1887

Microbial Genomics logo

Volume 7, Issue 9

The rise and the fall of a endemic lineage in a hospital Open Access

Abstract

The biological features that allow a pathogen to survive in the hospital environment are mostly unknown. The extinction of bacterial epidemics in hospitals is mostly attributed to changes in medical practice, including infection control, but the role of bacterial adaptation has never been documented. We analysed a collection of isolates belonging to the Besançon Epidemic Strain (BES), responsible for a 12year nosocomial outbreak, using a genotype-to-phenotype approach. Bayesian analysis estimated the emergence of the clone in the hospital 5 years before its opening, during the creation of its water distribution network made of copper. BES survived better than the reference strains PAO1 and PA14 in a copper solution due to a genomic island containing 13 metal-resistance genes and was specifically able to proliferate in the ubiquitous amoeba . Mutations affecting amino-acid metabolism, antibiotic resistance, lipopolysaccharide biosynthesis, and regulation were enriched during the spread of BES. Seven distinct regulatory mutations attenuated the overexpression of the genes encoding the efflux pump MexAB-OprM over time. The fitness of BES decreased over time in correlation with its genome size. Overall, the resistance to inhibitors and predators presumably aided the proliferation and propagation of BES in the plumbing system of the hospital. The pathogen further spread among patients via multiple routes of contamination. The decreased prevalence of patients infected by BES mirrored the parallel and convergent genomic evolution and reduction that affected bacterial fitness. Along with infection control measures, this may have participated in the extinction of BES in the hospital setting.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): bacterial pathogens , high-risk clone , outbreak and parallel evolution
Funding
This study was supported by the:
  • Conseil Régional de Franche-Comté
    • Principle Award Recipient: HélènePuja
  • Ministère de l’Enseignement Supérieur, de la Recherche Scientifique et des Technologies de l'Information et de la Communication
    • Principle Award Recipient: PauloJuarez
  • Conseil Régional de Franche-Comté
    • Principle Award Recipient: MariePetitjean
© 2021 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License.
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000629
2021-09-02
2024-04-25
Loading full text...

Full text loading...

/deliver/fulltext/mgen/7/9/mgen000629.html?itemId=/content/journal/mgen/10.1099/mgen.0.000629&mimeType=html&fmt=ahah

