Comparison of different biochemical and molecular methods for the identification of Vibrio parahaemolyticus

AIMS: Multicentre evaluation of biochemical and molecular methods for the identification of Vibrio parahaemolyticus. METHODS AND RESULTS: For the biochemical identification methods, API 20E and API 20NE and Alsina's scheme were evaluated in intra- and interlaboratory tests in order to determine the accuracy and concordance of each method. Both in intra- and interlaboratory tests, the Alsina's scheme showed the highest sensitivity (86% of correct identifications in the interlaboratory test). False-positive results were obtained by all methods (specificity was 95% for API 20E, 73% for API 20NE and 84% for Alsina's scheme) and concordance varied from 65% of API 20NE to 84% of API 20E. For the molecular identifications, polymerase chain reaction (PCR) for the detection of toxR gene, tl gene and pR72H fragment were tested on 30 strains by two laboratories. The PCR for toxR showed the highest inclusivity (96%), exclusivity (100%) and concordance (97%). CONCLUSIONS: Among the biochemical identification methods tested, the Alsina's scheme gave more reliable results; however, in order to avoid false-positive results, all the biochemical identifications should be confirmed by means of molecular methods. SIGNIFICANCE AND IMPACT OF THE STUDY: Availability of an efficient identification method of Vibrio parahaemolyticus to use in official control of fisheries products.     

Differences in the API 20E biochemical patterns of clinical and environmental Vibrio parahaemolyticus isolates

Genetic differences in clinical and environmental strains of Vibrio parahaemolyticus have been widely used as criteria in identifying pathogenic isolates. However, few studies have been carried out to assess the differences in biochemical characteristics of V. parahaemolyticus isolates from human and environmental sources. We compared the biochemical profiles obtained by the characterization of V. parahaemolyticus isolates from human infections and the marine environment using the API 20E system. Environmental and clinical isolates showed significant differences in the gelatin and arabinose tests. Additionally, clinical isolates were correctly identified according to the API 20E profile using 0.85% NaCl diluent, but they presented nonspecific profiles with 2% NaCl diluent. In contrast, use of 2% NaCl diluent facilitated correct identification of the environmental isolates. Clinical isolates showed significant differences in up to five biochemical tests with respect to the API 20E database. The API 20E system is widely used in routine identification of bacteria in clinical laboratories, and this discrepancy in an important number of biochemical tests may lead to misidentification of V. parahaemolyticus infection.     

Standardization of broth microdilution method for Mycobacterium tuberculosis

Indirect drug susceptibility tests of Mycobacterium tuberculosis was done to investigate the accuracy and feasibility of a broth microdilution method (BMM) for determining minimal inhibitory concentrations of conventional drugs against M. tuberculosis. Test drugs included isoniazid (H), rifampicin (R), ethambutol (E), streptomycin (S) and pyrazinamide (Z). Fifty isolates of M. tuberculosis from patients who had never received drug therapy, and H37Rv strain for control, were evaluated in the system. When comparing this method with the gold standard proportional method in Lowenstein-Jensen medium, sensitivity of 100% for all drugs and specifities of 91, 100, 96, 98 and 85% were observed respectively for H, R, E, S and Z. The BMM was read faster (14-20 days) than the proportional method (20-28 days). The microdilution method evaluated allows the testing of multiple drugs in multiple concentrations. It is easy to perform and does not require special equipment or expensive supplies. In contrast to radiometric method it does not use radioactive material.     

Characteristics of maltose transporter activity in an ale and larger strain of the yeast Saccharomyces cerevisiae

R.R. BEUMER, M.C. TE GIFFEL, M.T.C. KOK AND F.M. ROMBOUTS. 1996. All confirmation and identification methods used in this study can be used for the screening of suspected colonies on isolation media for Listeria spp. In traditional enrichment procedures the Microscreen Listeria latex test gives fast results. The DNA probes (Accuprobe and Gene-Trak) are very specific in detecting Listeria monocytogenes . For identification of Listeria spp. both tests (API and Micro-ID) performed equally well. Preference may be given to the API test, since differentiation of L. monocytogenes from L. innocua is based on the absence of arylamidase, through which tests for haemolytic activity and/or CAMP reactions can be omitted. However, the use of Enhanced Haemolysis Agar as isolation medium makes further testing essentially superfluous, since L. monocytogenes strains can be differentiated from L. innocua .     

