A probability matrix for the identification of vibrios

A probability matrix for computer-assisted identification of vibrios has been constructed, based on the API 20E system. Data were gathered from 173 strains representing 31 taxa of vibrios and related organisms, from a variety of sources. The matrix was tested internally by four statistical programs. Program OVERMAT tested the separation and program MOSTTYP the discretion and homogeneity of the taxa. Most of the taxa were satisfactory but a few were less so; reasons for this are discussed. Program CHARSEP and program DIACHAR tested the separation and diagnostic values, respectively, of the characters used. The overall test error was 4–5%. The matrix was assessed externally by its performance in the identification of vibrio-like strains isolated from freshwater. Of 243 wild strains, 79–4% were identified with ten taxa, with a Willcox score of ζ 0–99.     

A reappraisal of the terverticillate penicillia using biochemical, physiological and morphological features. II. Identification

The data from an integrated numerical classification was used to construct identification schemes for some fasciculate penicillia. The identification schemes were presented as a synoptic key and a frequency matrix for computer-assisted identification. Statistical testing of the frequency matrix showed that although character separation values were generally low, only four pairs of taxa showed overlap greater than that expected for a rectangular distribution. The identification schemes were tested practically with 52 previously studied strains and 51 further cultures. A synoptic key based on 10 and 90% cutoff limits was used to correctly identify 44 of the 51 additional strains, although this proved very sensitive to single test discrepancies. The frequency matrix was used to correctly identify 45 of the additional strains with a Willcox probability score and this was compared to identifications based on the modal likelihood fraction.     

Numerical classification and identification of Bacillus sphaericus including some strains pathogenic for mosquito larvae

Ninety-one strains of Bacillus sphaericus, including representatives of all the established DNA homology groups, related round-spored and oval-spored species, and six strains pathogenic for mosquito larvae, were examined for 155 characters. Numerical analyses (Jaccard coefficient/average linkage clustering) based on the 88 variable features revealed 14 clusters at the 79% similarity level that contained more than one strain and 17 single member clusters. All insect pathogenic strains were recovered in a single cluster and the classification was in accord with an established classification based on DNA sequence homology. Two frequency matrices for probabilistic identification were constructed and tested. A comprehensive matrix comprising 14 mesophilic, round-spored taxa and 27 tests gave good results for identification of hypothetical median organisms, cluster overlap and identifications of representative strains (based on data generated in the classification study). Reference strains for the 14 taxa and eight additional insect pathogenic strains were examined for the 27 tests and were correctly identified with high scores using this matrix. A second matrix comprising seven taxa and 13 tests also performed well in the theoretical evaluation and correctly identified the reference strains and insect pathogenic strains.     

Distribution and ecology of Vibrio vulnificus and other lactose-fermenting marine vibrios in coastal waters of the southeastern United States.

Water, sediment, plankton, and animal samples from five coastal sites from North Carolina to Georgia were sampled for their lactose-fermenting vibrio populations. Over 20% of all vibrios tested were sucrose negative and o-nitrophenyl-beta-D-galactopyranoside (ONPG) positive, suggesting identification as the human pathogen Vibrio vulnificus. These vibrios were isolated from all sample sites and sources (water, sediment, plankton, and animals). Correlations with several of 19 environmental parameters monitored at each site were found for total vibrios. The presence of ONPG-positive, sucrose-negative vibrios was correlated with hydrocarbon levels in the water and, in the case of plankton samples, with salinity. A total of 279 sucrose-negative, ONPG-positive isolates were subjected to numerical taxonomic analysis, which resulted in three major clusters. Cluster I corresponded to and included 11 reference strains of V. vulnificus. Cluster II contained the largest number (133) of isolates, of which the great majority were bioluminescent. Although having a resemblance to V. harveyi, the isolates were ONPG positive and many were H2S positive. Cluster III consisted of strains similar to the group F vibrios (V. fluvialis). Of all of the isolates, 55% were luminescent, of which over 20% were lethal when injected into mice. Problems involved in detecting lactose fermentation among marine vibrios and the potential pathogenicity of these organisms are discussed.     

Characterization of toxigenic vibrios isolated from the freshwater environment of Hiroshima, Japan.

