1887

Abstract

Variable number tandem repeat (VNTR) analysis at nine loci of isolates of submitted to the national reference laboratory from UK hospitals, from over 2000 patients, between June 2010 and June 2012 revealed four widely found types that collectively were received from approximately a fifth of patients, including from those with cystic fibrosis. These types were also prevalent among related submissions from the clinical environment and were received from up to 54 (out of 143) hospitals. Multi-locus sequence typing and sequencing confirmed the clonal relationship within each cluster, and representatives from multiple centres clustered within about 70 % by pulsed-field gel electrophoresis. Illumina sequencing of 12 isolates of cluster A of VNTR profile 8, 3, 4, 5, 2, 3, 5, 2, (where the repeat number at the last, most discriminatory locus is variable) revealed a large number of variably present targets in the accessory genome and seven of these were sought by PCR among a larger set of isolates. Representatives from patients within a single centre mostly had distinct accessory gene profiles, suggesting that these patients acquired the strain independently, while those with clear epidemiological links shared the same profile. Profiles also varied between representatives from different centres. Epidemiological investigations of widely found types such as these require the use of finer-typing methods, which increasingly will be informed by next generation sequencing.

Loading

Article metrics loading...

/content/journal/jmm/10.1099/jmm.0.054841-0
2013-07-01
2020-08-05
Loading full text...

Full text loading...

/deliver/fulltext/jmm/62/7/988.html?itemId=/content/journal/jmm/10.1099/jmm.0.054841-0&mimeType=html&fmt=ahah