Comparison of rapid NFT and API 20E with conventional methods for identification of gram-negative nonfermentative bacilli from pharmaceuticals and cosmetics

The accuracy of the Rapid NFT and the API 20E identification systems was evaluated by comparing them with conventional biochemical methods for the identification of gram-negative, nonfermentative bacilli. The organisms were recovered from preserved, nonsterile pharmaceutical and cosmetic products. A total of 123 test isolates that are commonly encountered in these products were used. By using the criteria of accurate and reliable identification without employing additional tests, Rapid NFT was found to be more accurate after 48 h of incubation than API 20E for characterizing isolates to the species level. Therefore, close agreement between NFT and conventional methods for identification of industrial gram-negative isolates provides evidence that the Rapid NFT system is an improved and rapid method for identifying these organisms to the species level with minimal use of supplementary tests.     

Comparison of rapid NFT and API 20E with conventional methods for identification of gram-negative nonfermentative bacilli from pharmaceuticals and cosmetics.

The accuracy of the Rapid NFT and the API 20E identification systems was evaluated by comparing them with conventional biochemical methods for the identification of gram-negative, nonfermentative bacilli. The organisms were recovered from preserved, nonsterile pharmaceutical and cosmetic products. A total of 123 test isolates that are commonly encountered in these products were used. By using the criteria of accurate and reliable identification without employing additional tests, Rapid NFT was found to be more accurate after 48 h of incubation than API 20E for characterizing isolates to the species level. Therefore, close agreement between NFT and conventional methods for identification of industrial gram-negative isolates provides evidence that the Rapid NFT system is an improved and rapid method for identifying these organisms to the species level with minimal use of supplementary tests.     

A convenient microtitre tray procedure for yeast identification

Media for yeast identification tests were incorporated into the wells of a microtitre tray. The tests included fermentation and assimilation of carbohydrates, assimilation of nitrogen compounds, growth in vitamin-free medium, resistance to cycloheximide, and observations for cell morphology and sporulation. Results of tests conducted in the trays showed very good agreement with those obtained by conventional methods. Eighteen reference yeasts were correctly identified from tests conducted in the trays. The trays of media could be stored, and provided a convenient system for yeast identification.     

A convenient microtitre tray procedure for yeast identification

Media for yeast identification tests were incorporated into the wells of a microtitre tray. The tests included fermentation and assimilation of carbohydrates, assimilation of nitrogen compounds, growth in vitamin-free medium, resistance to cycloheximide, and observations for cell morphology and sporulation. Results of tests conducted in the trays showed very good agreement with those obtained by conventional methods. Eighteen reference yeasts were correctly identified from tests conducted in the trays. The trays of media could be stored, and provided a convenient system for yeast identification.     

Comparison of two chromogenic media and evaluation of two molecular based identification systems for Enterobacter sakazakii detection

Background  

Enterobacter sakazakii is a foodborne pathogen that has been associated with sporadic cases and outbreaks causing meningitis, necrotizing enterocolitis and sepsis especially in neonates. The current FDA detection method includes two enrichment steps, the subculturing of the second enrichment broth on a selective agar (VRBG), a further subculturing of selected grown colonies on TSA and the subsequent biochemical identification of yellow-pigmented colonies by API20E. However, there is a strong need for simplified methods for isolation and identification of E. sakazakii. In this study, two chromogenic media, which allow to indicate presumptive E. sakazakii colonies by the alpha glucosidase activity, as well as a newly developed 1,6-alpha-glucosidase based conventional PCR assay and a rRNA oligonucleotide probe based commercial test system for identification of presumptive E. sakazakii were evaluated on 98 target and non-target strains. The methods were compared with respect to specifiCity aspects.     

Identification of enterococci isolated from cow's milk cheese: comparison of the classical methods and the API 20 STREP system (technical note)

A comparison of the results obtained using the classical methods with those of the API 20 Strep system was carried out in identifying 24 enterococci strains isolated from San Simón cow's milk cheese, a traditional Spanish variety. The results of both identification systems coincided exactly in 9 strains (37.5% of the strains studied). In one strain the results obtained using the classical methods did not coincide with those using the API 20 Strep method. 3 strains (12.5%) could not be identified using the API 20 Strep system. However, 11 strains (45%), that remained doubtful between both species E. faecalis and E. faecium on the basis of the classical methods, were identified using the API 20 Strep system. The API 20 Strep system does not include some biochemical tests of importance in identifying of foodborne enterococci and could not identify the atypical strains of Enterococcus. Moreover, this system is adapted to the identification of enterococci of clinical origin and their database does not include some species common in foods. However, it could have an application in combination with the classical methods in order to carry out a reasonably rapid and reliable identification of enterococci related to cheese.     

