1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 6

sp. nov., isolated from birds and water in New Zealand Open Access

Abstract

Six isolates of with similar non-standard colonial morphologies were identified during studies isolating from bird faeces and rivers in New Zealand. Genomic (16S rRNA gene sequencing and whole genome analysis) and phenotypic (MALDI-TOF analysis and conventional biochemical tests) showed that the isolates form a monophyletic clade with genetic relationships to / and /. They may be distinguished from other by their MALDI-TOF spectral pattern, their florid α-haemolysis, their ability to grow anaerobically at 37 °C, and on 2 % NaCl nutrient agar, and their lack of hippuricase. This study shows that these isolates represent a novel species within the genus for which the name sp. nov. is proposed. The presence of in water may be a confounder for freshwater microbial risk assessment as they may not be pathogenic for humans. The type strain is B423b (=NZRM 4741=ATCC TSD-167).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): birds , Campylobacter , genomics and New Zealand
Funding
This study was supported by the:
  • Marsden Fund (Award MAU0802)
    • Principle Award Recipient: Nigel French
© 2020 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004231
2020-06-05
2023-06-03
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/6/3775.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004231&mimeType=html&fmt=ahah

References

  1. Sebald M, Veron M. Teneur en bases de l’ADN et classification des vibrions. Ann Inst Pasteur 1963; 105:897–910
     [Google Scholar]
  2. Gilbert MJ, Zomer AL, Timmerman AJ, Spaninks MP, Rubio-García A et al. Campylobacter blaseri sp. nov., isolated from common seals (Phoca vitulina). Int J Syst Evol Microbiol 2018; 68:1787–1794 [View Article][PubMed]
     [Google Scholar]
  3. Samuel MC, Vugia DJ, Shallow S, Marcus R, Segler S et al. Epidemiology of sporadic Campylobacter infection in the United States and declining trend in incidence, FoodNet 1996–1999. Clin Infect Dis 2004; 38:S165–S174 [View Article][PubMed]
     [Google Scholar]
  4. Baker M, Wilson N, Edwards R. Campylobacter infection and chicken: an update on New Zealand’s largest ‘common source outbreak’. N Z Med J 2007; 120:75–79
     [Google Scholar]
  5. Waldenström J, Broman T, Carlsson I, Hasselquist D, Achterberg RP et al. Prevalence of Campylobacter jejuni, Campylobacter lari, and Campylobacter coli in different ecological guilds and taxa of migrating birds. Appl Environ Microbiol 2002; 68:5911–5917 [View Article][PubMed]
     [Google Scholar]
  6. Newell DG, Fearnley C. Sources of Campylobacter colonization in broiler chickens. Appl Environ Microbiol 2003; 69:4343–4351 [View Article][PubMed]
     [Google Scholar]
  7. Debruyne L, Broman T, Bergström S, Olsen B, On SLW et al. Campylobacter subantarcticus sp. nov., isolated from birds in the sub-Antarctic region. Int J Syst Evol Microbiol 2010; 60:815–819 [View Article][PubMed]
     [Google Scholar]
  8. Benskin CMH, Rhodes G, Pickup RW, Wilson K, Hartley IR. Diversity and temporal stability of bacterial communities in a model passerine bird, the zebra finch. Mol Ecol 2010; 19:5531–5544 [View Article][PubMed]
     [Google Scholar]
  9. Carter PE, McTavish SM, Brooks HJL, Campbell D, Collins-Emerson JM et al. Novel clonal complexes with an unknown animal reservoir dominate Campylobacter jejuni isolates from river water in New Zealand. Appl Environ Microbiol 2009; 75:6038–6046 [View Article][PubMed]
     [Google Scholar]
  10. French N, Yu S, Biggs P, Holland B, Fearnhead P et al. Evolution of Campylobacter species in New Zealand. In Sheppard SK. editor Campylobacter Ecology and Evolution Caister Academic Press; 2014 pp 221–240
     [Google Scholar]
