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1 Unidad de Diagnóstico Molecular, EPSO, Universidad Miguel Hernández, Ctra Beniel Km 3, E-03312 Orihuela (Alicante), Spain
2 Labaqua SA, Alona 33, E-03007 Alicante, Spain
3 Unidad de Microbiología, Departamento de Ciencias Médicas Básicas, Facultad de Medicina y Ciencias de la Salud, Universidad Rovira y Virgili, Reus, E-43201 Tarragona, Spain
Correspondence
A. J. Martínez-Murcia
ammurcia{at}umh.es
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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Published online ahead of print on 29 November 2002 as DOI 10.1099/ijs.0.02443-0.
The GenBank/EMBL/DDBJ accession numbers for the gyrB sequences of Aeromonas species determined in this study are AY101772–AY101824.
Tables showing percentage similarities and percentage nucleotide substitutions in gyrB in the genus Aeromonas are available as supplementary data in IJSEM Online.
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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). Aeromonads are autochthonous to aquatic environments worldwide and have been implicated in the aetiology of a variety of fish and human diseases, frequently including diarrhoea and occasionally systemic infections (Janda, 1991). Over the past few years, interest in the genus Aeromonas as an emergent human pathogen has increased significantly (Abbott et al., 1998; Janda & Abbott, 1998; Joseph & Carnahan, 2000).
The classification of the genus Aeromonas has been dogged by confusion and controversy. In Bergey's Manual of Systematic Bacteriology (Popoff, 1984), the genus was divided into three mesophilic and motile species (Aeromonas hydrophila, Aeromonas caviae and Aeromonas sobria) and the psychrophilic, non-motile species Aeromonas salmonicida. Extensive DNA–DNA hybridization studies (Popoff et al., 1981; Hickman-Brenner et al., 1987, 1988; Kuijper et al., 1989; Carnahan et al., 1991) have resulted in the recognition of 14 so-called DNA homology groups (HGs): A. hydrophila (HG1), Aeromonas sp. (unnamed; HG2), A. salmonicida (HG3), A. caviae (HG4), Aeromonas media (HG5), Aeromonas eucrenophila (HG6), A. sobria (HG7), Aeromonas veronii biogroup sobria (HG8), Aeromonas jandaei (HG9), A. veronii biogroup veronii (HG10), Aeromonas sp. (unnamed; HG11), A. schubertii (HG12), Aeromonas group 501 (HG13; formerly Enteric group 501) and Aeromonas trota (HG14). The name Aeromonas bestiarum has been proposed for strains included in HG2 (Ali et al., 1996). During the past decade, three novel species have been described: Aeromonas allosaccharophila (Martínez-Murcia et al., 1992b), Aeromonas encheleia (Esteve et al., 1995b) and Aeromonas popoffii (Huys et al., 1997b). The species names Aeromonas enteropelogenes and Aeromonas ichthiosmia (Schubert et al., 1990a, b) are now considered to be synonyms of A. trota and A. veronii, respectively (Carnahan, 1993; Collins et al., 1993). Phylogenetic analyses based on 16S rRNA genes indicated that aeromonads are a very tight group of species (Martinez-Murcia et al., 1992a). In almost all species of the genus, rDNA-derived relationships correlated well with DNA–DNA hybridization. DNA probes and RFLP profiles designed from 16S rDNA diagnostic regions have served to identify Aeromonas at the species level (Ash et al., 1993a, b; Dorsch et al., 1994; Borrell et al., 1997; Khan & Cerniglia, 1997; Figueras et al., 2000). However, there are reported discrepancies between different sets of DNA–DNA hybridization data (Hickman-Brenner et al., 1987; Schubert & Hegazi, 1988; Esteve et al., 1995a, b; Huys et al., 1996a, b, 2001), and the fact that 16S rRNA is highly conserved (Martínez-Murcia, 1999) brings the latest descriptions of some species into question (Nair & Holmes, 1999).
