Arcobacter lanthieri sp. Nov., isolated from pig and dairy cattle manure

International Journal of Systematic and Evolutionary Microbiology

Volumn 65, Issue 8, 2015, Pages 2709-2716

  Whiteduck Léveillée, Kerri ^a   Whiteduck Léveillée, Jenni ^a   Cloutier, Michel ^a   Tambong, James T ^a   Xu, Renlin ^a   Topp, Edward ^b   Arts, Michael T ^c   Chao, Jerry ^d   Adam, Zaky ^a   Lévesque, C André ^a   Lapen, David R ^a   Villemur, Richard ^e   Talbot, Guylaine ^f   Khan, Izhar U H ^a  

^a OTTAWA RESEARCH AND DEVELOPMENT CENTRE   (Canada)

^b AGRICULTURE AND AGRI FOOD CANADA   (Canada)

^c RYERSON UNIVERSITY   (Canada)

^d ONTARIO MINISTRY OF THE ENVIRONMENT   (Canada)

^e INRS INSTITUT ARMAND FRAPPIER   (Canada)

^f SHERBROOKE RESEARCH AND DEVELOPMENT CENTRE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ACETOIN; ALPHA AMINO 5 TERT BUTYL 3 HYDROXY 4 ISOXAZOLEPROPIONIC ACID; DNA TOPOISOMERASE (ATP HYDROLYSING) B; NITRITE; RNA 16S; RNA POLYMERASE BETA SUBUNIT; BACTERIAL DNA; FATTY ACID; MANURE;

ANTIBIOTIC RESISTANCE; ARCOBACTER; ARCOBACTER BUTZLERI; ARCOBACTER LANTHIERI; ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM ISOLATE; BACTERIUM ISOLATION; CONTROLLED STUDY; DAIRY CATTLE; DNA BASE COMPOSITION; DNA DNA HYBRIDIZATION; GENETIC VARIABILITY; LIPID COMPOSITION; MANURE; MICROBIAL DIVERSITY; MULTIPLEX POLYMERASE CHAIN REACTION; NONHUMAN; PHENOTYPIC VARIATION; PIG; PRIORITY JOURNAL; RNA SEQUENCE; SEQUENCE ALIGNMENT; SPECIES DIVERSITY; TAXONOMY; ANIMAL; BACTERIAL GENE; BOVINE; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEIC ACID HYBRIDIZATION; ONTARIO; PHYLOGENY; POLYMERASE CHAIN REACTION;

ANIMALS; ARCOBACTER; BASE COMPOSITION; CATTLE; DNA, BACTERIAL; FATTY ACIDS; GENES, BACTERIAL; MANURE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; ONTARIO; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SWINE;

EID: 84935032755     PISSN: 14665026     EISSN: 14665034     Source Type: Journal    
DOI: 10.1099/ijs.0.000318     Document Type: Article

References (45)

