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Journal of Clinical Microbiology, February 2009, p. 300-310, Vol. 47, No. 2
0095-1137/09/$08.00+0 doi:10.1128/JCM.01916-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
Phylogeny and Identification of Pantoea Species and Typing of Pantoea agglomerans Strains by Multilocus Gene Sequencing 
,
Alexis Delétoile,1,2
Dominique Decré,3,4
Stéphanie Courant,3
Virginie Passet,1,2
Jennifer Audo,3
Patrick Grimont,2
Guillaume Arlet,3,5 and
Sylvain Brisse1,2*
Genotyping of Pathogens and Public Health,1 Biodiversity of Emerging Bacterial Pathogens,2 Institut Pasteur, Université Pierre et Marie Curie (Paris VI), UPRES EA 2392 Antibiotiques et Flore Digestive,3 Service de Microbiologie, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine,4 Service de Bactériologie, Assistance Publique-Hôpitaux de Paris, Hôpital Tenon, Paris, France5
Received 3 October 2008/ Returned for modification 15 November 2008/ Accepted 22 November 2008
Pantoea agglomerans and other Pantoea species cause infections in humans and are also pathogenic to plants, but the diversity of Pantoea strains and their possible association with hosts and disease remain poorly known, and identification of Pantoea species is difficult. We characterized 36 Pantoea strains, including 28 strains of diverse origins initially identified as P. agglomerans, by multilocus gene sequencing based on six protein-coding genes, by biochemical tests, and by antimicrobial susceptibility testing. Phylogenetic analysis and comparison with other species of Enterobacteriaceae revealed that the genus Pantoea is highly diverse. Most strains initially identified as P. agglomerans by use of API 20E strips belonged to a compact sequence cluster together with the type strain, but other strains belonged to diverse phylogenetic branches corresponding to other species of Pantoea or Enterobacteriaceae and to probable novel species. Biochemical characteristics such as fosfomycin resistance and utilization of D-tartrate could differentiate P. agglomerans from other Pantoea species. All 20 strains of P. agglomerans could be distinguished by multilocus sequence typing, revealing the very high discrimination power of this method for strain typing and population structure in this species, which is subdivided into two phylogenetic groups. PCR detection of the repA gene, associated with pathogenicity in plants, was positive in all clinical strains of P. agglomerans, suggesting that clinical and plant-associated strains do not form distinct populations. We provide a multilocus gene sequencing method that is a powerful tool for Pantoea species delineation and identification and for strain tracking.
* Corresponding author. Mailing address: Genotyping of Pathogens and Public Health Platform (PF8), Institut Pasteur, 28 rue du Dr Roux, F-75724 Paris, France. Phone: 33 1 40 61 36 58. Fax: 33 1 40 61 39 43. E-mail: sylvain.brisse{at}pasteur.fr
Published ahead of print on 3 December 2008.
Supplemental material for this article may be found at http://jcm.asm.org/.
Journal of Clinical Microbiology, February 2009, p. 300-310, Vol. 47, No. 2
0095-1137/09/$08.00+0 doi:10.1128/JCM.01916-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
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