References

  1. Otter JA, Doumith M, Davies F, Mookerjee S, Dyakova E et al. Emergence and clonal spread of colistin resistance due to multiple mutational mechanisms in carbapenemase-producing Klebsiella pneumoniae in London. Sci Rep 2017; 7:12711 [View Article] [PubMed]
     [Google Scholar]
  2. Bertrand X, Bailly P, Blasco G, Balvay P, Boillot A et al. Large outbreak in a surgical intensive care unit of colonization or infection with Pseudomonas aeruginosa that overexpressed an active efflux pump. Clin Infect Dis 2000; 31:E9–E14 [View Article] [PubMed]
     [Google Scholar]
  3. Quick J, Cumley N, Wearn CM, Niebel M, Constantinidou C et al. Seeking the source of Pseudomonas aeruginosa infections in a recently opened hospital: an observational study using whole-genome sequencing. BMJ Open 2014; 4:e006278 [View Article] [PubMed]
     [Google Scholar]
  4. Eppinger M, Pearson T, Koenig SS, Pearson O, Hicks N et al. Genomic epidemiology of the Haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic. mBio 2014; 5:e01721 [View Article] [PubMed]
     [Google Scholar]
  5. Merker M, Blin C, Mona S, Duforet-Frebourg N, Lecher S et al. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nat Genet 2015; 47:242–249 [View Article] [PubMed]
     [Google Scholar]
  6. Mathee K, Narasimhan G, Valdes C, Qiu X, Matewish JM et al. Dynamics of Pseudomonas aeruginosa genome evolution. Proc Natl Acad Sci USA 2008; 105:3100–3105 [View Article] [PubMed]
     [Google Scholar]
  7. Koser CU, Holden MT, Ellington MJ, Cartwright EJ, Brown NM et al. Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N Engl J Med 2012; 366:2267–2275 [View Article] [PubMed]
     [Google Scholar]
  8. Buhl M, Kastle C, Geyer A, Autenrieth IB, Peter S et al. Molecular evolution of extensively drug-resistant (XDR) Pseudomonas aeruginosa strains from patients and hospital environment in a prolonged outbreak. Front Microbiol 2019; 10:1742 [View Article] [PubMed]
     [Google Scholar]
  9. Marsh JW, Mustapha MM, Griffith MP, Evans DR, Ezeonwuka C et al. Evolution of outbreak-causing carbapenem-resistant Klebsiella pneumoniae ST258 at a tertiary care hospital over 8 years. mBio 2019; 10: [View Article] [PubMed]
     [Google Scholar]
  10. French CE, Coope C, Conway L, Higgins JP, McCulloch J et al. Control of carbapenemase-producing Enterobacteriaceae outbreaks in acute settings: an evidence review. J Hosp Infect 2017; 95:3–45 [View Article] [PubMed]
     [Google Scholar]
  11. Aujoulat F, Roger F, Bourdier A, Lotthe A, Lamy B et al. From environment to man: genome evolution and adaptation of human opportunistic bacterial pathogens. Genes (Basel) 2012; 3:191–232 [View Article] [PubMed]
     [Google Scholar]
  12. Lyczak JB, Cannon CL, Pier GB. Establishment of Pseudomonas aeruginosa infection: lessons from a versatile opportunist. Microbes Infect 2000; 2:1051–1060 [View Article] [PubMed]
     [Google Scholar]
  13. Breidenstein EBM, de la Fuente-Núñez C, Hancock REW. Pseudomonas aeruginosa: all roads lead to resistance. Trends Microbiol 2011; 19:419–426 [View Article] [PubMed]
     [Google Scholar]
  14. CDC 2019. Antibiotic Resistance Threats in the United States. In Department of Health and Human Services, CDC U.S: Atlanta, GA; 2019
     [Google Scholar]
  15. Hota S, Hirji Z, Stockton K, Lemieux C, Dedier H et al. Outbreak of multidrug-resistant Pseudomonas aeruginosa colonization and infection secondary to imperfect intensive care unit room design. Infect Control Hosp Epidemiol 2009; 30:25–33 [View Article] [PubMed]
     [Google Scholar]
  16. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  17. Petitjean M, Martak D, Silvant A, Bertrand X, Valot B et al. Genomic characterization of a local epidemic Pseudomonas aeruginosa reveals specific features of the widespread clone ST395. Microb Genom 2017; 3:e000129 [View Article] [PubMed]
     [Google Scholar]
  18. Kolmogorov M, Raney B, Paten B, Pham S. Ragout - a reference-assisted assembly tool for bacterial genomes. Bioinformatics 2014; 30:i302–9 [View Article] [PubMed]
     [Google Scholar]
  19. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M et al. Versatile and open software for comparing large genomes. Genome Biol 2004; 5:R12 [View Article] [PubMed]
     [Google Scholar]
  20. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article] [PubMed]
     [Google Scholar]
  21. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
     [Google Scholar]
  22. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 2012; 67:2640–2644 [View Article] [PubMed]
     [Google Scholar]
  23. Chen L, Xiong Z, Sun L, Yang J, Jin Q. VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res 2012; 40:641–645
     [Google Scholar]