1. Adam, Z., Whiteduck-Leveillee, K., Cloutier, M., Tambong, J. T., Chen, W., Lewis, C. T., Lévesque, C. A., Topp, E., Lapen, D. R. & other authors (2014). Draft genome sequences of three Arcobacter strains of pig and dairy cattle manure origin. Genome Announc 2, e00377–e00314.
2. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997). Gapped blast and psi-blast: a new generation of pr otein database search programs. Nucleic Acids Res 25, 3389–3402.
3. Bruce, K. D., Hiorns, W. D., Hobman, J. L., Osborn, A. M., Strike, P. & Ritchie, D. A. (1992). Amplification of DNA from native populations of soil bacteria by using the polymerase chain reaction. Appl Environ Microbiol 58, 3413–3416.
4. Chao, J., Wolfaardt, G. M. & Arts, M. T. (2010). Characterization of Pseudomonas aeruginosa fatty acid profiles in biofilms and batch planktonic cultures. Can J Microbiol 56, 1028–1039.
5. CLSI (2010). Methods for antimicrobial dilution and disk susceptibility testing of infrequently isolated fastidious bacteria; Approved Guideline, 2nd edn. CLSI document M45-A2. Wayne, PA: Clinical and Laboratory Standards Institute.
6. CLSI (2011). Performance standards for antimicrobial susceptibility testing, 21st Informational Supplement. CLSI M100-S21. Wayne, PA: Clinical and Laboratory Standards Institute.
7. Collado, L., Levican, A., Perez, J. & Figueras, M. J. (2011). Arcobacter defluvii sp. nov., isolated from sewage samples. Int J Syst Evol Microbiol 61, 2155–2161.
8. Douidah, L., De Zutter, L., Vandamme, P. & Houf, K. (2010). Identification of five human and mammal associated Arcobacter species by a novel multiplex-PCR assay. J Microbiol Methods 80, 281–286.
9. Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368–376.
10. Fera, M. T., La Camera, E., Carbone, M., Malara, D. & Pennisi, M. G. (2009). Pet cats as carriers of Arcobacter spp. in Southern Italy. J Appl Microbiol 106, 1661–1666.
11. Figueras, M. J., Collado, L., Levican, A., Perez, J., Solsona, M. J. & Yustes, C. (2011). Arcobacter molluscorum sp. nov., a new species isolated from shellfish. Syst Appl Microbiol 34, 105–109.
12. Greco-Stewart, V. S., Brown, E. E., Parr, C., Kalab, M., Jacobs, M. R., Yomtovian, R. A. & Ramírez-Arcos, S. M. (2012). Serratia marcescens strains implicated in adverse transfusion reactions form biofilms in platelet concentrates and demonstrate reduced detection by automated culture. Vox Sang 102, 212–220.
13. Harmon, K. M. & Wesley, I. V. (1996). Identification of Arcobacter isolates by PCR. Lett Appl Microbiol 23, 241–244.
14. Hayat, M. A. (1989). Principles and Techniques of Electron Microscopy: Biological Applications, 3rd edn. Boca Raton, FL: CRC Press.
15. Hill, J. E., Paccagnella, A., Law, K., Melito, P. L., Woodward, D. L., Price, L., Leung, A. H., Ng, L. K., Hemmingsen, S. M. & Goh, S. H. (2006). Identification of Campylobacter spp. and discrimination from Helicobacter and Arcobacter spp. by direct sequencing of PCRamplified cpn60 sequences and comparison to cpnDB, a chaperonin reference sequence database. J Med Microbiol 55, 393–399.
16. Ho, H. T. K., Lipman, L. J. & Gaastra, W. (2006). Arcobacter, what is known and unknown about a potential foodborne zoonotic agent! Vet Microbiol 115, 1–13.
17. Houf, K. & Stephan, R. (2007). Isolation and characterization of the emerging foodborn pathogen Arcobacter from human stool. J Microbiol Methods 68, 408–413.
18. Houf, K., Tutenel, A., De Zutter, L., Van Hoof, J. & Vandamme, P. (2000). Development of a multiplex PCR assay for the simultaneous detection and identification of Arcobacter butzleri, Arcobacter cryaerophilus and Arcobacter skirrowii. FEMS Microbiol Lett 193, 89–94.
19. Houf, K., Devriese, L. A., De Zutter, L., Van Hoof, J. & Vandamme, P. (2001). Development of a new protocol for the isolation and quantification of Arcobacter species from poultry products. Int J Food Microbiol 71, 189–196.
20. Houf, K., De Zutter, L., Van Hoof, J. & Vandamme, P. (2002). Assessment of the genetic diversity among arcobacters isolated from poultry products by using two PCR-based typing methods. Appl Environ Microbiol 68, 2172–2178.
21. Houf, K., On, S. L., Coenye, T., Mast, J., Van Hoof, J. & Vandamme, P. (2005). Arcobacter cibarius sp. nov., isolated from broiler carcasses. Int J Syst Evol Microbiol 55, 713–717.