It has been reported that gyrB (which encodes the B-subunit of DNA gyrase, a type-II DNA topoisomerase) could be a suitable phylogenetic marker for bacterial systematics (Yamamoto & Harayama, 1995, 1996, 1998; Huang, 1996; Venkateswaran et al., 1998; Yamamoto et al., 1999, 2000; Kasai et al., 2000; Watanabe et al., 2001; Stackebrandt et al., 2002). This protein plays a crucial role in the DNA replication process, and its gene sequence has a mean synonymous substitution rate that is almost four times that of 16S rDNA (Yamamoto & Harayama, 1996).
In the present study, gyrB nucleotide sequences were determined from 53 Aeromonas strains, including type strains of all described species (or HGs), reference strains and some new isolates, which were also characterized by analysis of the 16S rDNA variable regions. This phylogenetic study was designed to clarify the interspecies phylogenetic relationships within Aeromonas, and to assess the congruence of gyrB groupings with those of both 16S rDNA sequencing and DNA–DNA hybridization.
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METHODS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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. New isolates and reference strains from culture collections were identified genetically by 16S rDNA RFLP typing and further sequencing. Most Aeromonas strains were grown aerobically on trypticase soy agar (Oxoid) overnight at 28 °C. The only exception was the psychrophilic species A. salmonicida, which was incubated at 22 °C.
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Oligonucleotide primers.
Primers gyrB3F and gyrB14R were designed from the most conserved regions in a preliminary alignment of published A. hydrophila gyrB sequences (GenBank accession numbers AF074917 and AF208250–AF208260). These primers were used to amplify a gyrB fragment of approximately 1100 bp. Primers gyrB7F, gyrB9R and gyrB9Rs were then designed from alignments that included the first few gyrB sequences obtained in the present study. The five Cy5-labelled primers (Table 2) were purchased from Amersham Biosciences and were used for gyrB sequencing reactions as required. Primers for amplification and sequencing of 16S rDNA were described previously (Martínez-Murcia et al., 1999).
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Phylogenetic data analysis.
The gyrB nucleotide sequences were aligned by using the CLUSTAL X program, version 1.8 (Thompson et al., 1997). Genetic distances were obtained using Kimura's two-parameter model (Kimura, 1980) and evolutionary trees were constructed by the neighbour-joining method (Saitou & Nei, 1987) with the MEGA program (Kumar et al., 2001).
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RESULTS AND DISCUSSION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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). Experiments were repeated at least twice from single colonies of original cultures, to confirm readings and solve ambiguities. The derived gyrB sequences were 960–1100 nt in length, covering more than 70 % of the ATPase domain (amino acid residues 2–392 in Escherichia coli; Huang, 1996) and 191 nt of the 3' flanking region. Species identification by 16S rDNA sequence is shown in Table 1.
Phylogenetic location of the genus Aeromonas
A multiple alignment of the GyrB subunit amino acid sequences, deduced from the gene sequences, was obtained. Amino acid (289 aa) and nucleotide (869 bp) sequences from type strains of all known Aeromonas species (or HGs) were compared with the corresponding sequences of the species E. coli, Vibrio cholerae, P. shigelloides, Neisseria gonorrhoeae and Myxococcus xanthus. Percentage similarities for both proteins and genes are given in Table A, which is available as supplementary data in IJSEM Online. On average, protein sequences showed a higher level of conservation than nucleotide sequences. Ranges of nucleotide and protein sequence similarity values between Aeromonas and species of other genera were, respectively: 68·5–70·9 % and 75·1–77·2 % to V. cholerae; 72·0–74·0 % and 74·7– 76·8 % to P. shigelloides; and 73·9–76·1 % and 75·7–76·5 % to E. coli. A phylogenetic tree constructed from the nucleotide alignment is shown in Fig. 1.
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that the genus Aeromonas formed a distinct line, separate from V. cholerae and E. coli, as it did from P. shigelloides. Species of these four genera belong to the 
-subclass of the Proteobacteria, clearly separated from representatives of the 
- (N. gonorrhoeae) and 
- (M. xanthus) subclasses. These findings agree with a previous phylogenetic study based on 16S rRNA gene sequences (Martinez-Murcia et al., 1992a) and support recognition of the family Aeromonadaceae (Colwell et al., 1986). In addition, the aeromonads showed a lower interspecies gyrB substitution rate than that of other genera (Yamamoto et al., 1999, 2000), in agreement with the former hypothesis that Aeromonas are a group of bacteria that have evolved relatively recently (Martínez-Murcia, 1999; Martínez-Murcia et al., 1999).
