Bacteria belonging to the genera Afipia and Bosea are amoeba-resisting bacteria that have been recently reported to colonize hospital water supplies and are suspected of being responsible for intensive care unitacquired pneumonia. Identification of these bacteria is now based on determination of the 16S ribosomal DNA sequence. However, the 16S rRNA gene is not polymorphic enough to ensure discrimination of species defined by DNA-DNA relatedness. The complete rpoB sequences of 20 strains were first determined by both PCR and genome walking methods. The percentage of homology between different species ranged from 83 to 97% and was in all cases lower than that observed with the 16S rRNA gene; this was true even for species that differed in only one position. The taxonomy of Bosea and Afipia is discussed in light of these results. For strain identification that does not require the complete rpoB sequence (4,113 to 4,137 bp), we propose a simple computerized method that allows determination of nucleotide positions of high variability in the sequence that are bordered by conserved sequences and that could be useful for design of universal primers. A fragment of 740 to 752 bp that contained the most highly variable area (positions 408 to 420) was amplified and sequenced with these universal primers for 47 strains. The variability of this sequence allowed identification of all strains and correlated well with results of DNA-DNA relatedness. In the future, this method could be also used for the determination of variability "hot spots" in sets of housekeeping genes, not only for identification purposes but also for increasing the discriminatory power of sequence typing techniques such as multilocus sequence typing.Aquatic bacteria such as Legionella, Pseudomonas, Stenotrophomonas, Burkholderia spp., and Acinetobacter spp. may colonize hospital water supplies and have previously been shown to be causally associated with cases of nosocomial infections (23). Free-living amoebae have been shown to be a reservoir of pathogens, such as Legionella spp., Burkholderia pickettii, and Cryptococcus neoformans (2, 26). The most studied of amoebaresisting bacteria (ARB) is Legionella pneumophila, the agent of Legionnaires' disease (27), which frequently results from exposure to contaminated aerosols. There are growing hints that additional ARB might be implicated in community-acquired pneumonia, including Legionella-like amoebal pathogens and members of the genus Parachlamydia (19). As part of the research into the diversity of bacterial agents associated with amoebae in hospital water supplies, we previously identified new ␣-proteobacteria belonging to the Bradyrhizobiaceae (13). Moreover, we demonstrated that patients with nosocomial pneumonia who were hospitalized in a public hospital where contaminated water was found had elevated titers of antibodies against these bacteria (14) and that patient seroconversion to Bosea massiliensis was frequent in patients hospitalized in intensive care units and was associated with the occurrence ...