22. Houf, K., On, S. L., Coenye, T., Debruyne, L., De Smet, S. & Vandamme, P. (2009). Arcobacter thereius sp. nov., isolated from pigs and ducks. Int J Syst Evol Microbiol 59, 2599–2604.
23. Kabeya, H., Maruyama, S., Morita, Y., Kubo, M., Yamamoto, K., Arai, S., Izumi, T., Kobayashi, Y., Katsube, Y. & Mikami, T. (2003). Distribution of Arcobacter species among livestock in Japan. Vet Microbiol 93, 153–158.
24. Kim, H. M., Hwang, C. Y. & Cho, B. C. (2010). Arcobacter marinus sp. nov. Int J Syst Evol Microbiol 60, 531–536.
25. Kluge, A. G. & Farris, F. S. (1969). Quantitative phyletics and the evolution of anurans. Syst Zool 18, 1–32.
26. Korczak, B. M., Stieber, R., Emler, S., Burnens, A. P., Frey, J. & Kuhnert, P. (2006). Genetic relatedness within the genus Campylobacter inferred from rpoB sequences. Int J Syst Evol Microbiol 56, 937–945.
27. Lanave, C., Preparata, G., Sacone, C. & Serio, G. (1984). A new method for calculating evolutionary substitution rates. J Mol Evol 20, 86–93.
28. Lee, C., Agidi, S., Marion, J. W. & Lee, J. (2012). Arcobacter in Lake Erie beach waters: an emerging gastrointestinal pathogen linked with human-associated fecal contamination. Appl Environ Microbiol 78, 5511–5519.
29. Levican, A., Rubio-Arcos, S., Martinez-Murcia, A., Collado, L. & Figueras, M. J. (2015). Arcobacter ebronensis sp. nov. and Arcobacter aquimarinus sp. nov., two new species isolated from marine environment. Syst Appl Microbiol 38, 30–35.
30. On, S. L., Stacey, A. & Smyth, J. (1995). Isolation of Arcobacter butzleri from a neonate with bacteraemia. J Infect 31, 225–227.
31. Prakash, O., Verma, M., Sharma, P., Kumar, M., Kumari, K., Singh, A., Kumari, H., Jit, S., Gupta, S. K. & other authors (2007). Polyphasic approach of bacterial classification – an overview of recent advances. Indian J Microbiol 47, 98–108.
32. Ramisse, V., Balandreau, J., Thibault, F., Vidal, D., Vergnaud, G. & Normand, P. (2003). DNA-DNA hybridization study of Burkholderia species using genomic DNA macro-array analysis coupled to reverse genome probing. Int J Syst Evol Microbiol 53, 739–746.
33. Richter, M. & Rosselló-Móra, R. (2009). Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106, 19126–19131.
34. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
35. Sasi Jyothsna, T. S., Rahul, K., Ramaprasad, E. V. V., Sasikala, Ch. & Ramana, Ch. V. (2013). Arcobacter anaerophilus sp. nov., isolated from an estuarine sediment and emended description of the genus Arcobacter. Int J Syst Evol Microbiol 63, 4619–4625.
36. Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9, 671–675.
37. Stackebrandt, E. & Goebel, B. M. (1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44, 846–849.
38. Tambong, J. T., de Cock, A. W. A. M., Tinker, N. A. & Lévesque, C. A. (2006). Oligonucleotide array for identification and detection of Pythium species. Appl Environ Microbiol 72, 2691–2706.
39. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28, 2731–2739.
40. Teeling, H., Meyerdierks, A., Bauer, M., Amann, R. & Glo¨ ckner, F. O. (2004). Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ Microbiol 6, 938–947.
41. Van den Bulck, K., Decostere, A., Baele, M., Driessen, A., Debongnie, J. C., Burette, A., Stolte, M., Ducatelle, R. & Haesebrouck, F. (2005). Identification of non-Helicobacter pylori spiral organisms in gastric samples from humans, dogs, and cats. J Clin Microbiol 43, 2256–2260.
42. Van Driessche, E., Houf, K., Vangroenweghe, F., De Zutter, L. & Van Hoof, J. (2005). Prevalence, enumeration and strain variation of Arcobacter species in the faeces of healthy cattle in Belgium. Vet Microbiol 105, 149–154.
43. Vandamme, P., Falsen, E., Rossau, R., Hoste, B., Segers, P., Tytgat, R. & De Ley, J. (1991). Revision of Campylobacter, Helicobacter, and Wolinella taxonomy: emendation of generic descriptions and proposal of Arcobacter gen. nov. Int J Syst Bacteriol 41, 88–103.
44. Vandamme, P., Dewhirst, F. E., Paster, B. J. & On, S. L. W. (2005). Genus II. Arcobacter Vandamme, Falsen, Rossau, Segers, Tytgat and De Ley 1991a, 99VP. In Bergey’s Manual of Systematic Bacteriology, 2nd edn., vol. 2C. pp. 1161–1165. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
45. Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsky, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E. & other authors (1987). International Committee on Systematic Bacteriology, Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.