Oligonucleotide probes specific for the genus Salmonella and for Salm. typhimurium

The Crystal Enteric/Nonfermenter (E/NF) identification kit (Becton Dickinson Microbiology Systems, USA) was evaluated using water-derived bacterial isolates and results compared to those obtained by the API 20E system (BioMérieux, UK). Both the E/NF and 20E systems correctly identified 93% of the Enterobacteriaceae reference cultures. Both systems agreed in the identification of 64·9% of environmental isolates. The E/NF system gave a positive identification to 88·0% of isolates and the 20E to 79·5% of isolates. The principal tests which gave differing reactions between the two systems were arginine dihydrolase, lysine decarboxylase, urease and citrate utilization.     

Antimicrobial susceptibility tests for anaerobic bacteria. Comparison of Wilkins-Chalgren agar reference method and a microdilution method,and determination of stability of antimicrobics frozen in broth

Susceptibility results for anaerobic bacteria obtained with a microdilution method with either Wilkins-Chalgren broth or Brain Heart Infusion broth were compared to results obtained with the reference agar dilution method proposed by the National Committee for Clinical Laboratory Standards. Results were generally comparable, but the minimal inhibitory concentrations obtained with the microdilution method were slightly lower than those obtained with the agar dilution method. Antibiotics stored in these broths in microdilution trays at-20°C were stable for up to 130 days.     

Comparison of the Vitek, API 20E and Gene-trak® systems for the identification of Yersinia enterocolitica

The current improvements in nucleic acid hybridization technology provide new techniques for the identification of micro-organisms. One such technique is the Gene-trak® DNA hybridization system (Framingham, MA, USA), which was introduced in 1983. The objective for this study was to evaluate the new Gene-trak® Yersinia enterocolitica kit in comparison with the API 20E and Vitek systems. A total of 101 strains including 18 reference non- Yersinia strains from the authors' stock culture collection and 83 suspected positive isolates from CIN agar were tested. Of these 83 isolates, 40 were identified as Y. enterocolitica after incubation at 37°C for 24 with the API 20E system; 37 strains were identified at 30°C for 48 h. The Gene-trak® method gave positive results with 39 strains. The Vitek system gave positive results with 27 strains.
With the Gene-trak® method, Y. enterocolitica was detectable in mixed cultures provided that the numbers of cfu ml^-1 were equal to or above 10⁶ Y. enterocolitica ml^-1. Although enrichment procedures are still needed, the system provides a quick detection of these food-borne pathogens.     

Biochemical properties of Corynebacterium amycolatum strains

C. amycolatum is the most commonly isolated nonlipophilic species of Corynebacterium from clinical samples. However, the lack of good commercial identification tests in microbiology laboratories causes some difficulties in C. amycolatum diagnostics. We decided to examine biochemical and enzymatic properties of isolated strains and analyze the occurrence of particular biochemical profiles (biotypes). Perhaps it would let improve the identification schemes. 70 strains of C. amycolatum were analyzed. The estimation of biochemical properties consisted of the results of API Coryne and API ZYM tests (bioMérieux), the ability of excreting of protease, esterase, lipase and lecithinase. Analyzed strains had various biochemical and enzymatic properties. Almost all strains fermented glucose (98.6%) and maltose (95.7%) and produced pyrasinamidase (94.3%). All strains produced alkaline phosphatase and phosphohydrolase, and 95.7%--acid phosphatase. Biotypes of particular strains were determined on the biochemical reactions included in the API Coryne tests. In the group of 70 strains 21 profiles were distinguished among which 3100325 biotype (35.7%) was dominant. The lipolysis was defined on Tween 20, Tween 40, Tween 60, Tween 80 medium and with the API ZYM test usage. All strains produced esterase-lipase (esterase C-8), 95.7% of strains-esterase C-4, and 21.4% lipase C-14. Among analyzed strains 18.6% hydrolyzed Tween 20, 14.3% Tween 60, and 1.4% Tween 40. None of these strains demonstrated lipase and lecithinase activity. Difficulties in concerning C. amycolatum as pathogens justify further investigations.     

Numerical taxonomy of alpha-amylase producing Bacillus species

A total of 134 alpha-amylase producing Bacillus isolates and 21 reference strains were divided into 12 groups according to their similarities (% SSM). Phenotypic characteristics determined by the API 20E and API 50CHB galleries, other biochemical tests and morphological characteristics were used for the numerical analysis. The API Computer Service identified 45% of the isolates. The amylase yields of 16 alpha-amylase hyperproducing (AHP) isolates were compared with those of seven amylolytic reference and type strains. The AHP isolates were related to Bacillus subtilis, B. licheniformis and 'B. amyloliquefaciens'.     

