Numerical classification and identification of Aeromonas genospecies

Non-uniqueness in probabilistic numerical identification of bacteria

In this note we point out an inherent difficulty in numerical identification of bacteria. The problem is that of uniqueness of the taxonomic structure or, in mathematical terms, the lack of statistical identifiability of finite mixtures of multivariate Bernoulli probability distributions shown here.

Phenotypic characteristics of human clinical and environmental Aeromonas in Western Australia

AIM

To determine the phenotypic characteristics of 199 Aeromonas strains comprising 146 clinical and 53 environmental isolates.

METHODS

Identification was based on a scheme consisting of 62 biochemical tests including two novel tests introduced as potential phenotypic markers.

RESULTS

One hundred and eighty-five strains (93%) were identified to species level while eight (4%) resembled members of the Aeromonas hydrophila complex and six (3%) could not be assigned to any taxon. There were no significant phenotypic differences between clinical and environmental strains of the three most commonly isolated species A. hydrophila, Aeromonas veronii subspecies sobria and Aeromonas caviae. The most frequently isolated species in human clinical material and environmental samples was A. hydrophila (54.8% and 45.3%, respectively).

CONCLUSIONS

Phenotypical identification showed that A. hydrophila was the most frequently isolated Aeromonas from clinical and water samples. The introduction of novel tests did not improve the discriminatory power of the scheme and the lack of definitive phenotypical markers continues to hinder Aeromonas taxonomy.

Sphingomonas fennica sp. nov. and Sphingomonas haloaromaticamans sp. nov., outliers of the genus Sphingomonas

Bacterial isolates obtained from polychlorophenol-contaminated sites in Finland (strain K101T) and from a Dutch drinking water well (strain A175T) were characterized taxonomically. 16S rRNA gene sequence analysis, determination of DNA G+C content, physiological characterization, estimation of the ubiquinone and polar lipid patterns and fatty acid content revealed that strains K101T and A175T were similar to Sphingomonas wittichii RW1T but also showed pronounced differences. The DNA G+C contents of the two novel strains were 63.6 and 66.1 mol%, respectively. On the basis of these results, two novel species of the genus Sphingomonas are described, for which the names Sphingomonas haloaromaticamans sp. nov. [type strain A175T (=DSM 13477T=CCUG 53463T)] and Sphingomonas fennica sp. nov. [type strain K101T (=DSM 13665T=CCUG 53462T)] are proposed.

Isolation and characterization of thermo-acidophilic endospore-forming bacteria from the concentrated apple juice-processing environment

Forty-five thermo-acidophilic, spore-forming bacteria were isolated from a concentrated apple juice-processing environment. All of them were Gram-positive, rod shaped, and strictly aerobic that most likely belong to the genus of Alicyclobacillus. A fast identification method-16S rDNA PCR-RFLP was used to identify them. The results indicated that at the similarity level of 87%, apple juice isolates strains of 1-4 and 1-2-4 clustered with the reference strain of A. acidoterrstris DSM 3922T, and 4-2-1, S-22 and 5-1 with A. cycloheptanicus DSM 4006T, respectively. The other tested strains were different from all the reference strains in this study and may be new species of Alicyclobacillus genus or the other. In order to confirm this conclusion, we selected 7 16S rDNA PCR-RFLP identified strains and 5 type strains of Alicyclobacillus genus, carried on 51 kinds of phenotypic characteristics and analysis the data by unweighted pair group method with arithmetic mean (UPGMA). The results showed that the similarity degree between every two strains was lower than 80%. It also suggested that they may be different from each other and the unidentified strains may be new species. In addition, spoilage effects of them on 12 Brix apple juice were also studied. The result suggested that all 19 tested bacterial strains caused apple juice to become turbid, form a precipitate and off odor at varying rates when incubated at 37 degrees C up to 12 days. It suggested that these bacteria are associated with the spoilage of apple juice during storage.

