, Ciofu O, Tamm S, Høiby N et al. Molecular epidemiology of chronic Pseudomonas aeruginosa airway infections in cystic fibrosis. PLoS One 2012; 7:e50731 [View Article]
     [Google Scholar]
  43. Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C et al. Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology 2012; 158:1005–1015 [View Article]
     [Google Scholar]
  44. Stewart L, Ford A, Sangal V, Jeukens J, Boyle B et al. Draft genomes of 12 host-adapted and environmental isolates of Pseudomonas aeruginosa and their positions in the core genome phylogeny. Pathog Dis 2014; 71:20–25 [View Article]
     [Google Scholar]
  45. Freschi L, Jeukens J, Kukavica-Ibrulj I, Boyle B, Dupont M-J et al. Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium. Front Microbiol 2015; 6:1036 [View Article]
     [Google Scholar]
  46. Kukavica-Ibrulj I, Bragonzi A, Paroni M, Winstanley C, Sanschagrin F et al. In vivo growth of Pseudomonas aeruginosa strains PAO1 and PA14 and the hypervirulent strain LESB58 in a rat model of chronic lung infection. J Bacteriol 2008; 190:2804–2813 [View Article]
     [Google Scholar]
  47. Petersen J. Phylogeny and compatibility: plasmid classification in the genomics era. Arch Microbiol 2011; 193:313–321 [View Article]
     [Google Scholar]
  48. Botelho J, Grosso F, Quinteira S, Mabrouk A, Peixe L. The complete nucleotide sequence of an IncP-2 megaplasmid unveils a mosaic architecture comprising a putative novel blaVIM-2-harbouring transposon in Pseudomonas aeruginosa . J Antimicrob Chemother 2017; 72:2225–2229 [View Article]
     [Google Scholar]
  49. Xiong J, Alexander DC, Ma JH, Déraspe M, Low DE et al. Complete sequence of pOZ176, a 500-kilobase IncP-2 plasmid encoding IMP-9-mediated carbapenem resistance, from outbreak isolate Pseudomonas aeruginosa 96. Antimicrob Agents Chemother 2013; 57:3775–3782 [View Article]
     [Google Scholar]
  50. McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA et al. The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 2013; 57:3348–3357 [View Article]
     [Google Scholar]
  51. Podnecky NL, Wuthiekanun V, Peacock SJ, Schweizer HP. The BpeEF-OprC efflux pump is responsible for widespread trimethoprim resistance in clinical and environmental Burkholderia pseudomallei isolates. Antimicrob Agents Chemother 2013; 57:4381–4386 [View Article]
     [Google Scholar]
  52. Gilbert P, McBain AJ. Potential impact of increased use of biocides in consumer products on prevalence of antibiotic resistance. Clin Microbiol Rev 2003; 16:189–208 [View Article]
     [Google Scholar]
  53. European Commission Scientific committee on emerging and newly identified health risks: effects of the active substances in biocidal products on antibiotic resistance; 2008
  54. Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P et al. Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 2000; 406:959–964 [View Article]
     [Google Scholar]
  55. Winstanley C, Langille MGI, Fothergill JL, Kukavica-Ibrulj I, Paradis-Bleau C et al. Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the liverpool epidemic strain of Pseudomonas aeruginosa . Genome Res 2009; 19:12–23 [View Article]
     [Google Scholar]
  56. Lee DG, Urbach JM, Wu G, Liberati NT, Feinbaum RL et al. Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial. Genome Biol 2006; 7:R90 [View Article]
     [Google Scholar]
  57. Roy PH, Tetu SG, Larouche A, Elbourne L, Tremblay S et al. Complete genome sequence of the multiresistant taxonomic outlier Pseudomonas aeruginosa PA7. PLoS One 2010; 5:e8842 [View Article]
     [Google Scholar]
  58. Stewart RMK, Wiehlmann L, Ashelford KE, Preston SJ, Frimmersdorf E et al. Genetic characterization indicates that a specific subpopulation of Pseudomonas aeruginosa is associated with keratitis infections. J Clin Microbiol 2011; 49:993–1003 [View Article]
     [Google Scholar]
  59. van Mansfeld R, Jongerden I, Bootsma M, Buiting A, Bonten M et al. The population genetics of Pseudomonas aeruginosa isolates from different patient populations exhibits high-level host specificity. PLoS One 2010; 5:e13482 [View Article]
     [Google Scholar]
  60. Selezska K, Kazmierczak M, Müsken M, Garbe J, Schobert M et al. Pseudomonas aeruginosa population structure revisited under environmental focus: impact of water quality and phage pressure. Environ Microbiol 2012; 14:1952–1967 [View Article]
     [Google Scholar]
  61. Haenni M, Hocquet D, Ponsin C, Cholley P, Guyeux C et al. Population structure and antimicrobial susceptibility of Pseudomonas aeruginosa from animal infections in France. BMC Vet Res 2015; 11:9 [View Article]
     [Google Scholar]
  62. Valot B, Guyeux C, Rolland JY, Mazouzi K, Bertrand X et al. What it takes to be a Pseudomonas aeruginosa? the core genome of the opportunistic pathogen updated. PLoS One 2015; 10:e0126468 [View Article]
     [Google Scholar]
  63. Mahenthiralingam E, Urban TA, Goldberg JB. The multifarious, multireplicon Burkholderia cepacia complex . Nat Rev Microbiol 2005; 3:144–156 [View Article]
     [Google Scholar]
  64. Yuan M, Chen H, Zhu X, Feng J, Zhan Z et al. pSY153-MDR, a p12969-DIM-related mega plasmid carrying bla IMP-45 and armA, from clinical Pseudomonas putida . Oncotarget 107 8:68439–68447
     [Google Scholar]
  65. Zheng D, Wang X, Wang P, Peng W, Ji N et al. Genome sequence of Pseudomonas citronellolis SJTE-3, an estrogen- and polycyclic aromatic hydrocarbon-degrading bacterium. Genome Announc 2016; 4: [View Article]
     [Google Scholar]
  66. Kuepper J, Ruijssenaars HJ, Blank LM, de Winde JH, Wierckx N. Complete genome sequence of solvent-tolerant Pseudomonas putida S12 including megaplasmid pTTS12. J Biotechnol 2015; 200:17–18 [View Article]
     [Google Scholar]
  67. Cazares R, Moore MP, Grimes M, Emond-Rheault JG, Wright LL et al. A megaplasmid family responsible for dissemination of multidrug resistance in Pseudomonas . BioRxiv 2019
     [Google Scholar]
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Not all Pseudomonas aeruginosa are equal: strains from industrial sources possess uniquely large multireplicon genomes
M Gen 5, e000276 (2019); https://doi.org/10.1099/mgen.0.000276
/content/journal/mgen/10.1099/mgen.0.000276
/content/journal/mgen/10.1099/mgen.0.000276
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