Molecular and phenotypic characterization of Pseudomonas spp. isolated from milk

Putative Pseudomonas spp. isolated predominantly from raw and processed milk were characterized by automated ribotyping and by biochemical reactions. Isolates were biochemically profiled using the Biolog system and API 20 NE and by determining the production of proteases, lipases, and lecithinases for each isolate. Isolates grouped into five coherent clusters, predominated by the species P. putida (cluster A), P. fluorescens (cluster B), P. fragi (as identified by Biolog) or P. fluorescens (as identified by API 20 NE) (cluster C), P. fragi (as identified by Biolog) or P. putida (as identified by API 20 NE) (cluster D), and P. fluorescens (cluster E). Isolates within each cluster also displayed similar enzyme activities. Isolates in clusters A, C, and D were generally negative for all three enzyme activities; isolates in cluster B were predominantly positive for all three enzyme activities; and isolates in cluster E were negative for lecithinase but predominantly positive for protease and lipase activities. Thus, only isolates from clusters B and E produced enzyme activities associated with dairy product flavor defects. Thirty-eight ribogroups were differentiated among the 70 isolates. Ribotyping was highly discriminatory for dairy Pseudomonas isolates, with a Simpson's index of discrimination of 0.955. Isolates of the same ribotype were never classified into different clusters, and ribotypes within a given cluster generally showed similar ribotype patterns; thus, specific ribotype fragments may be useful markers for tracking the sources of pseudomonads in dairy production systems. Our results suggest that ribogroups are generally homogeneous with respect to nomenspecies and biovars, confirming the identification potential of ribotyping for Pseudomonas spp.     

Comparison of a commercial biochemical kit and an oligonucleotide probe for identification of environmental isolates of Vibrio vulnificus

A. DALSGAARD, I. DALSGAARD, L. HØI AND J.L. LARSEN. 1996. Methods for the identification and isolation of environmental isolates of Vibrio vulnificus were evaluated. Alkaline peptone water supplemented with polymyxin B and colistin-polymyxin B-cellobiose agar were employed for the isolation of suspected V. vulnificus from water, sediment and shellfish samples. When comparing the identification of putative V. vulnificus obtained with the API 20E assay and an oligonucleotide probe, 29 API 20E profiles were obtained with only four profiles (representing 20 isolates) reaching the identification threshold of V. vulnificus among a total of 66 isolates hybridizing with the probe. The results indicated that, compared with colony hybridization, the API 20E assay was not adequate for the identification of environmental isolates of V. vulnificus .     

Numerical taxonomy of α-amylase producing Bacillus species

A total of 134 α-amylase producing Bacillus isolates and 21 reference strains were divided into 12 groups according to their similarities (% S_SM). Phenotypic characteristics determined by the API 20E and API 50CHB galleries, other biochemical tests and morphological characteristics were used for the numerical analysis. The API Computer Service identified 45% of the isolates. The amylase yields of 16 α-amylase hyperproducing (AHP) isolates were compared with those of seven amylolytic reference and type strains. The AHP isolates were related to Bacillus subtilis, B. licheniformis and 'B. amyloliquefaciens' .     

New host plants of Erwinia amylovora in Bulgaria

Nine strains of Erwinia amylovora were isolated from new host plants in Bulgaria--chokeberry and strawberry. The strains were characterized morphologically and biochemically using the API 20E and BIOLOG system. It was established that they showed three different API 20E metabolic profiles, not found by previous studies of E. amylovora. All strains were identified as E. amylovora due to their metabolic fingerprint patterns obtained by the BIOLOG system. The identification was confirmed by PCR amplification of a specific region of plasmid pEA29 and genome ams-region. This study is the first characterization and identification of E. amylovora strains isolated from chokeberry and strawberry by the API 20E and BIOLOG system and by polymerase chain reaction.     

Fluconazole susceptibility of Italian Candida dubliniensis clinical isolates determined by reference and simplified tests.

Candida dubliniensis ia an opportunistic pathogen mainly associated with oral candidiasis in human immunodeficiency virus (HIV)-infected individuals. We recently recovered the first Italian clinical isolates of C. dubliniensis from the oral cavities of seven HIV-seropositive subjects. The in vitro susceptibility to fluconazole (FLCZ) of these isolates was determined according to the National Committee for Clinical Laboratory Standards (NCCLS) M27-A broth microdilution method for yeasts. All seven isolates of C. dubliniensis were susceptible to FLCZ (MICs < or =0.5 microg/ml). Results of this reference method were compared to those obtained with simplified tests, more adapted to routine evaluation in hospital laboratories. Fungitest and Sensititre YeastOne colorimetric microplate-based methods have been evaluated. The agar disk diffusion method has also been tested on two different media: RPMI 1640-2% glucose and High Resolution-2% glucose-0.5 microg/ml methylene blue. All of the simplified methods tested were able to correctly identify FLCZ-susceptibility of this group of Italian C. dubliniensis isolates.