Aeromonas culicicola Pidiyar et al. 2002 is a later subjective synonym of Aeromonas veronii Hickman-Brenner et al. 1987

We re-investigated the taxonomic affiliation between Aeromonas culicicola Pidiyar et al. 2002 and Aeromonas veronii Hickman Brenner et al. 1987, two species that have previously been shown to be closely related on the basis of gyrB and rpoD gene sequencing and amplified fragment length polymorphism fingerprinting. From extended biochemical characterization and fatty acid analysis, it was concluded that A. culicicola did not constitute a unique phenotypic group in the genus Aeromonas but instead clearly fitted the phenotypic description of A. veronii biovar (bv.) sobria. Concordant with the phenotypic results, new DNA-DNA hybridizations revealed reassociation values in the range of 79-88% between the type strains of A. culicicola and A. veronii which indicates that both taxa belong to the same DNA hybridization group. Together with previously reported evidence, we conclude from the new taxonomic data that A. culicicola is a typical member of A. veronii bv. sobria and that its status as a new Aeromonas species is not justified. On the basis of nomenclatural priority, it is therefore proposed that A. culicicola Pidiyar et al. 2002 should be considered as later subjective synonym of A. veronii Hickman-Brenner et al. 1987.

Restriction Fragment Length Polymorphism of 16S–23S rDNA Intergenic Spacer of Aeromonas spp

We analyzed restriction fragment length polymorphism (RFLP) of 16S-23S rDNA intergenic spacer region (ISR) of Aeromonas species. A total of 69 isolates belonging to 18 DNA hybridization groups (HG; equivalent of genomic species) were used in this study. ISRs were amplified by PCR and the products were digested with four restriction endonucleases: Hin6I, Csp6I, TaqI, and TasI. The RFLP patterns obtained after digesting by particular enzymes revealed ISR polymorphism of isolates allocated to individual genomic species. The combined Hin6I, Csp6I, TaqI, and TasI restriction profiles were examined by Dice coefficient (SD) and unweighted pair group method of clustering (UPGMA). The isolates were allocated into 15 groups, three strains were unclustered. The strains belonging to the following genomic species: A. hydrophila, A. bestiarum, A. salmonicida, A. caviae, A. media, A. schubertii, A. allosaccharophila, A. popoffii, and A. culicicola formed distinct clusters. Strains belonging to HG 6, HG 7, HG 11, and HG 16 revealed similar combined RFLP patterns and constituted one group. Similarly, the strains of A. jandaei (HG 9) and the type strain of A. trota were allocated into one cluster. Two isolates of HG 14 formed distinct cluster. We noticed a genetic diversity among A. veronii isolates, the strains were clustered in two groups. Our study showed that combined ISR-RFLP analysis may be used for identification of some species of Aeromonas.

Genetic diversity and population structure of Aeromonas hydrophila, Aer. bestiarum, Aer. salmonicida and Aer. popoffii by multilocus enzyme electrophoresis (MLEE)

Genetic diversity, genetic relationship, identification and population structure of 120 Aeromonas strains (including Aer. hydrophila, Aer. bestiarum, Aer. salmonicida and Aer. popoffii) isolated from various sources were studied by analysis of 15 genetic loci by multilocus enzyme electrophoresis (MLEE). All 15 loci were polymorphic, with an average of 9.4 alleles per locus and a mean genetic diversity (H) of 0.64. Cluster analysis defined at H < or = 0.7 differentiated most of the taxa analysed except the Aer. popoffii and Aer. bestiarum strains, which showed a close genetic relationship. Allelic frequencies of five loci (EST1, HEX, IDH, LDH1 and MDH) identified 94% of the strains. The index of association (IA) for the total sample was 2.38 and IA values calculated for the different populations were always significantly different from zero. These results suggest that the population structure of this Aeromonas sample is strongly clonal, confirm the taxonomic status of the analysed species in population genetics terms, and show the usefulness of MLEE for identifying Aeromonas species.

Taxonomic study of sucrose-positive Aeromonas jandaei-like isolates from faeces, water and eels: emendation of A. jandaei Carnahan et al. 1992