  24. Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 2014; 30:923–930 [View Article] [PubMed]
     [Google Scholar]
  25. Rohart F, Gautier B, Singh A, Lê Cao K-A. mixOmics: An R package for omics feature selection and multiple data integration. PLoS Comput Biol 2017; 13:e1005752 [View Article] [PubMed]
     [Google Scholar]
  26. Treepong P, Guyeux C, Meunier A, Couchoud C, Hocquet D et al. panISa: ab initio detection of insertion sequences in bacterial genomes from short read sequence data. Bioinformatics 2018; 34:3795–3800 [View Article] [PubMed]
     [Google Scholar]
  27. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 2012; 61:539–542 [View Article] [PubMed]
     [Google Scholar]
  28. Rambaut A, Lam TT, Max Carvalho L, Pybus OG. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen. Virus Evol 2016; 2:vew007 [View Article] [PubMed]
     [Google Scholar]
  29. Hocquet D, Nordmann P, El Garch F, Cabanne L, Plésiat P. Involvement of the MexXY-OprM efflux system in emergence of cefepime resistance in clinical strains of Pseudomonas aeruginosa. Antimicrob Agents Chemother 2006; 50:1347–1351 [View Article] [PubMed]
     [Google Scholar]
  30. CLSI Method for dilution antimicrobial susceptibility tests for bacteria that grow aerobically. In CLSI document M7-A10 Approved standard, 10th. edn Wayne, Pa: National Committee for Clinical Laboratory Standards; 2015
     [Google Scholar]
  31. Jeanvoine A, Meunier A, Puja H, Bertrand X, Valot B et al. Contamination of a hospital plumbing system by persister cells of a copper-tolerant high-risk clone of Pseudomonas aeruginosa. Water Res 2019; 157:579–586 [View Article] [PubMed]
     [Google Scholar]
  32. Thomas V, Herrera-Rimann K, Blanc DS, Greub G. Biodiversity of amoebae and amoeba-resisting bacteria in a hospital water network. Appl Environ Microbiol 2006; 72:2428–2438 [View Article] [PubMed]
     [Google Scholar]
  33. Horcajada JP, Montero M, Oliver A, Sorli L, Luque S et al. Epidemiology and treatment of multidrug-resistant and extensively drug-resistant Pseudomonas aeruginosa infections. Clin Microbiol Rev 2019; 32: [View Article] [PubMed]
     [Google Scholar]
  34. Deleo FR, Chen L, Porcella SF, Martens CA, Kobayashi SD et al. Molecular dissection of the evolution of carbapenem-resistant multilocus sequence type 258 Klebsiella pneumoniae. Proc Natl Acad Sci USA 2014; 111:4988–4993 [View Article] [PubMed]
     [Google Scholar]
  35. Marvig RL, Johansen HK, Molin S, Jelsbak L. Genome analysis of a transmissible lineage of Pseudomonas aeruginosa reveals pathoadaptive mutations and distinct evolutionary paths of hypermutators. PLoS Genet 2013; 9:e1003741 [View Article] [PubMed]
     [Google Scholar]
  36. Martin K, Baddal B, Mustafa N, Perry C, Underwood A et al. Clusters of genetically similar isolates of Pseudomonas aeruginosa from multiple hospitals in the UK. J Med Microbiol 2013; 62:988–1000 [View Article] [PubMed]
     [Google Scholar]
  37. Teixeira P, Tacao M, Alves A, Henriques I. Antibiotic and metal resistance in a ST395 Pseudomonas aeruginosa environmental isolate: A genomics approach. Mar Pollut Bull 2016; 110:75–81 [View Article] [PubMed]
     [Google Scholar]
  38. Schelstraete P, Van Daele S, De Boeck K, Proesmans M, Lebecque P et al. Pseudomonas aeruginosa in the home environment of newly infected cystic fibrosis patients. Eur Respir J 2008; 31:822–829 [View Article] [PubMed]
     [Google Scholar]
  39. Heirali A, McKeon S, Purighalla S, Storey DG, Rossi L et al. Assessment of the microbial constituents of the home environment of individuals with cystic fibrosis (CF) and their association with lower airways infections. PLoS One 2016; 11:e0148534 [View Article] [PubMed]
     [Google Scholar]
  40. Treepong P, Kos VN, Guyeux C, Blanc DS, Bertrand X et al. Global emergence of the widespread Pseudomonas aeruginosa ST235 clone. Clin Microbiol Infect 2018; 24:258–266 [View Article] [PubMed]
     [Google Scholar]
  41. Matz C, Kjelleberg S. Off the hook - how bacteria survive protozoan grazing. Trends Microbiol 2005; 13:302–307 [View Article] [PubMed]
     [Google Scholar]
  42. Thomas JM, Ashbolt NJ. Do free-living amoebae in treated drinking water systems present an emerging health risk. Environ Sci Technol 2011; 45:860–869 [View Article] [PubMed]
     [Google Scholar]
  43. Cateau E, Imbert C, Rodier MH. Hartmanella vermiformis can be permissive for Pseudomonas aeruginosa. Lett Appl Microbiol 2008; 47:475–477 [View Article] [PubMed]
     [Google Scholar]
  44. Hao X, Luthje F, Ronn R, German NA, Li X et al. A role for copper in protozoan grazing - two billion years selecting for bacterial copper resistance. Mol Microbiol 2016; 102:628–641
     [Google Scholar]
