International Journal of Systematic and Evolutionary Microbiology (2002), 52, 165–171 Printed in Great Britain Phylogenetic classification of Bartonella species by comparing groEL sequences 1 Unite! des Rickettsies, CNRS Zaher Zeaiter,1 Pierre-Edouard Fournier,1 Hiroyuki Ogata2 UPRES-A 6020, Faculte! de 1 Me! decine, 27 boulevard and Didier Raoult Jean Moulin, 13385 Marseille Cedex 05, France Author for correspondence: Didier Raoult. Tel: 33491324375.Fax: 33491830390. 2 j j Information Ge! ne! tique & e-mail: Didier.Raoult!medecine.univ-mrs.fr Structurale, CNRS UMR 1889, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France Bartonella is a bacterial genus classified in the α-Proteobacteria on the basis of 16S rDNA sequence comparison. The highly conserved heat-shock chaperonin protein, GroEL, has proved to be a valuable resolving tool to classify ten Bartonella species. The groEL gene was amplified and sequenced from ten Bartonella isolates: Bartonella alsatica, Bartonella vinsonii subsp. arupensis, Bartonella taylorii, Bartonella tribocorum, Bartonella birtlesii, Bartonella henselae Marseille (URLLY8), B. henselae (90-615), B. henselae (Fizz), B. henselae (CAL-1) and B. henselae (SA-2). Then, phylogenetic relationships were inferred between our isolates and eight other species and subspecies from the comparison of both 16S rDNA and groEL sequences using parsimony, neighbour-joining and maximum-likelihood methods. By using groEL sequences, the first reliable classification of most known Bartonella species and subspecies was established. Four strongly supported subgroups were distinguished: firstly, the two human pathogens B. henselae and Bartonella quintana; secondly, a cluster including four rodent isolates, Bartonella elizabethae, B. tribocorum, Bartonella grahamii and B. taylorii; thirdly, a cluster including the B. vinsonii subspecies (B. vinsonii subsp. vinsonii, arupensis and berkhoffii); and lastly, B. birtlesii and ‘Bartonella weissi’. ‘Bartonella washoensis’, B. alsatica, Bartonella doshiae, Bartonella bacilliformis and Bartonella clarridgeiae did not reliably cluster with any other Bartonella species. In addition, the groEL gene was shown to be useful in subtyping six B. henselae isolates into three variants: Houston, Marseille and Fizz. Keywords: Bartonella, 16S rDNA, groEL, phylogeny, subtyping INTRODUCTION et al., 2000); Bartonella grahamii, Bartonella vinsonii subsp. vinsonii and Bartonella doshiae were recovered Bacteria within the genus Bartonella are aerobic, from voles (Birtles et al., 1995; Brenner et al., 1993); B. Gram-negative, fastidious, oxidase-negative, slow- vinsonii subsp. arupensis was isolated from mice (Welch growing, pleiomorphic organisms, which belong to the et al., 1999); Bartonella alsatica was isolated from α-Proteobacteria on the basis of their 16S rDNA rabbits (Heller et al., 1999); ‘Bartonella weissi’, Bar- sequences (Brenner et al., 1993; Birtles et al., 1995). tonella clarridgeiae, Bartonella henselae and Bartonella These bacteria are considered to be emerging patho- koehlerae were obtained from cats (Droz et al., 1999; gens (Anderson & Neuman, 1997). Currently, 18 Kelly et al., 1998; Koehler et al., 1994; Lawson & Bartonella species are recognized. All of them are Collins, 1996); B. vinsonii subsp. berkhoffii was cul- associated with mammalian hosts. Bartonella taylorii, tivated from dogs (Breitschwerdt et al., 1995) and from Bartonella elizabethae, Bartonella tribocorum and Bar- coyotes (Chang et al., 2000); ‘Bartonella washoensis’ tonella birtlesii were isolated from rats (Birtles et al., was evidenced in rodents (R. L. Regnery, personal 1995; Brenner et al., 1993; Heller et al., 1998; Bermond communication); and Bartonella quintana and Bar- tonella bacilliformis were isolated from humans ................................................................................................................................................. (McNee et al., 1916; Gray et al., 1990). As Bartonella Abbreviation: ITS, intergenic spacer. species express few remarkable phenotypic characteris- 01915 # 2002 IUMS 165 Z. Zeaiter and others tics, their precise identification and phylogenetic classi- denaturation at 94 mC was followed by 40 cycles of denatura- fication has mainly relied on the study of various tion for 30 s at 94 mC, annealing for 30 s at 54 mC and genes. The 16S rDNA sequence, which was considered extension for 90 s at 72 mC. The amplification was completed to be one of the most useful and informative tools for by holding for 7 min at 72 mC to allow complete extension of the identification and phylogenetic studies of bacteria the PCR products. PCR products were separated by electro- (Olsen & Woese, 1993), was the first gene to be studied phoresis on 1% agarose gels, visualized