Fourteen sucrose-positive Aeromonas jandaei-like isolates from fresh water and reared European eels were subjected to a polyphasic study to determine their taxonomic position. Numerical taxonomy was used to analyse phenotypic data obtained for these isolates and 43 type and reference strains representative of recognized Aeromonas species. The A. jandaei cluster (phenon 1) was defined at 81.6 % similarity (S(J)); this included the A. jandaei-like isolates, the sucrose-positive strain Aeromonas veronii biogroup sobria CECT 4910 and nearly all A. jandaei reference strains used in the study. Four other reference strains of A. veronii biogroup sobria and the type strain of Aeromonas ichthiosmia were peripheral to the A. jandaei cluster. The supra-group 'A. jandaei-A.veronii biogroup sobria-A. ichthiosmia' was linked at 80.7 % similarity (S(J)) and was clearly segregated from the phenotypic core of the A. veronii biogroup sobria species, which was related to the reference strain Popoff 224 (CECT 4835). DNA relatedness between strains grouped in the A. jandaei cluster (phenon 1) and A. jandaei CECT 4228(T) ranged from 70 to 100 %, but was below 50 % when DNAs from A. veronii biogroup sobria CECT 4835, A. veronii biogroup veronii CECT 4257(T) and A. ichthiosmia CECT 4486(T) were used. In addition, DNA relatedness between peripheral A. veronii biogroup sobria strains and the species A. jandaei (CECT 4228(T)), A. veronii (CECT 4257(T), CECT 4835) and A. ichthiosmia (CECT 4486(T)) was always below 54 %, as it was between the species A. ichthiosmia (CECT 4486(T)) and A. veronii (CECT 4257(T), CECT 4835). Emendation of A. jandaei is proposed; this taxon now includes sucrose-positive clinical and environmental strains as well as environmental isolates that are pathogenic for fish and humans. Other new traits for this species are the ability to grow at 4-42 degrees C, acid production from glycerol but not from lactose, D-melibiose or D-raffinose, the use of D-gluconate, L-glutamate or L-proline but not L-lactate, L-alanine, L-arabinose or L-arginine, hydrolytic activity against casein, elastin, starch and lecithin and the inability to lyse arbutin. The DNA G+C content of A. jandaei is also reported for the first time; it ranges from 58.1 to 61.1 mol%. On the other hand, the DNA relatedness data support the classification of peripheral reference strains of A. veronii biogroup sobria outside this taxon, indicating that biogroup sobria requires further revision.

Aeromonas hydrophila subsp. ranae subsp. nov., isolated from septicaemic farmed frogs in Thailand

A group of seven sucrose-negative Aeromonas strains (referred to as group Au) isolated from the internal organs of septicaemic farmed frogs (Rana rugulosa) in Thailand was subjected to a polyphasic taxonomic study including fluorescent amplified fragment length polymorphism (FAFLP) and ERIC-PCR fingerprinting, 16S rDNA sequencing, microplate DNA-DNA hybridizations and extensive phenotypic characterization. Comparison of FAFLP and ERIC-PCR fingerprints indicated that the group Au isolates belonged to the species Aeromonas hydrophila DNA hybridization group (HG) 1 in which they represent a genotypic subgroup closely affiliated to A. hydrophila subsp. hydrophila and subsp. dhakensis. One representative of the Au group exhibited > or = 99.0% 16S rDNA sequence similarity with the type strains of the two A. hydrophila subspecies. DNA-DNA hybridization with type and reference strains of all known Aeromonas taxa revealed that the Au group represented a homogeneous taxon that exhibited the highest relatedness with members of the two A. hydrophila subspecies, ranging from 75 to 93%. Phenotypic characterization on the basis of 152 features further revealed that the Au group isolates differed from A. hydrophila subsp. hydrophila or subsp. dhakensis in a total of 13 biochemical properties. Of these, assimilation of L-glycine and isobutyrate as sole carbon source, acid production from salicin and D-sucrose, and aesculin hydrolysis were of diagnostic value. From the results of this study, it can be concluded that the Aeromonas frog isolates of the Au group represent a new subspecies of A. hydrophila, for which the name Aeromonas hydrophila subsp. ranae subsp. nov. is proposed. Its type strain is Au-1D12(T) (=LMG 19707(T) = CCUG 46211(T)).

Biochemical identification and numerical taxonomy of Aeromonas spp. isolated from environmental and clinical samples in Spain

AIMS

To study the phenotypic characteristics of Aeromonas spp. from environmental and clinical samples in Spain and to cluster these strains by numerical taxonomy.

METHODS AND RESULTS

A collection of 202 Aeromonas strains isolated from bivalve molluscs, water and clinical samples was tested for 64 phenotypic properties; 91% of these isolates were identified at species level. Aeromonas caviae was predominant in bivalve molluscs and Aerom. bestiarum in freshwater samples. Cluster analyses revealed eight different phena: three containing more than one DNA-DNA hybridization group but including strains that belong to the same phenospecies complex (Aerom. hydrophila, Aerom. sobria and Aerom. caviae), Aerom. encheleia, Aerom. trota and three containing unidentified Aeromonas strains isolated from bivalve molluscs.