The occurrence and characterization of toxigenic vibrios in surface water and sediment samples of the fresh water environment of the Ohta River were studied. The membrane filter, pad preenrichment technique, followed by the placement of membranes onto thiosulfate citrate-bile salt-sucrose agar, was used for the enumeration of total vibrios. Qualitative examination of pathogenic vibrios was also attempted. In addition, a survey was conducted to determine the incidence of Clostridium botulinum in sediment samples of the Ohta River and the Hiroshima coast. In the identification of 361 strains, 12 species of Vibrio and two species of Listonella were observed. Non-01 Vibrio cholerae was prevalent among the members of the genus Vibrio. Vibrio parahaemolyticus (serotype 04:K34), isolated in fresh water, is significant and suggests that some still unknown conditions promote the survival of these organisms in fresh water. An estimated 132 strains were hemolytic by a simple agar method, and further characterization revealed that 82% of the hemolytic vibrios (107 strains) produced various toxins. About 71% (93 strains) elaborated cytotoxin, 55% (72 strains) produced hemolysin, and 44% (58 strains) responded for both cytotoxin and hemolysin in the crude toxin extracts. All the non-01 V. cholerae showed cytotoxic activity, and the virulent strains of Vibrio fluvialis and Vibrio spp. showed cytotonic responses in RK-13 cells. Of 36 sediment samples tested, 10 harbored C. botulinum spores (28%) and were isolated invariably in all the regions of the Hiroshima coast and in the Ohta River, except the upper region of the Ohta River.     

Characterization of toxigenic vibrios isolated from the freshwater environment of Hiroshima, Japan

The occurrence and characterization of toxigenic vibrios in surface water and sediment samples of the fresh water environment of the Ohta River were studied. The membrane filter, pad preenrichment technique, followed by the placement of membranes onto thiosulfate citrate-bile salt-sucrose agar, was used for the enumeration of total vibrios. Qualitative examination of pathogenic vibrios was also attempted. In addition, a survey was conducted to determine the incidence of Clostridium botulinum in sediment samples of the Ohta River and the Hiroshima coast. In the identification of 361 strains, 12 species of Vibrio and two species of Listonella were observed. Non-01 Vibrio cholerae was prevalent among the members of the genus Vibrio. Vibrio parahaemolyticus (serotype 04:K34), isolated in fresh water, is significant and suggests that some still unknown conditions promote the survival of these organisms in fresh water. An estimated 132 strains were hemolytic by a simple agar method, and further characterization revealed that 82% of the hemolytic vibrios (107 strains) produced various toxins. About 71% (93 strains) elaborated cytotoxin, 55% (72 strains) produced hemolysin, and 44% (58 strains) responded for both cytotoxin and hemolysin in the crude toxin extracts. All the non-01 V. cholerae showed cytotoxic activity, and the virulent strains of Vibrio fluvialis and Vibrio spp. showed cytotonic responses in RK-13 cells. Of 36 sediment samples tested, 10 harbored C. botulinum spores (28%) and were isolated invariably in all the regions of the Hiroshima coast and in the Ohta River, except the upper region of the Ohta River.     

Software for the development and evaluation of probabilistic identification matrices

A number of programs are described for the development and evaluationof probabilistic identification matrices for use with computer-assistedidentification. The program BEST reads an initial matrix ofper cent probabilities for all the binary characters examinedduring a cluster analysis and determines the most useful setof tests for distinguishing taxa in the matrix. Program RESORTcreates from the initial matrix an identification matrix inwhich the order of the tests may be different or the numberof tests reduced. A printed version of a matrix can be producedby MATPRJNT, which creates tables giving the per cent probabilityof a positive test result and the test results presented as‘–’, ‘v’ and ‘+’ dependingon a user-specified threshold. Program IDSC evaluates an identificationmatrix by calculating the best identification score for eachtaxon in the matrix using the expected result for each test.The programs were written in FORTRAN 77 and can be run on anymicrocomputer using the PC/MS-DOS operating system. Received on April 27, 1990; accepted on November 5, 1990     

A frequency matrix for probabilistic identification of some bacilli

A matrix comprising frequencies for positive results for 44 Bacillus taxa for 30 characters has been constructed. The 44 taxa include most of the common species and several clusters of environmental isolates including those described as B. firmus-B. lentus intermediates. The tests, which were chosen for their high diagnostic value, included some of the traditional tests used for identification of bacilli supplemented with a range of sugar fermentations and other characterization tests. The matrix was evaluated by identifying hypothetical median organisms, cluster representatives and a panel of 23 reference strains. All reference strains achieved Willcox probabilities above 0.995. Fifty-eight environmental isolates were also subjected to the 30 tests and identification was attempted. Forty-one strains (70%) achieved a Willcox probability greater than 0.95, which was considered an acceptable identification, and were assigned to 12 taxa. If the SE of taxonomic distance was also considered in the identification score (an acceptable value being less than 7.0), the number of acceptable identifications was reduced to 34 (59%). It was encouraging that bacteria from garden soils identified to the common species such as B. subtilis, B. cereus and B. licheniformis whereas some of the bacteria from an estuarine habitat were identified as species such as B. firmus which are normally identified with that habitat.     

Numerical classification and identification of Aeromonas genospecies.