Phylogenetic relationships of Aeromonas species
The gyrB sequences from all Aeromonas strains in this study were aligned, and percentage nucleotide substitutions (Table B, available as supplementary data in IJSEM Online) were calculated for a continuous stretch of 957 nt (positions 404–1364 according to the E. coli numbering). Sequence similarity between Aeromonas strains ranged from 86·7 to 100 %, corresponding to 0–127 nucleotide differences. At the intraspecies level, the rate of nucleotide substitution ranged from 0 to 2·6 %, and was <2 % for most Aeromonas species. However, interspecies nucleotide substitutions were usually >3 %, except for the following two pairs of species: A. salmonicida and A. bestiarum (2·2–3·3 %), and A. encheleia and Aeromonas sp. HG11 (2·1–2·7 %). Fig. 2 shows an unrooted tree that was constructed from the derived genetic distance matrix by the neighbour-joining method. The same topology (phylogenetic distances and branching points) was obtained when only 772 bp, corresponding to approximately 70 % of the ATPase domain, was used (not shown).
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). This faster rate is an expected consequence of the chronometric nature of the gyrB gene as, although relatively conserved because it encodes a housekeeping enzyme, it is subject to a degenerative code which allows most silent mutations to occur (i.e. different codons may encode the same amino acid). Such evolutionary differences between the gyrB gene and protein chronometers are shown in Table A (available as supplementary data in IJSEM Online) where, apart from a higher level of protein conservation, different nucleotide sequences often encode almost-identical GyrB proteins. As a consequence, phylogenetic trees obtained from the protein sequences (not shown) show poor branching resolution and many strains of different species appear intermixed. Instead, gyrB gene sequences were found to be extremely useful in the current phylogenetic study of the genus Aeromonas.
Sequence analysis of gyrB shows considerable divergence between all Aeromonas species and DNA HGs. Moreover, apart from the strains A. media CECT 4234 and A. allosaccharophila CECT 4200, which showed sequences identical to those of the corresponding type strains of these species, a significant number of differences were found between strains of the same species. The two exceptions may suggest that these strains are duplicates of the type strains of their respective species. All other strains had a unique gyrB sequence; it therefore appears that gyrB sequences may be used not only for species identification, but also for simultaneous research of the phylogenetic depth of species. Despite the observed sequence diversity at the strain level, the groupings shown in Fig. 2 indicate a phylogenetic taxonomy consistent with that described in most previous genetic and phylogenetic studies of the genus Aeromonas. Almost all species formed separate lines on the basis of their gyrB sequences and clearly represent distinct genospecies. Due to the fact that gyrB sequence divergence is greater than that of 16S rRNA, we found the former gene more advantageous for Aeromonas species delineation. For example, A. trota and A. caviae, distinguishable by only a single nucleotide of their 16S rDNA sequences, are separated at a relatively large phylogenetic distance (Fig. 2) on the basis of partial gyrB sequence (6·0–7·2 % nucleotide substitutions, corresponding to 57–69 bp; see Table B in the supplementary data available in IJSEM Online). Similarly, A. hydrophila and A. media, which show only three nucleotide differences in 16S rDNA, are clearly separated by gyrB sequences (Fig. 2). A. schubertii clustered at the deepest branch of the genus (near the ancestral root), which is consistent with the 16S rRNA tree (Martínez-Murcia, 1999). The present analysis confirms that A. veronii biogroup sobria (HG8) and biogroup veronii (HG10) represent two heterogeneous phenotypes of a single species. Strain CECT 4911 (LMG 13073), largely classified as A. veronii (Huys et al., 1996b), possessed a gyrB sequence that was clearly related to that of A. allosaccharophila (Fig. 2). 16S rDNA sequencing results (Table 1) confirmed that CECT 4911 actually belongs to A. allosaccharophila.