CONCLUSIONS

Aeromonas spp. are widely distributed in environmental and clinical sources. A selection of 16 of the phenotypical tests chosen allowed the identification of most isolates (91%), although some strains remain unidentified, mainly isolates from bivalve molluscs, suggesting the presence of new Aeromonas species. Numerical taxonomy was not in total concordance with the identification of the studied strains.

SIGNIFICANCE AND IMPACT OF THE STUDY

Numerical taxonomy of Aeromonas strains isolated from different sources revealed the presence of potentially pathogenic Aeromonas spp., especially in bivalve molluscs, and phena with unidentified strains that suggest new Aeromonas species.

Phenotypic study by numerical taxonomy of strains belonging to the genus Aeromonas

AIMS

This study was undertaken to cluster and identify a large collection of Aeromonas strains.

METHODS AND RESULTS

Numerical taxonomy was used to analyse phenotypic data obtained on 54 new isolates taken from water, fish, snails, sputum and 99 type and reference strains. Each strain was tested for 121 characters but only the data for 71 were analysed using the 'SSM' and 'SJ' coefficients, and the UPGMA clustering algorithm. At SJ values of > or = 81.6% the strains clustered into 22 phenons which were identified as Aer. jandaei, Aer. hydrophila, Aer. encheleia, Aer. veronii biogroup veronii, Aer. trota, Aer. caviae, Aer. eucrenophila, Aer. ichthiosmia, Aer. sobria, Aer. allosaccharophila, Aer. media, Aer. schubertii and Aer. salmonicida. The species Aer. veronii biogroup sobria was represented by several clusters which formed two phenotypic cores, the first related to reference strain CECT 4246 and the second related to CECT 4835. A good correlation was generally observed among this phenotypic clustering and previous genomic and phylogenetic data. In addition, three new phenotypic groups were found, which may represent new Aeromonas species.

CONCLUSIONS

The phenetic approach was found to be a necessary tool to delimitate and identify the Aeromonas species.

SIGNIFICANCE AND IMPACT OF THE STUDY

Valuable traits for identifying Aeromonas as well as the possible existence of new Aeromonas species or biotypes are indicated.

Miniaturized tests for computer-assisted identification of motile Aeromonas species with an improved probability matrix

AIMS

To develop miniaturized tests for the phenotypic identification of motile Aeromonas species using an improved probability matrix.

METHODS AND RESULTS

Conventional tests were miniaturized for use in 96-well plates, and their performance assessed using 60 aeromonads comprising type and reference strains as well as clinical, fish and water isolates. A revised probability matrix for Aeromonas hybridization groups 1-14, including A. allosaccharophila, A. bestiarum, A. encheleia and A. popoffii, was developed. Using 26 tests, all the reference strains were correctly identified with the revised probability matrix, and 80% of the isolates were correctly identified at a Willcox probability level of 95%.

CONCLUSION

The compact test format, coupled with a robust identification matrix, provides a convenient basis for identifying motile aeromonads.

SIGNIFICANCE AND IMPACT OF THE STUDY

The identification system for identifying aeromonads will be of use to medical and veterinary laboratories undertaking disease diagnosis.

Characterization of oxytetracycline-resistant heterotrophic bacteria originating from hospital and freshwater fishfarm environments in England and Ireland