References

  1. Aaron S. D., Vandemheen K. L., Ramotar K., Giesbrecht-Lewis T., Tullis E., Freitag A., Paterson N., Jackson M., Lougheed M. D. et al. 2010; Infection with transmissible strains of Pseudomonas aeruginosa and clinical outcomes in adults with cystic fibrosis. JAMA 304:2145–2153 [CrossRef][PubMed]
    [Google Scholar]
  2. Armstrong D., Bell S., Robinson M., Bye P., Rose B., Harbour C., Lee C., Service H., Nissen M. et al. 2003; Evidence for spread of a clonal strain of Pseudomonas aeruginosa among cystic fibrosis clinics. J Clin Microbiol 41:2266–2267 [CrossRef][PubMed]
    [Google Scholar]
  3. Ashish A., Shaw M., Winstanley C., Ledson M. J., Walshaw M. J. 2012a; Increasing resistance of the Liverpool Epidemic Strain (LES) of Pseudomonas aeruginosa (Psa) to antibiotics in cystic fibrosis (CF)–a cause for concern?. J Cyst Fibros 11:173–179 [CrossRef][PubMed]
    [Google Scholar]
  4. Ashish A., Shaw M., McShane J., Ledson M. J., Walshaw M. J. 2012b; Health-related quality of life in cystic fibrosis patients infected with transmissible Pseudomonas aeruginosa strains: cohort study. JRSM Short Rep 3:12 [CrossRef][PubMed]
    [Google Scholar]
  5. Ballarini A., Scalet G., Kos M., Cramer N., Wiehlmann L., Jousson O. 2012; Molecular typing and epidemiological investigation of clinical populations of Pseudomonas aeruginosa using an oligonucleotide-microarray. BMC Microbiol 12:152 [CrossRef][PubMed]
    [Google Scholar]
  6. Cramer N., Wiehlmann L., Tümmler B. 2010; Clonal epidemiology of Pseudomonas aeruginosa in cystic fibrosis. Int J Med Microbiol 300:526–533 [CrossRef][PubMed]
    [Google Scholar]
  7. Cramer N., Klockgether J., Wrasman K., Schmidt M., Davenport C. F., Tümmler B. 2011; Microevolution of the major common Pseudomonas aeruginosa clones C and PA14 in cystic fibrosis lungs. Environ Microbiol 13:1690–1704 [CrossRef][PubMed]
    [Google Scholar]
  8. Cramer N., Wiehlmann L., Ciofu O., Tamm S., Høiby N., Tümmler B. 2012; Molecular epidemiology of chronic Pseudomonas aeruginosa airway infections in cystic fibrosis. PLoS ONE 7:e50731 [CrossRef][PubMed]
    [Google Scholar]
  9. Curran B., Jonas D., Grundmann H., Pitt T., Dowson C. G. 2004; Development of a multilocus sequence typing scheme for the opportunistic pathogen Pseudomonas aeruginosa. . J Clin Microbiol 42:5644–5649 [CrossRef][PubMed]
    [Google Scholar]
  10. Davies T. A., Marie Queenan A., Morrow B. J., Shang W., Amsler K., He W., Lynch A. S., Pillar C., Flamm R. K. 2011; Longitudinal survey of carbapenem resistance and resistance mechanisms in Enterobacteriaceae and non-fermenters from the USA in 2007–09. J Antimicrob Chemother 66:2298–2307 [CrossRef][PubMed]
    [Google Scholar]
  11. Delcher A. L., Bratke K. A., Powers E. C., Salzberg S. L. 2007; Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673–679 [CrossRef][PubMed]
    [Google Scholar]
  12. Fera M. T., Zummo S., de Sarro A. 2011; In vitro activity studies of doripenem and two other carbapenems tested against Pseudomonas aeruginosa and other non-fermentative bacilli. J Chemother 23:335–340[PubMed] [CrossRef]
    [Google Scholar]
  13. Fothergill J. L., Upton A. L., Pitt T. L., Hart C. A., Winstanley C. 2008; Diagnostic multiplex PCR assay for the identification of the Liverpool, Midlands 1 and Manchester CF epidemic strains of Pseudomonas aeruginosa . J Cyst Fibros 7:258–261 [CrossRef][PubMed]
    [Google Scholar]
  14. Fothergill J. L., White J., Foweraker J. E., Walshaw M. J., Ledson M. J., Mahenthiralingam E., Winstanley C. 2010; Impact of Pseudomonas aeruginosa genomic instability on the application of typing methods for chronic cystic fibrosis infections. J Clin Microbiol 48:2053–2059 [CrossRef][PubMed]
    [Google Scholar]
  15. Fothergill J. L., Walshaw M. J., Winstanley C. 2012; Transmissible strains of Pseudomonas aeruginosa in cystic fibrosis lung infections. Eur Respir J 40:227–238 [CrossRef][PubMed]
    [Google Scholar]
  16. Griffiths A. L., Wurzel D. F., Robinson P. J., Carzino R., Massie J. 2012; Australian epidemic strain pseudomonas (AES-1) declines further in a cohort segregated cystic fibrosis clinic. J Cyst Fibros 11:49–52 [CrossRef][PubMed]
    [Google Scholar]
  17. Jolley K. A., Chan M. S., Maiden M. C. 2004; mlstdbNet - distributed multi-locus sequence typing (MLST) databases. BMC Bioinformatics 5:86 [CrossRef]
    [Google Scholar]
  18. Jones A. M., Dodd M. E., Morris J., Doherty C., Govan J. R., Webb A. K. 2010; Clinical outcome for cystic fibrosis patients infected with transmissible Pseudomonas aeruginosa: an 8-year prospective study. Chest 137:1405–1409 [CrossRef][PubMed]
    [Google Scholar]
  19. Kerr K. G., Snelling A. M. 2009; Pseudomonas aeruginosa: a formidable and ever-present adversary. J Hosp Infect 73:338–344 [CrossRef][PubMed]
    [Google Scholar]