Our study included the gyrB sequence from the type strain of the recently described species Aeromonas culicicola (Pidiyar et al., 2002), available in GenBank (accession no. AF175891). This taxon, together with isolate CFAE 35 (previously identified as A. eucrenophila; Singh & Sanyal, 1999), formed a separate phylogenetic line as shown in the tree in Fig. 2. The closest relatives of this species were A. veronii and A. allosaccharophila (3·4–4·0 and 3·9–4·4 % sequence divergence, respectively; Table B); therefore, these three species are equidistant from each other. The 16S rRNA gene of A. culicicola showed only a single nucleotide difference from that of A. jandaei CECT 4228T. On the other hand, 56 differences (in approx. 1000 nt) were found in the gyrB gene, once again demonstrating the advantage of this gene in separating closely related species.
The species A. allosaccharophila
Previous amplified fragment length polymorphism (AFLP) and DNA–DNA hybridization studies by Huys et al. (1996b, 2001) have questioned the original proposal of the species A. allosaccharophila, which was based on phylogenetic and phenotypic analyses (Martínez-Murcia et al., 1992b) and subsequent DNA–DNA reassociation results obtained by Esteve et al. (1995a). The latter study found that strains of A. allosaccharophila exhibited 0–40 % DNA relatedness with A. veronii, although later DNA–DNA hybridization studies by Huys et al. (2001) indicated a much higher range of 78–84 %, using the same reference strains. Apart from the striking lack of correlation between these hybridization studies, another inconsistency was found for the strain A. allosaccharophila CECT 4220 (ATCC 35942) when compared with DNA–DNA hybridization data obtained by Hickman-Brenner et al. (1987). It is worth nothing that Huys et al. often reported relatively high DNA relatedness values between very unrelated Aeromonas species (Martínez-Murcia, 1999; Huys et al., 2001). In the original description of A. allosaccharophila (Martínez-Murcia et al., 1992b), it was concluded that the species shows a clear phylogenetic divergence, demonstrated by qualitative evolutionary events (as well as the quantitative differences indicated) that support its phylogenetic distinctiveness from other species and particularly from A. veronii. The 16S rDNA of A. allosaccharophila shows six unique bases, i.e. different composition at positions where all other known Aeromonas species have the same conserved nucleotides (a fact that obviously gives more support to the distinctiveness of this species); also, A. allosaccharophila can be readily distinguished from A. veronii in region V2 (by two paired signature triplets at positions 154–156 and 167–165), the most relevant evolutionary event that splits the genus Aeromonas between A. hydrophila and A. schubertii. In the present study, A. allosaccharophila, although one of the closest phylogenetic relatives of A. veronii, undoubtedly formed a separate line on the basis of the gyrB sequence analysis, a result consistent with the phylogenetic analysis based on 16S rDNA (Martínez-Murcia et al., 1992b). The rate of nucleotide differences in their gyrB sequences varies from 2·9 to 4·1 %, which is notable considering the mean intraspecies value in Aeromonas (approx. 2 %). In comparison, similar phylogenetic distances were found between A. veronii and A. culicicola, or between A. popoffii and A. bestiarum. In view of the present and previous studies, we consider that A. allosaccharophila shows sufficient phylogenetic divergence to be considered as a separate species.
Controversial taxonomic issues
An insertion of 3 bp at positions 484–485 (E. coli numbering) was only detected in all strains of the species A. salmonicida and A. bestiarum (triplet AGC), A. popoffii and Aeromonas sp. HG11 (triplet AGT) and A. encheleia and A. eucrenophila (triplet TCC). All of these species clustered together in the same sub-branch of the tree (Fig. 2). Although this codon encodes serine in all strains of these species, its composition was found to be variable, even in the first codon position (i.e. AGC, AGT and TCC). Because the insertion was found neither in other Aeromonas species nor in representatives of the other genera studied, we consider this to be an exclusive character of this group of species, and as support for the hypothesis that these species have evolved from each other relatively recently. Curiously, this group contains species that show the lowest range of gyrB nucleotide differences; this has been considered to be one of the most controversial taxonomic issues of the genus Aeromonas.