This ecotaxonomic study compared the antibiotic tolerance among culturable oxytetracyline-resistant (Ot(r)) heterotrophic strains isolated from two aquatic environments representing human activities in health care and aquaculture, namely hospital effluents and freshwater fishfarms. Using a standardized methodology, samples taken in England and Ireland were analyzed to determine the antibiotic tolerance profiles of two groups of culturable Ot(r) bacterial isolates at the intergeneric and intrageneric level comprising heterotrophs (189 strains) and mesophilic Aeromonas spp. (153 strains), respectively. Antibiogram data of heterotrophic isolates revealed that Irish hospital strains comprised higher frequencies of multi-tolerance than those originating from fishfarm environments whereas a reverse correlation was found among the English heterotrophs. Polyphasic identification of the isolates using fatty acid analysis and API 20E profiling showed that this difference arose from the unique taxonomic diversity within each heterotrophic strain set. Acinetobacter (27%) and Brevundimonas (22%) were predominant among the Irish Ot(r) fishfarm isolates, whereas isolates originating from the English aquaculture site almost entirely consisted of Stenotrophomonas maltophilia (86%) exhibiting high frequencies of tolerance to ampicillin and streptomycin. Within both the English and the Irish Ot(r) Aeromonas strain sets, on the other hand, the hospital strain sets displayed higher numbers of multi-tolerant isolates than to fishfarm isolates although country-specific differences were observed for individual antimicrobial agents. The typical occurrence of kanamycin-tolerant aeromonads in the Irish hospital site could to some extent be linked to the typical presence of A. hydrophila DNA hybridization group (HG) 3 strains as determined by fatty acid analysis and fluorescent amplified fragment length polymorphism (FAFLP) fingerprinting. Essentially, these data indicate that tolerance profiles in a specific environment of one country do not necessarily reflect the corresponding tolerance profiles of the same type of environment in another country, and this mainly as a result of the unique taxonomic composition of each site. Ot(r) representatives of Acinetobacter, S. maltophilia, and A. veronii biovar sobria HG8 were common to most if not all of the four sites under study, indicating that these three taxa may serve as potential indicator organisms for monitoring antibiotic tolerance among indigenous bacterial populations in various aquatic environments.

Diverse restriction fragment length polymorphism patterns of the PCR-amplified 16S rRNA genes in Aeromonas veronii strains and possible misidentification of Aeromonas species

Restriction fragment length polymorphism analysis after PCR amplification (RFLP-PCR) of the 16S rRNA gene has been previously proposed as a rapid method to identify Aeromonas species. In the present study, the precision of RFLP-PCR was evaluated with 62 Aeromonas reference strains. The analysis revealed that Aeromonas veronii biovar sobria strains produce various patterns, possibly leading to its misidentification as an environmental species. For most other Aeromonas species little variation was noted. This study supports the usefulness of RFLP-PCR analysis to separate three clinically important species but also reveals possible misidentifications that necessitate further biochemical tests to validate the preliminary identification.

Taxonomic relationships among spotted fever group rickettsiae as revealed by antigenic analysis with monoclonal antibodies

The spotted fever group (SFG) is made up of more than 20 different rickettsial species and strains. Study of the taxonomic relationships among the group has been attempted by phenotypic, genotypic, and phylogenetic analyses. In this study, we determined taxonomic relationships among the SFG rickettsiae by comparative analysis of immunogenic epitopes reactive against a panel of monoclonal antibodies. A total of 98 monoclonal antibodies, which were directed against epitopes on the major immunodominant proteins or on the lipopolysaccharide-like antigens of strains of Rickettsia africae, Rickettsia conorii, Rickettsia massiliae, Rickettsia akari, Rickettsia sibirica, and Rickettsia slovaca, were used in the study. The distribution and expression of the epitopes among 29 SFG rickettsiae and Rickettsia bellii were assessed by determination of reaction titers in a microimmunofluorescence assay. The results were scored as numerical taxonomic data, and cluster analysis was used to construct a dendrogram. The architecture of this dendrogram was consistent with previous taxonomic studies, and the implications of this and other findings are discussed.

Multiresistant Staphylococcus epidermidis in a neonatal care unit

OBJECTIVE: To study the presence and diversity of types of Staphylococcus epidermidis in the neonatal intensive care unit of a university hospital. METHODS: During a period of 6 weeks, samples were taken from nose, external auditory canal, axilla, groin and umbilicus from consecutively admitted patients. Patients were sampled two times a week for up to 2 weeks. Isolates of S. epidermidis were characterized by antibiogram, plasmid pattern and biotype. RESULTS: Fifteen patients were included. Each patient was sampled in one to four successive surveys, depending on the admission period. A total of 128 isolates of S. epidermidis were obtained and allocated to seven antibiogram types, 36 plasmid types and 14 biotypes. One plasmid type found in 58 isolates (six patients) corresponded with one multiresistant antibiogram type. The number of isolates with these characteristics increased per neonate from the first survey to the fourth. Nineteen isolates from four patients were allocated to a second plasmid type and were of a common antibiogram type. The remaining 34 plasmid types were sporadic. No clear correspondence of biotypes with antibiogram or plasmid types was found. CONCLUSIONS: The present study revealed the increase in colonization of a multiresistant type of S. epidermidis in the compromised patients during admission to the ward. Further studies have to assess whether this type remains persistent in the ward.