  45. Donlan RM, Forster T, Murga R, Brown E, Lucas C et al. Legionella pneumophila associated with the protozoan Hartmannella vermiformis in a model multi-species biofilm has reduced susceptibility to disinfectants. Biofouling 2005; 21:1–7 [View Article] [PubMed]
     [Google Scholar]
  46. Sun S, Noorian P, McDougald D. Dual role of mechanisms involved in resistance to predation by protozoa and virulence to humans. Front Microbiol 2018; 9:1017 [View Article] [PubMed]
     [Google Scholar]
  47. Department of Health UK Health Technical Memorandum 04-01 Part A: Design, Installation and Commissioning 2016
     [Google Scholar]
  48. Smith EE, Buckley DG, Wu Z, Saenphimmachak C, Hoffman LR et al. Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc Natl Acad Sci USA 2006; 103:8487–8492 [View Article] [PubMed]
     [Google Scholar]
  49. King JD, Kocincova D, Westman EL, Lam JS. Review: Lipopolysaccharide biosynthesis in Pseudomonas aeruginosa. Innate Immun 2009; 15:261–312 [View Article] [PubMed]
     [Google Scholar]
  50. Maldonado RF, Sa-Correia I, Valvano MA. Lipopolysaccharide modification in Gram-negative bacteria during chronic infection. FEMS Microbiol Rev 2016; 40:480–493 [View Article] [PubMed]
     [Google Scholar]
  51. Magiorakos AP, Srinivasan A, Carey RB, Carmeli Y, Falagas ME et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect 2012; 18:268–281 [View Article] [PubMed]
     [Google Scholar]
  52. Hocquet D, Bertrand X, Köhler T, Talon D, Plésiat P. Genetic and phenotypic variations of a resistant Pseudomonas aeruginosa epidemic clone. Antimicrob Agents Chemother 2003; 47:1887–1894 [View Article] [PubMed]
     [Google Scholar]
  53. Piddock LJ. Multidrug-resistance efflux pumps - not just for resistance. Nat Rev Microbiol 2006; 4:629–636 [View Article] [PubMed]
     [Google Scholar]
  54. Skurnik D, Roux D, Cattoir V, Danilchanka O, Lu X et al. Enhanced in vivo fitness of carbapenem-resistant oprD mutants of Pseudomonas aeruginosa revealed through high-throughput sequencing. Proc Natl Acad Sci USA 2013; 110:20747–20752 [View Article] [PubMed]
     [Google Scholar]
  55. Tian ZX, Yi X-X, Cho A, O’Gara F, Wang YP. CpxR activates MexAB-OprM efflux pump expression and enhances antibiotic resistance in both laboratory and clinical nalB-type isolates of Pseudomonas aeruginosa. PLoS Pathog 2016; 12:e1005932
     [Google Scholar]
  56. Hirakata Y, Kondo A, Hoshino K, Yano H, Arai K et al. Efflux pump inhibitors reduce the invasiveness of Pseudomonas aeruginosa. Int J Antimicrob Agents 2009; 34:343–346 [View Article] [PubMed]
     [Google Scholar]
  57. Sanchez P, Linares JF, Ruiz-Diez B, Campanario E, Navas A et al. Fitness of in vitro selected Pseudomonas aeruginosa nalB and nfxB multidrug resistant mutants. J Antimicrob Chemother 2002; 50:657–664 [View Article] [PubMed]
     [Google Scholar]
  58. Vettoretti L, Plesiat P, Muller C, El Garch F, Phan G et al. Efflux unbalance in Pseudomonas aeruginosa isolates from cystic fibrosis patients. Antimicrob Agents Chemother 2009; 53:1987–1997 [View Article] [PubMed]
     [Google Scholar]
  59. Hirakata Y, Srikumar R, Poole K, Gotoh N, Suematsu T et al. Multidrug efflux systems play an important role in the invasiveness of Pseudomonas aeruginosa. J Exp Med 2002; 196:109–118 [View Article] [PubMed]
     [Google Scholar]
  60. Hocquet D, Petitjean M, Rohmer L, Valot B, Kulasekara HD et al. Pyomelanin-producing Pseudomonas aeruginosa selected during chronic infections have a large chromosomal deletion which confers resistance to pyocins. Environ Microbiol 2016; 18:3482–3493 [View Article] [PubMed]
     [Google Scholar]
  61. Tsuchiya K, Cao YY, Kurokawa M, Ashino K, Yomo T et al. A decay effect of the growth rate associated with genome reduction in Escherichia coli. BMC Microbiol 2018; 18:101 [View Article] [PubMed]
     [Google Scholar]
  62. Binet R, Maurelli AT. Fitness cost due to mutations in the 16S rRNA associated with spectinomycin resistance in Chlamydia psittaci 6BC. Antimicrob Agents Chemother 2005; 49:4455–4464 [View Article] [PubMed]
     [Google Scholar]
  63. Rohr U, Weber S, Michel R, Selenka F, Wilhelm M. Comparison of free-living amoebae in hot water systems of hospitals with isolates from moist sanitary areas by identifying genera and determining temperature tolerance. Appl Environ Microbiol 1998; 64:1822–1824 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000629
Loading
The rise and the fall of a Pseudomonas aeruginosa endemic lineage in a hospital
M Gen 7, 000629 (2021); https://doi.org/10.1099/mgen.0.000629
/content/journal/mgen/10.1099/mgen.0.000629
/content/journal/mgen/10.1099/mgen.0.000629
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL

Supplementary material 3

EXCEL

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error