1887

Abstract

Twelve isolates recovered from 10 cystic fibrosis/other patient types and a variety of clinical sources, were referred to Canada's National Microbiology Laboratory over 7 years. These were assignable to the genus but were unidentifiable to species level. Patients included five males and five females from two geographically separated provinces, ranging in age from 2 months to 84 years. In contrast, most species described to date have been derived from water, plants or contaminated soils. By 16S rRNA gene sequencing, the patient strains had ≥99.4 % similarity to each other but only 97.73–98.29 % to their closest relatives, or . Bacteria were studied by whole genome sequencing using average nucleotide identity by n, digital DNA–DNA hybridization, average amino acid identity, core genome and single nucleotide variant analyses, MALDI-TOF, biochemical and cellular fatty acid analyses, and by antimicrobial susceptibility testing. Bacterial structures were assessed using scanning and transmission electron microscopy. Strains were strict aerobes, yellowish-pigmented, oxidative, non-motile, Gram-stain-negative bacilli and generally unable to reduce nitrate. Strains were susceptible to most of the antibiotics tested; some resistance was observed towards carbapenems, several cephems and uniformly to nitrofurantoin. The single taxon group observed by 16S rRNA gene sequencing was supported by whole genome sequencing; genomes ranged in size from 4.36 to 4.73 Mb and had an average G+C content of 69.12 mol%. Based on this study we propose the name sp. nov. for this cluster. DSM 18855, acquired for this study, was found to be non-motile phenotypically and by electron microscopy; we therefore propose the emendation of Young . 2007 to document that observation.

Funding
This study was supported by the:
  • Kathryn A. Bernard , Public Health Agency of Canada- A Base
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004533
2020-10-29
2020-11-25
Loading full text...

Full text loading...