A total of 176 Aeromonas strains representing all currently characterized genospecies were tested for 329 biochemical characters. Overall similarities of all strains were determined by numerical taxonomic techniques, the UPGMA algorithm and the SSM and the SJ coefficients as measures of similarity. Sixteen clusters (two or more strains) and seven unclustered strains were recovered at the 93.5% similarity level (SSM). Genospecies 1, 4, 5, 6, 7, 9, 12 and 13 were largely represented by single phena, whereas strains of genospecies 2 and 3 were found in closely-related phena. Strains belonging to genospecies 8 formed two distinct biotypes. Strains belonging to genospecies 11 formed a subcluster within a cluster representing different genospecies. In general, similar groupings were obtained with the Jaccard coefficient at a similarity level of 80.0% (SJ) with minor changes in the definition of clusters. The phenetic data showed good correlation with the taxa defined by DNA/DNA hybridization and those obtained by multilocus enzyme analysis. For all genospecies (independent from cluster assignment) 30 diagnostic characters were selected to construct a matrix for probabilistic identification. The correct identification rate of the matrix was 71.51% taking a Willcox probability greater than 0.99, and 83.7% taking a Willcox probability greater than 0.9 as identification threshold levels.     

Makeup of a population El Tor vibrios according to their agglutinability by type-specific sera]

The authors studied population composition of 14 strains of EL Tor vibrios. Of 7 strains of Ogava serological type the population composition was homogeneous in 2, and heterogeneous in 5. All the 7 strains of EL Tor vibrios of Inaba serological type had homogeneous population composition. Changes of the existence conditions of EL Tor vibrios of Ogava serological type, containing in their population 5% cells of Hikoshima serological tupe, led to separation of the cells of Inaba serological type; under the same conditions, in El Tor vibrios of Ogava and Inaba serological type with homogeneous population the latter was stable.     

Numerical classification and identification of Aeromonas genospecies

P. KÄMPFER AND M. ALTWEGG. 1992. A total of 176 Aeromonas strains representing all currently characterized genospecies were tested for 329 biochemical characters. Overall similarities of all strains were determined by numerical taxonomic techniques, the UPGMA algorithm and the S _SM and the S _J coefficients as measures of similarity. Sixteen clusters (two or more strains) and seven unclustered strains were recovered at the 93.5% similarity level ( S _SM). Genospecies 1, 4, 5, 6, 7, 9, 12 and 13 were largely represented by single phena, whereas strains of genospecies 2 and 3 were found in closely-related phena. Strains belonging to genospecies 8 formed two distinct biotypes. Strains belonging to genospecies 11 formed a subcluster within a cluster representing different genospecies. In general, similar groupings were obtained with the Jaccard coefficient at a similarity level of 80.0% ( S _J) with minor changes in the definition of clusters. The phenetic data showed good correlation with the taxa defined by DNA/DNA hybridization and those obtained by multilocus enzyme analysis. For all genospecies (independent from cluster assignment) 30 diagnostic characters were selected to construct a matrix for probabilistic identification. The correct identification rate of the matrix was 71.51% taking a Willcox probability < 0.99, and 83.7% taking a Willcox probability > 0.9 as identification threshold levels.     

Ecological relationship between Vibrio parahaemolyticus and agar-digesting vibrios as evidenced by bacteriophage susceptibility patterns.

Twenty bacteriophages active against Vibrio parahaemolyticus and agar-digesting vibrios, isolated from oysters (Crassostrea gigas) and Dungeness crab (Cancer magister) and by induction of a lysogenic agar digester, were tested as to their host range. These phages were specific for V. parahaemolyticus and various agar-digesting vibrios, and interspecies lysis occurred only between these two groups. V. alginolyticus, V. anguillarum and related species, V. cholerae, and a group of marine psychrophilic and psychrotrophic vibrios were not affected. No correlation was observed between the O and K serotypes of V. parahaemolyticus strains and bacteriophage susceptibility patterns, and 7 of 28 strains of V. parahaemolyticus were not lysed by any of the phages. Only two of the phage isolates were capable of lysing all susceptible V. parahaemolyticus strains. No correlation was observed between the inter-and intraspecies genetic relatedness (DNA homologies) of V. parahaemolyticus and agar-digesting vibrios and susceptibility patterns to different bacteriophages. Some of the phages were capable of plaque formation on V. parahaemolyticus as well as on some strains of agar-digesting vibrios that were separated by 70 to 80% differences in their DNA homologies. The possible ecological significance of these vibrio bacteriophages, particularly those having a wide host range, is discussed.     