  11. Mohan V, Stevenson M, Marshall J, Fearnhead P, Holland BR et al. Campylobacter jejuni colonization and population structure in urban populations of ducks and starlings in New Zealand. Microbiologyopen 2013; 2:659–673 [View Article][PubMed]
     [Google Scholar]
  12. Mullner P, Shadbolt T, Collins-Emerson JM, Midwinter AC, Spencer SEF et al. Molecular and spatial epidemiology of human campylobacteriosis: source association and genotype-related risk factors. Epidemiol Infect 2010; 138:1372–1383 [View Article][PubMed]
     [Google Scholar]
  13. Wilkinson DA, O'Donnell AJ, Akhter RN, Fayaz A, Mack HJ et al. Updating the genomic taxonomy and epidemiology of Campylobacter hyointestinalis . Sci Rep 2018; 8:2393 [View Article][PubMed]
     [Google Scholar]
  14. Bojanić K, Midwinter AC, Marshall JC, Biggs PJ, Acke E et al. Isolation of emerging Campylobacter species in working farm dogs and their frozen home-killed raw meat diets. J Vet Diagn Invest 2019; 31:23–32 [View Article][PubMed]
     [Google Scholar]
  15. Bojanić K, Midwinter AC, Marshall JC, Rogers LE, Biggs PJ et al. Isolation of Campylobacter spp. from client-owned dogs and cats, and retail raw meat pet food in the Manawatu, New Zealand. Zoonoses Public Health 2017; 64:438–449 [View Article][PubMed]
     [Google Scholar]
  16. McBride G, Till D, Ryan T, Ball A, Lewis G et al. Pathogen occurence and human health risk assessment analysis; 2002
  17. Nohra A, Grinberg A, Midwinter AC, Marshall JC, Collins-Emerson JM et al. Molecular epidemiology of Campylobacter coli strains isolated from different sources in New Zealand between 2005 and 2014. Appl Environ Microbiol 2016; 82:AEM.00934-16 [View Article][PubMed]
     [Google Scholar]
  18. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chicester: John Wiley & Sons; 1991 pp 115–175
     [Google Scholar]
  19. Wilkinson DA, Midwinter AC, Kwan E, Bloomfield SJ, French NP et al. Draft whole-genome sequences of three isolates of a novel strain of a Campylobacter sp. isolated from New Zealand birds and water. Microbiol Resour Announc 2019; 8:1–2 [View Article][PubMed]
     [Google Scholar]
  20. Katoh K, Rozewicki J, Yamada KD. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform 2019; 20:1160–1166 [View Article][PubMed]
     [Google Scholar]
  21. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
     [Google Scholar]
  22. Taylor DE, Eaton M, Yan W, Chang N. Genome maps of Campylobacter jejuni and Campylobacter coli . J Bacteriol 1992; 174:2332–2337 [View Article][PubMed]
     [Google Scholar]
  23. Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A et al. Geneious.
  24. Debruyne L, Gevers D, Vandamme P. Taxonomy of the family Campylobacteraceae . In Nachamkin I, Szymanski C, Blaser M. (editors) Campylobacter Washington, DC, USA: ASM Press; 2008 pp 3–26
     [Google Scholar]
  25. Van TTH, Elshagmani E, Gor MC, Scott PC, Moore RJ. Campylobacter hepaticus sp. nov., isolated from chickens with spotty liver disease. Int J Syst Evol Microbiol 2016; 66:4518–4524 [View Article][PubMed]
     [Google Scholar]
  26. 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 [View Article][PubMed]
     [Google Scholar]
  27. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
     [Google Scholar]
  28. 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][PubMed]
     [Google Scholar]
  29. Hunt M, Mather AE, Sánchez-Busó L, Page AJ, Parkhill J et al. ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads. Microb Genom 2017; 3:1–11 [View Article][PubMed]
     [Google Scholar]
  30. 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]
  31. Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 2014; 58:3895–3903 [View Article][PubMed]
     [Google Scholar]
  32. Chen L, Yang J, Yu J, Yao Z, Sun L et al. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 2005; 33:D325–D328 [View Article][PubMed]
     [Google Scholar]