  20. Kidd T. J., Ritchie S. R., Ramsay K. A., Grimwood K., Bell S. C., Rainey P. B. 2012; Pseudomonas aeruginosa exhibits frequent recombination, but only a limited association between genotype and ecological setting. PLoS ONE 7:e44199 [CrossRef][PubMed]
    [Google Scholar]
  21. Kresse A. U., Blöcker H., Römling U. 2006; ISPa20 advances the individual evolution of Pseudomonas aeruginosa clone C subclone C13 strains isolated from cystic fibrosis patients by insertional mutagenesis and genomic rearrangements. Arch Microbiol 185:245–254 [CrossRef][PubMed]
    [Google Scholar]
  22. Li W., Godzik A. 2006; Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658–1659 [CrossRef][PubMed]
    [Google Scholar]
  23. Lister P. D., Wolter D. J., Hanson N. D. 2009; Antibacterial-resistant Pseudomonas aeruginosa: clinical impact and complex regulation of chromosomally encoded resistance mechanisms. Clin Microbiol Rev 22:582–610 [CrossRef][PubMed]
    [Google Scholar]
  24. Logan C., Habington A., Lennon G., Grogan J., Byrne M., O’Leary J., O’Sullivan N. 2012; Genetic relatedness of Pseudomonas aeruginosa isolates among a paediatric cystic fibrosis patient cohort in Ireland. J Med Microbiol 61:64–70 [CrossRef][PubMed]
    [Google Scholar]
  25. McPhail G. L., Acton J. D., Fenchel M. C., Amin R. S., Seid M. 2008; Improvements in lung function outcomes in children with cystic fibrosis are associated with better nutrition, fewer chronic Pseudomonas aeruginosa infections, and dornase alfa use. J Pediatr 153:752–757 [CrossRef][PubMed]
    [Google Scholar]
  26. Pirnay J. P., Bilocq F., Pot B., Cornelis P., Zizi M., Van Eldere J., Deschaght P., Vaneechoutte M., Jennes S. et al. 2009; Pseudomonas aeruginosa population structure revisited. PLoS ONE 4:e7740 [CrossRef][PubMed]
    [Google Scholar]
  27. Qin X., Zerr D. M., McNutt M. A., Berry J. E., Burns J. L., Kapur R. P. 2012; Pseudomonas aeruginosa syntrophy in chronically colonized airways of cystic fibrosis patients. Antimicrob Agents Chemother 56:5971–5981 [CrossRef][PubMed]
    [Google Scholar]
  28. Remold S. K., Brown C. K., Farris J. E., Hundley T. C., Perpich J. A., Purdy M. E. 2011; Differential habitat use and niche partitioning by Pseudomonas species in human homes. Microb Ecol 62:505–517 [CrossRef][PubMed]
    [Google Scholar]
  29. Römling U., Schmidt K. D., Tümmler B. 1997; Large genome rearrangements discovered by the detailed analysis of 21 Pseudomonas aeruginosa clone C isolates found in environment and disease habitats. J Mol Biol 271:386–404 [CrossRef][PubMed]
    [Google Scholar]
  30. Römling U., Kader A., Sriramulu D. D., Simm R., Kronvall G. 2005; Worldwide distribution of Pseudomonas aeruginosa clone C strains in the aquatic environment and cystic fibrosis patients. Environ Microbiol 7:1029–1038 [CrossRef][PubMed]
    [Google Scholar]
  31. Scott F. W., Pitt T. L. 2004; Identification and characterization of transmissible Pseudomonas aeruginosa strains in cystic fibrosis patients in England and Wales. J Med Microbiol 53:609–615 [CrossRef][PubMed]
    [Google Scholar]
  32. Tramper-Stranders G. A., van der Ent C. K., Wolfs T. F., Kimpen J. L., Fleer A., Johansen U., Johansen H. K., Høiby N. 2008; Pseudomonas aeruginosa diversity in distinct paediatric patient groups. Clin Microbiol Infect 14:935–941 [CrossRef][PubMed]
    [Google Scholar]
  33. Turton J. F., Turton S. E., Yearwood L., Yarde S., Kaufmann M. E., Pitt T. L. 2010; Evaluation of a nine-locus variable-number tandem-repeat scheme for typing of Pseudomonas aeruginosa. . Clin Microbiol Infect 16:1111–1116 [CrossRef][PubMed]
    [Google Scholar]
  34. van Mansfeld R., Jongerden I., Bootsma M., Buiting A., Bonten M., Willems R. 2010; The population genetics of Pseudomonas aeruginosa isolates from different patient populations exhibits high-level host specificity. PLoS ONE 5:e13482 [CrossRef][PubMed]
    [Google Scholar]
  35. Vu-Thien H., Corbineau G., Hormigos K., Fauroux B., Corvol H., Clément A., Vergnaud G., Pourcel C. 2007; Multiple-locus variable-number tandem-repeat analysis for longitudinal survey of sources of Pseudomonas aeruginosa infection in cystic fibrosis patients. J Clin Microbiol 45:3175–3183 [CrossRef][PubMed]
    [Google Scholar]
  36. Wiehlmann L., Wagner G., Cramer N., Siebert B., Gudowius P., Morales G., Köhler T., van Delden C., Weinel C. et al. 2007; Population structure of Pseudomonas aeruginosa. . Proc Natl Acad Sci U S A 104:8101–8106 [CrossRef][PubMed]
    [Google Scholar]
  37. Woodford N., Turton J. F., Livermore D. M. 2011; Multiresistant Gram-negative bacteria: the role of high-risk clones in the dissemination of antibiotic resistance. FEMS Microbiol Rev 35:736–755 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jmm/10.1099/jmm.0.054841-0
Loading
/content/journal/jmm/10.1099/jmm.0.054841-0
Loading

Data & Media loading...

Most cited this month 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