by staining with but has failed to establish a reliable phylogeny of ethidium bromide and then purified using the QIAquick Bartonella species. The high degree of conservation of PCR purification kit (QIAGEN) as described by the manu- this gene led to a small number of informative sites in facturer. PCR products were sequenced in both directions its sequence. Thus, it does not seem to be a good tool using the d-Rhodamine Terminator Cycle Sequencing Ready Reaction kit (Perkin Elmer) as described by the to reveal a precise and statistically supported phy- manufacturer. Each reaction was carried out using 5 µl logeny at the species level (Fox et al., 1992; Hasegawa purified DNA (" 200 ng), d-Rhodamine mix (4 µl) and 1 µl & Hashimoto, 1993; Teichmann & Mitchison, 1999). primer (10 pmol); sequencing primers are reported in Table Other genes have been investigated to classify Bar- 2. Conditions used for sequencing were 30 cycles of tonella species. The 16S–23S rDNA intergenic spacer denaturation for 20 s at 95 mC, annealing for 10 s at 50 mC (ITS) region (Roux & Raoult, 1995) and the citrate and extension for 2 min at 60 mC. Reaction products were synthase-encoding gene (gltA) (Birtles & Raoult, 1996) mixed with 80 µl 70% ethanol and 0n5 mM MgCl# and, after provided better bootstrap values for the nodes than being held for 20 min at room temperature in the dark, those obtained with the 16S rDNA sequence. Cur- precipitated DNA was collected by centrifugation for 25 min rently, the most recent and reliable classification of at 3000 r.p.m. at room temperature. The DNA pellet was Bartonella species was established by Marston et al. dried and resuspended in either 3 µl1\4(v\v) formamide\ (1999) who, using the 60 kDa heat-shock protein- 1% bromophenol blue solution and then denatured by encoding gene (groEL), which is one of the two highly heating for 2 min at 95 mCor12µl Template Suppression conserved components of the heat-shock chaper- reagent (Perkin Elmer). Sequencing products were resolved onin response system groES (Hsp10)\groEL (Hsp60) using an ABI 377 or an ABI 310 automated sequencer (Mayhew & Hartl, 1996), established the relationships (Perkin Elmer). between nine Bartonella strains. Analysis of sequences and construction of phylogenetic In the present study, sequences of the major portion of trees. Sequence analysis was performed with the software the groEL gene from ten additional Bartonella isolates packages ABI Prism DNA Sequencing Analysis Software were determined. From the alignment of these se- version 3.0 (Perkin Elmer) and multisequence alignment was quences and those available for another eight species made with software, version 1.81 (Thompson et and subspecies, the phylogenetic relationships within al., 1994). Phylogenetic trees were obtained from DNA the Bartonella genus were inferred. The utility of this sequences by using the maximum-parsimony method (- gene as a tool in subtyping B. henselae and B. quintana software in ; Felsenstein, 1989), distance isolates was also tested. methods (, distance matrix with Kimura two- parameter or Jukes–Cantor parameters; and , neighbour-joining) and the maximum-likelihood method METHODS ( software in ). Phylogenetic trees were inferred from amino acid sequences using the maximum- Bartonella strains and DNA extraction. The strains used in parsimony method ( software in ) and this study are summarized in Table 1. Bartonella isolates distance methods (, dayhoff PAM matrix or were grown on 5% sheep blood agar (bioMe! rieux) at 37 mC Kimura formula; and , neighbour-joining) Boot- ina5%CO#-enriched atmosphere. Bacteria were harvested after 7 d cultivation and DNA was extracted using the strap replicates were performed to estimate the node Chelex method (de Lamballerie et al., 1992). Supernatants reliability of the phylogenetic trees obtained by the three containing the genomic DNAs were stored at 4 mC until their methods (Brown, 1994). Bootstrap values were obtained use as templates in PCR. from 100 trees (Efron et al., 1996) generated randomly with and in the software package. Only PCR amplification and DNA sequencing. Primers used for values above 90 were considered significant. Trees were amplification and sequencing are presented in Table 2. drawn using the version 1.5 (Page, 1996) software. Primer positions are numbered relative to the groEL gene of Agrobacteriun tumefaciens and Brucella abortus, two other B. bacilliformis (Table 1). Primers were selected using the α-Proteobacteria, were used as the outgroup in all our Primer3 software (Rozen & Skaletsky, 2000; code avail- phylogenetic trees (Table 1). Only the neighbour-joining tree able at http:\\www-genome.wi.mit.edu\genomeIsoftware\ other\primer3.html) and were purchased from Eurobio. is presented in this article.