A. salmonicida and A. bestiarum have 2·2–3·3 % nucleotide substitutions in gyrB, which is on the border between the intra- and interspecies ranges observed in the present study. Previous 16S rDNA results have indicated that these two species are only distinguishable by two paired nucleotides at positions 1011 and 1018 (Martínez-Murcia, 1999). However, some strains of A. salmonicida have shown 16S rDNA sequences identical to that of the type strain of A. bestiarum, which is consistent with the difficulties found in the separation of strains of HG2 and HG3 by DNA–DNA hybridization (Hänninen, 1994; Ali et al., 1996). Composition of the inserted codon in gyrB is the same for these two species (and different from all others), adding support for their close phylogenetic relationship. Strains of A. popoffii appear to be closely related to A. bestiarum on the basis of gyrB sequence (2·9–3·6 % divergence), in agreement with DNA–DNA hybridization data from the description of A. popoffii (Huys et al., 1997b), which showed the highest value (51–63 %) with A. bestiarum. Although the species are very closely related, A. popoffii warrants separate species status, as supported by 16S rDNA phylogeny (Martínez-Murcia, 1999) and RFLP analysis of the 16S–23S intergenic spacer region (A. J. Martínez-Murcia and others, unpublished data).
A second example of controversy within the genus Aeromonas is represented by A. encheleia and the unnamed Aeromonas sp. HG11. The gyrB sequences determined in the present study indicate that these species are closely related, as the interspecies divergence was in the range 2·1–2·7 %. The composition of the inserted codon is different for these two species. Classification of strains into one of these species has been very difficult (Martínez-Murcia, 1999). For example, strain CECT 4824 (LMG 13062), formerly classified as A. eucrenophila (Huys et al., 1996a), showed 94 % DNA–DNA hybridization with A. encheleia CECT 4342T (Huys et al., 1997a), but a value of 82 % hybridization with A. eucrenophila was reported in a previous study (Schubert & Hegazi, 1988). On the basis of gyrB sequence, this strain clearly clustered with Aeromonas sp. HG11, a result supported by 16S rDNA sequence analysis (Martínez-Murcia, 1999). Similarly, A. eucrenophila strain CECT 4825 (LMG 13691) has shown 50 % (Huys et al., 1997a) and 80 % (Schubert & Hegazi, 1988) DNA–DNA hybridization with A. eucrenophila LMG 3774T. The current gyrB sequence analysis indicates that this strain belongs to the Aeromonas sp. HG11 (Fig. 2), but its partial 16S rDNA sequence shows highest similarity to A. encheleia (Table 1). The 16S rDNA divergence between A. encheleia and Aeromonas sp. HG11 is based on eight nucleotide differences (Martínez-Murcia, 1999), which at first seems sufficient for a genus as tight as Aeromonas. All eight nucleotide differences were located at hypervariable positions (457–476) of a stem–loop with secondary structure base-pairing, rather than being dispersed around the molecule. This causes some concerns, as molecular clock ‘distortions' (i.e. plesiomorphy) detected on variable stem–loops have previously been reported for closely related individuals (Sneath, 1993; Martínez-Murcia et al., 1999). Consequently, further investigation using a considerable number of newly isolated A. encheleia/HG11 strains is recommended.
A similar case has been detected in the present study. Three isolates, 610, 520c and 531c, formed a separate cluster on the basis of gyrB sequences (Fig. 2), but the cluster was closely related to A. media (2·7–3·1 % substitutions). The distinctiveness of these isolates from A. media was also supported by 16S rDNA sequencing (data not shown); however, nucleotide differences were again located in the stem–loop at position 460 in the V3 region.
In conclusion, the gyrB gene sequence has proved to be an excellent molecular chronometer for phylogenetic inference in the genus Aeromonas. This phylogenetic marker revealed strain groupings consistent with the taxonomy proposed in most previous genetic and phylogenetic studies, particularly in agreement with 16S rDNA sequence analysis. The present analysis may serve to elucidate reported discrepancies between different DNA–DNA hybridization datasets. In addition, the observed sequence diversity at the intraspecies level allows us to propose that gyrB may be useful for strain differentiation and, at the same time, for identification of species following a phylogenetic frame.
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ACKNOWLEDGEMENTS |
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REFERENCES |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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