DNA-DNA hybridization (DDH) values have been used by bacterial taxonomists since the 1960s to determine relatedness between strains and are still the most important criterion in the delineation of bacterial species. Since the extent of hybridization between a pair of strains is ultimately governed by their respective genomic sequences, we examined the quantitative relationship between DDH values and genome sequence-derived parameters, such as the average nucleotide identity (ANI) of common genes and the percentage of conserved DNA. A total of 124 DDH values were determined for 28 strains for which genome sequences were available. The strains belong to six important and diverse groups of bacteria for which the intra-group 16S rRNA gene sequence identity was greater than 94 %. The results revealed a close relationship between DDH values and ANI and between DNA-DNA hybridization and the percentage of conserved DNA for each pair of strains. The recommended cut-off point of 70 % DDH for species delineation corresponded to 95 % ANI and 69 % conserved DNA. When the analysis was restricted to the protein-coding portion of the genome, 70 % DDH corresponded to 85 % conserved genes for a pair of strains. These results reveal extensive gene diversity within the current concept of "species". Examination of reciprocal values indicated that the level of experimental error associated with the DDH method is too high to reveal the subtle differences in genome size among the strains sampled. It is concluded that ANI can accurately replace DDH values for strains for which genome sequences are available.

DNA–DNA hybridization values and their relationship to whole-genome sequence similarities

In this paper minimal standards for the description of new genera and cultivable species in the family Flavobacteriaceae are proposed in accordance with Recommendation 30b of the Bacteriological Code (1990 Revision). In addition to specified phenotypic characteristics, the description of new species should be based on DNA-DNA hybridization data, and the placement of new taxa should be consistent with phylogenetic data derived from 16S rRNA sequencing. An emended description of the family is also proposed as several new taxa have been described since 1996. These proposals have been endorsed by the members of the Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes.

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Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family.

Polyphasic taxonomy, a consensus approach to bacterial systematics.

Summary: Over the past decade, the genus Aeromonas has undergone a number of significant changes of practical importance to clinical microbiologists and scientists alike. In parallel with the molecular revolution in microbiology, several new species have been identified on a phylogenetic basis, and the genome of the type species, A. hydrophila ATCC 7966, has been sequenced. In addition to established disease associations, Aeromonas has been shown to be a significant cause of infections associated with natural disasters (hurricanes, tsunamis, and earthquakes) and has been linked to emerging or new illnesses, including near-drowning events, prostatitis, and hemolytic-uremic syndrome. Despite these achievements, issues still remain regarding the role that Aeromonas plays in bacterial gastroenteritis, the extent to which species identification should be attempted in the clinical laboratory, and laboratory reporting of test results from contaminated body sites containing aeromonads. This article provides an extensive review of these topics, in addition to others, such as taxonomic issues, microbial pathogenicity, and antimicrobial resistance markers.

The Genus Aeromonas: Taxonomy, Pathogenicity, and Infection

The species concept is a recurrent controversial issue that preoccupies philosophers as well as biologists of all disciplines. Prokaryotic species concept has its own history and results from a series of empirical improvements parallel to the development of the techniques of analysis. Among the microbial taxonomists, there is general agreement that the species concept currently in use is useful, pragmatic and universally applicable within the prokaryotic world. However, this empirically designed concept is not encompassed by any of the, at least, 22 concepts described for eukaryotes. The species could be described as ‘a monophyletic and genomically coherent cluster of individual organisms that show a high degree of overall similarity in many independent characteristics, and is diagnosable by a discriminative phenotypic property’. We suggest to refer it as a phylo-phenetic species concept. Here, we discuss the validity of the concept in use which we believe is more pragmatic in comparison with those concepts described for eukaryotes.

The species concept for prokaryotes.

Reproducibility of relative binding ratios (RBR) was studied with 26 labeled DNA-unlabeled DNA hybridization reactions carried out at two temperatures (60 and 75°C) and following three procedures: the S1-nuclease method with precipitation of S1-resistant DNA by trichloroacetic acid (S1-TCA), the S1-nuclease method with adsorption of S1-resistant DNA onto DE81 filters (S1-DE81), and the hydroxyapatite (HA) method. Analyses of variance indicated that different hybridization methods give different RBR, but similar percent divirgence (ΔT
 m) results. A curvilinear relationship was found between RBR data obtained with S1-TCA and HA procedures at 60 or 75°C, and between 60°C RBR data obtained with S1-DE81 and HA procedures. At 75°C, RBR obtained with S1-DE81 and HA methods are comparable without any transformation of the data.

Reproducibility and correlation study of three deoxyribonucleic acid hybridization procedures

The alternative sigma factor RpoS (sigma S) is required for Salmonella virulence in mice. We report the immunizing capacity of Salmonella typhimurium rpoS and rpoS aroA mutants to protect susceptible BALB/c mice against subsequent oral challenge with virulent S. typhimurium. When administered orally or intraperitoneally, rpoS derivatives of the mouse-virulent S. typhimurium strains, C52 and SL1344, were highly attenuated and were efficient single-dose live vaccines. rpoS aroA mutants were more attenuated than corresponding single aroA or rpoS mutants, as assessed after oral or intraperitoneal administration, but retained significant ability to protect mice against salmonellosis. Salmonella rpoS and rpoS aroA mutants therefore deserve serious consideration for rational vaccine design. Consistent with this, Salmonella typhi Ty2, a 'wild-type' strain used widely for the development of human live-vaccine candidates against typhoid fever, was shown to be defective for rpoS. In addition, our results demonstrate that rpoS not only controls the growth and persistence of S. typhimurium in deep lymphoid organs, but also plays a role during the initial stages of oral infection.