Incidence of Vibrio cholerae and related vibrios in a coastal lagoon and seawater influenced by lake discharges along an annual cycle

Most probable numbers of Vibrio cholerae and related vibrios were determined in Albufera Lake, Valencia, Spain, and in coastal waters under the influence of the lake discharges over the course of an annual cycle. The influence of temperature, kind of water, and characteristics of the different sampling sites on the numbers of vibrios recovered was evaluated. Maximum recovery of vibrios reached 10(3)/ml in both types of waters analyzed. V. cholerae numbers reached 10(3)/ml in the lake and 10(2) in one of the coastal sites. Frequently during the warm season, all vibrios isolated were identified as V. cholerae. Occasionally, no V. cholerae was recovered. The recovery of vibrios was significantly influenced by the temperature of the water and the type of water analyzed. Most of the V. cholerae isolates were included in Heiberg groups I and II, and nearly 50% of the strains used chitin as sole carbon source. Indole was not produced by 100% of the strains. All strains tested were non-O1 serovars.     

Incidence of Vibrio cholerae and related vibrios in a coastal lagoon and seawater influenced by lake discharges along an annual cycle.

Most probable numbers of Vibrio cholerae and related vibrios were determined in Albufera Lake, Valencia, Spain, and in coastal waters under the influence of the lake discharges over the course of an annual cycle. The influence of temperature, kind of water, and characteristics of the different sampling sites on the numbers of vibrios recovered was evaluated. Maximum recovery of vibrios reached 10(3)/ml in both types of waters analyzed. V. cholerae numbers reached 10(3)/ml in the lake and 10(2) in one of the coastal sites. Frequently during the warm season, all vibrios isolated were identified as V. cholerae. Occasionally, no V. cholerae was recovered. The recovery of vibrios was significantly influenced by the temperature of the water and the type of water analyzed. Most of the V. cholerae isolates were included in Heiberg groups I and II, and nearly 50% of the strains used chitin as sole carbon source. Indole was not produced by 100% of the strains. All strains tested were non-O1 serovars.     

A simplified strategy for the identification of Gram negative fermenting rods using a desk-top computer

A total of 845 strains of Gram negative, fermenting rods isolated from humans were routinely identified using a desk-top computer. A reduced matrix of 54 taxa x 29 tests was used for a multistep procedure. By an average number of 24 tests, 97–5% of strains reached an identification score of P < 0.9.     

The agglutinability of cholera O-monoclonal immunoglobulins]

A set of 10 monoclonal antibodies specific for vibrio species and of 5 monoclonal antibodies specific for serovar (Ogawa) was studied. These monoclonal antibodies were directed toward V. cholerae O1 antigen in agglutination reaction and on slide plates. Monoclonal antibodies agglutinating typical strains of cholera vibrios with titration range from 1: 6000 to 1: 25,000 were selected. MA were revealed to interact with cholera vibrio strains with reduced agglutinability. The set of agglutinating O monoclonal immunoglobulins was developed for laboratory identification of cholera O1 vibrios.     

The phages of halophilic vibrios and their use]

The range of the lytic activity of 46 phages of parahemolytic vibrios isolated from lysogenic strains, sea water samples, crabs and mussels has been studied. The phages are represented by virions belonging to morphological groups II, IV, V according to the phage classification currently used in Russia and to different serological groups. No relationship between the sensitivity of vibrio strains to the phages under study and the specificity of serotypes O and K has been established. The preparation of diagnostic phage [see text] suitable for the identification of 82% of strains of parahemolytic vibrios has been proposed.     

酵母鉴定程序在酵母分类鉴定中的应用

本文介绍了Barnett等1985年编制并由剑桥大学发行的计算机软件《酵母鉴定程序》,以及如何使用该程序在IBM PC DOS操作系统上进行酵母菌的分类鉴定。我们使用该程序对从云南鸡足山和紫金山两地森林土壤中分离到的82株酵母菌进行了分类鉴定,其中:鉴定到种的有47株,占总株数的57.3％;鉴定到属但未能直接定到种的有21株,占总株数的25.6％;暂未定名的有14株,占总株数的17.1％。     

Numerical characterization study of Micrococcaceae associated with lamb spoilage

A computer-assisted characterization of 296 Micrococcaceae isolates obtained from aerobically chill-stored lamb carcasses was carried out using a probability matrix and Bayesian identification theorems, complemented with cluster analysis. Preliminary identification was done with an original probability matrix comprising 37 previously described taxa and 32 tests. Although its statistical quality was adequate, the percentage of identification of field strains to species level was only 70% (96.6% identified with genera). To achieve an improved characterization, cluster analysis was subsequently performed on this group and an additional 26% could be associated with defined species, with five more taxa defined. The combined use of both approaches was judged positive as new identifications and better discrimination could be achieved. The majority of our isolates belonged to the Staphylococcus species group. Many species and groups of staphylococci increased as the spoilage progressed.