A biochemical protocol for the differentiation of current genomospecies of Aeromonas

A data file consisting of 40 biochemical and physiological tests for the differentiation of aeromonads was constructed based upon existing published data from various geographical locations and laboratories. The data file covers all the current genomospecies (or hybridisation groups) of Aeromonas and is therefore applicable to bacteriologists from a wide variety of fields. The protocol derived from the data file was adapted for use with a semi-interactive computer identification program. This program was challenged with the type strains of all the currently recognised genomospecies and each genomospecies was correctly identified, with only one strain (ATCC 7966, HG1) having an identification probability of less than 90%. The program was also tested with environmental and clinical isolates and again identifications were achieved with high probabilities. This protocol is designed for use on presumptive isolates of Aeromonas spp. and can be carried out in routine laboratories not equipped to perform the complex DNA hybridisation techniques which are currently used for the differentiation of genomospecies of Aeromonas.

Study of the intergenic exeF-exeG region and its application as a simple preliminary test for Aeromonas spp

The exeF-exeG intergenic regions from different hybridization groups (HG) of Aeromonas were studied by PCR amplification using a single pair of primers. Six main classes of PCR products were identified according to size: 360 bp, 320 bp, 280 bp, 230-240 bp, 220 bp and 160 bp. Direct sequencing of the PCR products indicated that the shorter intergenic regions had probably originated from deletion of DNA segments between direct repeats. Correlation of certain PCR products with Aeromonas caviae (HG4), A. caviae (HG5), A. veronii (HG8) and A. salmonicida (HG3) was revealed. The PCR reaction was also shown to be generally specific for Aeromonas spp. Thus, the usefulness of this rapid, single colony-based PCR test for both identification and preliminary differentiation of Aeromonas spp. is demonstrated.

Application of a colorimetric DNA-DNA hybridization method for identification of Aeromonas genomic species, isolated from diarrheal stools

The colorimetric DNA-DNA hybridization method for the identification of 18 strains of Aeromonas spp. isolated from human stools was used. Bacterial isolates were also examined by phenotypic characteristics. On the basis of biochemical tests 13 strains were included in phenogroup A. caviae and 5 strains in A. sobria. Identification to the species level was obtained by colorimetric hybridization method. DNA-DNA similarity values showed that isolates of A. caviae group belong to hybridization group (HG) 4 whereas isolates of A. sobria belong to HG 8/10. DNA relatedness results obtained by the colorimetric method showed good agreement with values detected by the spectrophotometric method. The background in the colorimetric method is lower than in the spectrophotometric one. Results of this study indicate the usefulness of the colorimetric DNA-DNA hybridization in microplates method for the identification of Aeromonas genomic species, isolated from human diarrheal stools.

Distribution of Aeromonas phenospecies and genospecies among strains isolated from water, foods or from human clinical samples

A total of 332 Aeromonas spp. originating from drinking water (n = 75), fresh water (n = 57), chicken and ground beef (107), human faecal samples in association with travelling (n = 49), human faecal samples not associated with travelling (n = 38), and six strains from human blood cultures were studied by phenotypic methods and by using analysis of ribopatterns as a molecular method for the identification of the 13 known hybridization groups (HGs). Also included were the reference strains of each HG. A. hydrophila HG 1, A. caviae HG 4 and A. veronii biotype sobria HG 8/10 were the most important genospecies identified in human faecal samples. A. hydrophila HG 2 and A. media HG 5B predominated in drinking water and A. hydrophila HG 2 and HG 3, A. media HG 5A and HG 5B predominated in fresh water. In drinking water only one isolate was A. hydrophila HG 1 and two isolates were A. caviae HG 4. Clinically important Aeromonas spp. HG 1 (A. hydrophila), HG 4 (A. caviae) and HG 8/10 (A. veronii biotype sobria) were common in chicken and ground beef. In contrast to the drinking water samples, HG 5A was common in chicken and ground beef samples. Atypical, unidentified isolates were most often found in fresh water samples (12/57 strains). Although water has been suspected of being an important source of human aeromonas infections, clinically important HGs were found to be in the minority among Aeromonas spp. identified in drinking water or fresh water. The distribution of Aeromonas spp. HGs among drinking water, chicken and ground beef samples was also different, suggesting that contamination of meat or chicken may not originate from water.