Virulence and vaccine potential of Salmonella typhimurium mutants deficient in the expression of the RpoS (sigma S) regulon.

Relatedness among 55 motileAeromonas strains was assessed by determining the extent of reassociation in heterologous DNA preparations. S1 nuclease and diethylaminoethyl-cellulose filters were used to separate reassociated nucleotide sequences from nonreassociated sequences and to determine the thermal stability of related nucleotide sequences. The motile aeromonads would presently consist of three species:A. hydrophila (type strain ATCC 7966),A. caviae (type strain ATCC 15468), andA. sobria (type strain CIP 7433). These three species are clearly separated on the basis of both biochemical characteristics and similarities in DNA. Each of these three species contains more than one hybridization group: three groups inA. hydrophila; two groups inA. caviae; and at least two groups inA. sobria. DNA hybridization groups are biochemically similar within each species. When additional data is available, these separate DNA hybridization groups may merit designation. Any decision to delineate species in terms of DNA hybridization groups must await a phenotypic basis for their separation.

Polynucleotide sequence relatedness among motileAeromonas species

Summary The growth pattern of Salmonella enterica subsp. enterica serotype Typhimurium (Typhimurium) was studied in mice to examine the role of the 60-Mdal virulence-associated plasmid in the pathogenesis of mouse typhoid. After repeated subcultures at 45°C, isogenic variants harbouring the virulence-associated plasmid (strains C52, TM122 and TM332) or having lost this large plasmid (strains C53, TM123 and TM333) were obtained from three parental strains (strains C5, TM 12 and TM33, respectively). Plasmid plP1350, present in strain C52, was tagged by Tn10 and transferred by successive conjugations to strains C53, TM123 and TM333. The behaviour of these three Typhimurium lines was studied in C57BL/6, DBA2, 136132 (C57BL/6 x DBA2 F1 hybrid) and OF, mice after oral infection, subcutaneous injection into the hind footpad or intravenous inoculation. The kinetics of organ colonization were followed at intervals after injection by enumeration of viable bacteria in caecum, mesenteric or popliteal lymph node, spleen, liver, kidney and lung depending on the route of infection. Strains harbouring virulence plasmid and their cured derivatives did not differ significantly in their ability to colonize caecal content and to translocate to draining lymph nodes. Elimination of the virulence plasmid was correlated with a significant reduction in the ability of cured variants to colonize spleen and liver. Reintroduction of the virulence plasmid into plasmidless variants restored the virulence to the level originally observed. These data demonstrate that a 60-Mdal plasmid in Typhimurium strains is necessary to ensure colonization of spleen and liver of experimentally infected mice.

Virulence-associated plasmids of Salmonella serotype Typhimurium in experimental murine infection.

We report the identification and functional analysis of katN, a gene encoding a non-haem catalase of Salmonella enterica serotype Typhimurium. katN, which is not present in Escherichia coli, is located between the yciGFE and yciD E. coli homologues in the Salmonella genome. Its predicted protein product has a molecular weight of 31 826 Da and is similar to the Mn-catalases of Lactobacillus plantarum and Thermus spp. Its product, KatN, was visualized as a 37 kDa protein in E. coli maxicells. A KatN recombinant protein, containing six histidine residues at its C-terminus, was purified, and its catalase activity was observed on a non-denaturing polyacrylamide gel. KatN was also visualized by catalase activity gel staining of bacterial cell extracts. Its expression was shown to be regulated by growth phase and rpoS. Northern blotting indicated that kat forms an operon with the upstream yciGFE genes. A putative rpoS-regulated promoter was identified upstream of yciG. Southern blotting revealed that katN is conserved within Salmonella serovars. katN homologues were found in Pseudomonas aeruginosa, Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter cloacae and Serratia marcescens. A katN mutation did not appear to affect the hydrogen peroxide (H2O2) response of Salmonella. However, the expression of katN increased the H2O2 resistance of unadapted cells in the exponential phase and of rpoS mutants in stationary phase. Thus, KatN may contribute to hydrogen peroxide resistance in Salmonella in certain environmental conditions.

Colette Coynault

Papers

Reproducibility and correlation study of three deoxyribonucleic acid hybridization procedures

Virulence and vaccine potential of Salmonella typhimurium mutants deficient in the expression of the RpoS (sigma S) regulon.

Polynucleotide sequence relatedness among motileAeromonas species

Virulence-associated plasmids of Salmonella serotype Typhimurium in experimental murine infection.

Identification of a non-haem catalase in Salmonella and its regulation by RpoS (sigmaS).