A bioinformatics tool for ensuring the backwards compatibility of Legionella pneumophila typing in the genomic era

Clinical Microbiology and Infection

Volumn 23, Issue 5, 2017, Pages 306-310

  Gordon, M ^a   Yakunin, E ^b   Valinsky, L ^b   Chalifa Caspi, V ^a   Moran Gilad, J ^a,b  

^a BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

^b MINISTRY OF HEALTH   (Israel)

Author keywords

Backwards compatibility; Bioinformatics; Legionella; Sequencing; Typing

Indexed keywords

BACTERIAL DNA;

BACTERIAL GENE; BACTERIUM IDENTIFICATION; BIOLOGY; CLASSIFICATION; DNA SEQUENCE; GENETIC ASSOCIATION STUDY; GENETIC DATABASE; GENETICS; GENOMICS; LEGIONELLA PNEUMOPHILA; SINGLE NUCLEOTIDE POLYMORPHISM;

BACTERIAL TYPING TECHNIQUES; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA, BACTERIAL; GENES, BACTERIAL; GENETIC ASSOCIATION STUDIES; GENOMICS; LEGIONELLA PNEUMOPHILA; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 85013485261     PISSN: 1198743X     EISSN: 14690691     Source Type: Journal    
DOI: 10.1016/j.cmi.2017.01.002     Document Type: Article

References (15)

1. [1] Yu, V.L., Plouffe, J.F., Pastoris, M.C., Stout, J.E., Schousboe, M., Widmer, A., et al. Distribution of Legionella species and serogroups isolated by culture in patients with sporadic community acquired legionellosis: an international collaborative survey. J Infect Dis 186 (2002), 127–128.
2. [2] European Centre for Disease Prevention and Control, Annual Epidemiological Report 2012. Reporting on 2010 surveillance data and 2011 epidemic intelligence data., 2013, ECDC, Stockholm.
3. [3] Gaia, V., Fry, N.K., Afshar, B., Lück, P.C., Meugnier, H., Etienne, J., et al. A consensus sequence-based epidemiological typing scheme for clinical and environmental isolates of Legionella pneumophila. J Clin Microbiol 43 (2005), 2047–2052.
4. [4] Ratzow, S., Gaia, V., Helbig, J.H., Fry, N.K., Lück, P.C., Addition of neuA, the gene encoding N-acylneuraminate cytidylyl transferase, increases the discriminatory ability of the consensus sequence-based scheme for typing Legionella pneumophila serogroup 1 strains. J Clin Microbiol 45 (2007), 1965–1968.
5. [5] Harrison, T.G., Afshar, B., Doshi, N., Fry, N.K., Lee, J.V., Distribution of Legionella pneumophila serogroups, monoclonal antibody subgroups and DNA sequence types in recent clinical and environmental isolates from England and Wales (2000–2008). Eur J Clin Microbiol Infect Dis 28 (2009), 781–791.
6. [6] Moran-Gilad, J., Lazarovitch, T., Mentasti, M., Harrison, T., Weinberger, M., Mordish, Y., et al. Humidifier-associated paediatric Legionnaires’ disease, Israel, February 2012. Euro Surveill, 17, 2012 pii=20293.
7. [7] Bletz, S., Mellmann, A., Rothgänger, J., Harmsen, D., Ensuring backwards compatibility: traditional genotyping efforts in the era of whole genome sequencing. Clin Microbiol Infect, 21, 2015 347.e1–4.
8. [8] David, S., Mentasti, M., Tewolde, R., Aslett, M., Harris, S.R., Afshar, B., et al. Evaluation of an optimal epidemiologic typing scheme for Legionella pneumophila with whole genome sequence data using validation guidelines. J Clin Microbiol, 2016 pii: JCM.00432-16 [Epub ahead of print].
9. [9] Moran-Gilad, J., Prior, K., Yakunin, E., Harrison, T.G., Underwood, A., Lazarovitch, T., et al. Design and application of a core genome multilocus sequence typing scheme for investigation of Legionnaires’ disease incidents. Euro Surveill, 20, 2015 pii:21186.
10. [10] Raphael, B.H., Baker, D.J., Nazarian, E., Lapierre, P., Bopp, D., Kozak-Muiznieks, N.A., et al. Genomic resolution of outbreak-associated Legionella pneumophila serogroup 1 isolates from New York State. Appl Environ Microbiol 82 (2016), 3582–3590.
11. [11] Underwood, A.P., Jones, G., Mentasti, M., Fry, N.K., Harrison, T.G., Comparison of the Legionella pneumophila population structure as determined by sequence-based typing and whole genome sequencing. BMC Microbiol, 13, 2013, 302.
12. [12] Burckhardt, F., Brion, A., Lahm, J., Koch, H.U., Prior, K., Petzold, M., et al. Confirming Legionnaires’ disease outbreak by genome-based method, Germany, 2012. Emerg Infect Dis 22 (2016), 1303–1304.
13. [13] Lévesque, S., Plante, P.L., Mendis, N., Cantin, P., Marchand, G., Charest, H., et al. Genomic characterization of a large outbreak of Legionella pneumophila serogroup 1 strains in Quebec City, 2012. PLoS One, 9, 2014, e103852.
14. [14] Graham, R.M., Doyle, C.J., Jennison, A.V., Real-time investigation of a Legionella pneumophila outbreak using whole genome sequencing. Epidemiol Infect 142 (2014), 2347–2351.
15. [15] Reuter, S., Harrison, T.G., Köser, C.U., Ellington, M.J., Smith, G.P., Parkhill, J., et al. A pilot study of rapid whole-genome sequencing for the investigation of a Legionella outbreak. BMJ Open, 3, 2013 pii:e002175.