  33. Wong A, Lange D, Houle S, Arbatsky NP, Valvano MA et al. Role of capsular modified heptose in the virulence of Campylobacter jejuni . Mol Microbiol 2015; 96:1136–1158 [View Article][PubMed]
     [Google Scholar]
  34. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
     [Google Scholar]
  35. Yu G, Smith DK, Zhu H, Guan Y, Lam Tommy Tsan‐Yuk, Lam TT. ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol 2017; 8:28–36 [View Article]
     [Google Scholar]
  36. RStudio Team RStudio: integrated development environment for R; 2015
  37. Koziel M, O'Doherty P, Vandamme P, Corcoran GD, Sleator RD et al. Campylobacter corcagiensis sp. nov., isolated from faeces of captive lion-tailed macaques (Macaca silenus). Int J Syst Evol Microbiol 2014; 64:2878–2883 [View Article][PubMed]
     [Google Scholar]
  38. Gibb S, Strimmer K. MALDIquant: a versatile R package for the analysis of mass spectrometry data. Bioinformatics 2012; 28:2270–2271 [View Article]
     [Google Scholar]
  39. Ahdesmäki M, Strimmer K. Feature selection in omics prediction problems using cat scores and false nondiscovery rate control. Ann Appl Stat 2010; 4:503–519 [View Article]
     [Google Scholar]
  40. Strimmer K. Package ‘crossval’ Title Generic Functions for Cross Validation; 2015
  41. Wheeler NE, Blackmore T, Reynolds AD, Midwinter AC, Marshall J et al. Genomic correlates of extraintestinal infection are linked with changes in cell morphology in Campylobacter jejuni . Microb Genom 2019; 5:1–12 [View Article][PubMed]
     [Google Scholar]
  42. Champion OL, Karlyshev AV, Senior NJ, Woodward M, La Ragione R et al. Insect infection model for Campylobacter jejuni reveals that O-methyl phosphoramidate has insecticidal activity. J Infect Dis 2010; 201:776–782 [View Article][PubMed]
     [Google Scholar]
  43. Moran AP, Upton ME. Effect of medium supplements, illumination and superoxide dismutase on the production of coccoid forms of Campylobacter jejuni ATCC 29428. J Appl Bacteriol 1987; 62:43–51 [View Article][PubMed]
     [Google Scholar]
  44. Atlas R, Snyder J. Reagents, stains and media: Bacteriology. In Jorgensen JH, Pfaller MA. (editors) Manual of Clinical Microbiology American Society for Microbiology; 2015
     [Google Scholar]
  45. MacFaddin JF. Biochemical Tests for Identification of Medical Bacteria, 3rd ed. Philadelphia, USA: Lippincott Williams & Wilkins; 2000
     [Google Scholar]
  46. On SL, Holmes B. Assessment of enzyme detection tests useful in identification of campylobacteria. J Clin Microbiol 1992; 30:746–749[PubMed]
     [Google Scholar]
  47. Ma M, Amano T, Enokimoto M, Yano T, Moe KK et al. Influence of pH of TSI medium on the detection of hydrogen sulfide production by Campylobacter hyointestinalis . Lett Appl Microbiol 2007; 44:544–549 [View Article][PubMed]
     [Google Scholar]
  48. Sifré E, Salha BA, Ducournau A, Floch P, Chardon H et al. EUCAST recommendations for antimicrobial susceptibility testing applied to the three main Campylobacter species isolated in humans. J Microbiol Methods 2015; 119:206–213 [View Article][PubMed]
     [Google Scholar]
  49. On SL, Holmes B. Reproducibility of tolerance tests that are useful in the identification of campylobacteria. J Clin Microbiol 1991; 29:1785–1788[PubMed]
     [Google Scholar]
  50. Al-Edany AA, Khudor MH, Radhi LY. Isolation, identification and toxigenic aspects of Campylobacter jejuni isolated from slaughtered cattle and sheep at Basrah city. Basrah J Vet Res 2015; 14:316–327
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004231
Loading
Campylobacter novaezeelandiae sp. nov., isolated from birds and water in New Zealand
Int J Syst Evol Microbiol 70, 3775 (2020); https://doi.org/10.1099/ijsem.0.004231
/content/journal/ijsem/10.1099/ijsem.0.004231
/content/journal/ijsem/10.1099/ijsem.0.004231
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

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