References

  1. Finkmann W, Altendorf K, Stackebrandt E, Lipski A. Characterization of N2O-producing Xanthomonas-like isolates from biofilters as Stenotrophomonas nitritireducens sp. nov., Luteimonas mephitis gen. nov., sp. nov. and Pseudoxanthomonas broegbernensis gen. nov., sp. nov. Int J Syst Evol Microbiol 2000; 50 Pt 1:273–282 [CrossRef][PubMed]
    [Google Scholar]
  2. Thierry S, Macarie H, Iizuka T, Geißdörfer W, Assih EA et al. Pseudoxanthomonas mexicana sp. nov. and Pseudoxanthomonas japonensis sp. nov., isolated from diverse environments, and emended descriptions of the genus Pseudoxanthomonas Finkmann et al. 2000 and of its type species. Int J Syst Evol Microbiol 2004; 54:2245–2255 [CrossRef][PubMed]
    [Google Scholar]
  3. Kuo SF, Lee CH. An oil refinery worker at Kaohsiung, with Pseudoxanthomonas kaohsiungensis bloodstream infection presenting as chronic pericarditis and masquerading as tuberculosis pericarditis. J Microbiol Immunol Infect 2018; 51:575–577 [CrossRef][PubMed]
    [Google Scholar]
  4. Bernard KA, Shuttleworth L, Munro C, Forbes-Faulkner JC, Pitt D et al. Propionibacterium australiense sp. nov. derived from granulomatous bovine lesions. Anaerobe 2002; 8:41–47 [CrossRef]
    [Google Scholar]
  5. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
    [Google Scholar]
  6. Young CC, Ho MJ, Arun AB, Chen WM, Lai WA et al. Pseudoxanthomonas spadix sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2007; 57:1823–1827 [CrossRef][PubMed]
    [Google Scholar]
  7. Bernier AM, Bernard K. Draft genome sequence of Trueperella bernardiae LCDC 89-0504T, isolated from a human blood culture. Genome Announc 2016; 4:e01634-15 [CrossRef][PubMed]
    [Google Scholar]
  8. 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 [CrossRef][PubMed]
    [Google Scholar]
  9. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [CrossRef][PubMed]
    [Google Scholar]
  10. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J, Glockner O. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [CrossRef][PubMed]
    [Google Scholar]
  11. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [CrossRef][PubMed]
    [Google Scholar]
  12. Palmer M, Steenkamp ET, Blom J, Hedlund BP, Venter SN. All ANIs are not created equal: implications for prokaryotic species boundaries and integration of ANIs into polyphasic taxonomy. Int J Syst Evol Microbiol 2020; 70:2937–2948 [CrossRef][PubMed]
    [Google Scholar]
  13. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60-2105-14-60 [CrossRef][PubMed]
    [Google Scholar]
  14. Petkau A, Mabon P, Sieffert C, Knox NC, Cabral J et al. SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology. Microb Genom 2017; 3:e000116 [CrossRef][PubMed]
    [Google Scholar]
  15. 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 [CrossRef][PubMed]
    [Google Scholar]
  16. Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [CrossRef][PubMed]
    [Google Scholar]
  17. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118 [CrossRef]
    [Google Scholar]
  18. Bernard KA, Pacheco AL, Loomer C, Burdz T, Wiebe D et al. Corynebacterium lowii sp. nov. and Corynebacterium oculi sp. nov., derived from human clinical disease and an emended description of Corynebacterium mastitidis. Int J Syst Evol Microbiol 2016; 66:2803–2812 [CrossRef][PubMed]
    [Google Scholar]
  19. Weyant RS, Moss CW, Weaver RE, Hollis DG, Jordan JG et al. Identification of Unusual Pathogenic Gram-Negative Aerobic and Facultatively Anaerobic Bacteria, 2nd edn. Baltimore, MD: Williams & Wilkins; 1996
    [Google Scholar]
  20. Kittiwongwattana C, Thawai C. Pseudoxanthomonas helianthi sp. nov., isolated from roots of Jerusalem artichoke (Helianthus tuberosus). Int J Syst Evol Microbiol 2016; 66:5034–5038 [CrossRef][PubMed]
    [Google Scholar]
  21. Lee DS, Ryu SH, Hwang HW, Kim YJ, Park M et al. Pseudoxanthomonas sacheonensis sp. nov., isolated from BTEX-contaminated soil in Korea, transfer of Stenotrophomonas dokdonensis Yoon et al. 2006 to the genus Pseudoxanthomonas as Pseudoxanthomonas dokdonensis comb. nov. and emended description of the genus Pseudoxanthomonas. Int J Syst Evol Microbiol 2008; 58:2235–2240 [CrossRef][PubMed]
    [Google Scholar]
  22. Golding CG, Lamboo LL, Beniac DR, Booth TF. The scanning electron microscope in microbiology and diagnosis of infectious disease. Sci Rep 2016; 6:26516 [CrossRef][PubMed]
    [Google Scholar]
  23. Sasser M. MIDI technical note 101. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids MIDI, Newark: 1990 pp 1–6
    [Google Scholar]
  24. Patel NB, Tito RY, Obregón-Tito AJ, O'Neal L, Trujillo-Villaroel O et al. Ezakiella peruensis gen. nov., sp. nov. isolated from human fecal sample from a coastal traditional community in Peru. Anaerobe 2015; 32:43–48 [CrossRef][PubMed]
    [Google Scholar]
  25. Weinstein MP, Patel JB. Clinical Laboratory Standards Institute Performance Standards for Antimicrobial Susceptibility Testing; 28th Informational Supplement 250 Wayne, PA: CLSI document M100-S28. Wayne PA; 2018
    [Google Scholar]
  26. Cunha BA, Schoch PE, Hage JR. Nitrofurantoin: preferred empiric therapy for community-acquired lower urinary tract infections. Mayo Clin Proc 2011; 86:1243–1244 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004533
Loading
/content/journal/ijsem/10.1099/ijsem.0.004533
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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