Maximum growth temperature ranges of Aeromonas Spp. isolated from clinical or environmental sources

Only a limited number of phenotypic tests are available for the differentiation of all 13 known hybridization groups (HG) of Aeromonas spp. These organisms have a wide spectrum of warm-blooded and cold-blooded hosts. In the present study, the maximum growth temperatures (tmax) of the most common HGs of Aeromonas spp. originating from human fecal samples, food, water, and healthy and diseased fish were determined with a plate-type continuous temperature-gradient incubator. We observed that determination of the tmax can be applied for differentiation of HG 1 from HG 2 and 3 (phenospecies A. hydrophila); HG 6 from HG 4, 5A, and 5B (phenospecies A. caviae); HG 7 from HG 8/10 (phenospecies A. sobria); and HG 11 from HG 8/10 (phenospecies A. veronii). HG 1, 4, 8/10, and 13 strains occurring also in human clinical samples had a high tmax, about 40°C or higher. Hybridization group 2, 3, 5A, and 5B strains, which in most cases originated from water or food, had tmax values in the range of about 36-39°C, while HG 6, 7, and 11 had tmax values in the range of about 33-37°C. Fish pathogenic strains of A. salmonicida subsp. salmonicida and subsp. achromogenes had the lowest tmax values from about 30 to 35°C.

Diversity of Aeromonas sp. in Flemish drinking water production plants as determined by gas-liquid chromatographic analysis of cellular fatty acid methyl esters (FAMEs)

Gas-liquid chromatography of cellular fatty acid methyl esters (FAMEs) was used to determine the phenotypic and genotypic diversity among 489 presumptive Aeromonas strains isolated from five Flemish drinking water production plants. FAME profiles were compared with the predetermined library profiles of a representative database, AER48C, which contains the mean FAME data of all 14 currently established hybridization groups (HGs) or genospecies within Aeromonas. Using AER48C, more than 93% (457 strains) of all presumptive aeromonads isolated on ampicillin-dextrin agar were unequivocally identified as belonging to this genus. Moreover, 85.5% and 73.5% of these strains could be assigned to a particular phenospecies or HG, respectively. Raw and treated surface water samples were dominated by members of the Aer. hydrophila complex (38.8%, comprising HGs 1-3), followed by the Aer. caviae complex (22.7%, comprising HGs 4-6) and the Aer. sobria complex (16.7%, comprising HGs 7-9). HGs 3, 5A/B and 8 were the most prominent genospecies in this type of water. On the other hand, it was found that raw and treated phreatic groundwater samples displayed a much more limited species diversity since these were almost entirely dominated (95.8%) by strains belonging to HGs 2 and 3 of the Aer. hydrophila complex. In general, flocculation-decantation and sand filtration were not shown to influence the overall species distribution in any of the plants examined.

Non-uniqueness in probabilistic numerical identification of bacteria

In this note we point out an inherent difficulty in numerical identification of bacteria. The problem is that of uniqueness of the taxonomic structure or, in mathematical terms, the lack of statistical identifiability of finite mixtures of multivariate Bernoulli probability distributions shown here.

Numerical classification and identification of Acinetobacter genomic species

A total of 211 Acinetobacter strains (representing all currently recognized genomic species) were tested for 329 biochemical characters. Overall similarities of all strains were determined for 145 characters by numerical taxonomic techniques, the UPGMA algorithm and the S(SM)) and the S(J) coefficients as measures of similarity. Seven clusters (two or more strains) and three unclustered strains were recovered at a similarity level of 80.0% (S(SM). At this level a complete correspondence between phenotypic cluster and genomic species was found only for genomic species 12 (Ac. radioresistens). At higher similarity levels (84.0% to 84.6% (S(SM)), however, several subclusters were found, each representing a single genomic species. An exception were the strains belonging to the genetically closely related species of the Acinetobacter calcoaceticus-baumannii complex. These were recovered scattered in several subclusters. The degree of genomic relatedness between some DNA groups correlated with phenotypic similarities, especially for DNA group 8 (Ac. Iwoffii) and 15 of Tjernberg and Ursing, and for DNA group 4 (Ac. haemolyticus) and 6. For the majority of genomic species, two identification matrices were constructed consisting of 22 and 10 diagnostic characters, respectively. The correct identification rates for the matrices were 98.0% (22 tests) and 90.8% (10 tests) taking a Willcox probability > 0.9. For unambiguous identification of some genomic species, however, additional methods (preferably DNA-DNA hybridization or ribotyping) should be used.