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BACKGROUND: The bacterium Eikenella, classified as a gram-negative member of the phylum Proteobacteria, is distinguished by its rarity, corrosive nature, facultative anaerobic properties, and conditional pathogenicity. It represents the sole species within its genus-Eikenella corrodens (E. corrodens)-and can be found colonizing both human and animal oral and nasopharyngeal regions. Additionally, it occasionally inhabits the gastrointestinal or urogenital tracts. However, its slow growth rate can be attributed to its high nutritional requirements. However, there is an uneven distribution of construction and diagnostic capacity in China which poses undeniable challenges for the clinical examination and analysis of this case, especially in the basic hospitals. CASE SUMMARY: Here we presented a case of empyema associated with E. corrodens infection in a 67-year-old male patient without any previous history of infectious diseases in our primary hospital in Dongguan district of China. The patient was admitted due to recurrent worsening cough, sputum production, and dyspnea for 3 d, which had persisted for over 20 years. Moreover, the patient experienced a one-hour episode of unconsciousness. Upon admission, immediate comprehensive examinations were conducted on the patient which subsequently led to his admission to the intensive care unit. Meanwhile, the patient presented with drowsiness and profuse sweating along with bilateral conjunctival edema observed during initiation of non-invasive ventilation, suggesting empyema. A significant amount of coffee-colored malodorous pleural fluid was drained during the procedure above and sent to the laboratory department for inspection. Finally, laboratory culture results confirmed the presence of E. corrodens infection in the pleural fluid sample. The patient received antimicrobial therapy until died on day 22 in the hospital. CONCLUSION: In this report, we presented a case of empyema associated with E. corrodens infection. Multiple courses of morphological examination, viable culture analysis, and biochemical identification revealed its difficulties in detecting distinctive characteristics, as well as a detection model worth promoting. It's just that there were still certain deficiencies in terms of morphological assessment, biochemical identification, and drug susceptibility testing.

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Vibrio anguillarum is the most frequent pathogen affecting fish worldwide. The only known virulent strains of V. anguillarum are serotypes O1, O2, and O3. Genetic differences between the serotypes that could shed insight on the evolution and serotype differences of this marine pathogen are unknown. Here, we fully sequenced and characterized a strain of V. anguillarum O1 (J382) isolated from winter steelhead trout (Oncorhynchus mykiss irideus) in British Columbia, Canada. Koch's postulates using the O1 strain were replicated in naïve lumpfish (Cyclopterus lumpus) and compared to O2. Phenotypic and genotypic comparisons were conducted for serotypes O1, O2, and O3, using biochemical tests and bioinformatic tools, respectively. The genome of V. anguillarum O1 (J382) contains two chromosomes (3.13 Mb and 1.03 Mb) and two typical pJM1-like plasmids (65,573 and 76,959 bp). Furthermore, V. anguillarum O1 (J382) displayed resistance to colistin sulphate, which differs from serotype O2 and could be attributed to the presence of the ugd gene. Comparative genomic analysis, among the serotypes, showed that intra-species evolution is driven by insertion sequences, bacteriophages, and a different repertoire of putative ncRNAs. Genetic heterogeneity in the O-antigen biosynthesis gene cluster is characterized by the absence or the presence of unique genes, which could result in differences in the immune evasion mechanisms employed by the respective serotypes. This study contributes to understanding the genetic differences among V. anguillarum serovars and their evolution.

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In July 2021, a disease with a high mortality rate broke out in freshwater cultured hybrid sturgeon in Zhengzhou, Henan Province. A dominant strain, H-701, was isolated from diseased fish; physiological changes in diseased fish were investigated and molecular identification, biochemical characterization, and pathogenicity and drug sensitivity tests of H-701 were performed. The 16S rRNA gene sequence of H-701 was 99.86% homologous with that of Vibrio metschnikovii in GenBank. The 50% lethal dose of H-701 was 3.72 ± 0.929 × 104 CFU/g fish weight. The proportion of monocytes, neutrophils, and eosinophils in the blood of diseased sturgeon increased significantly, whereas the proportion of lymphocytes decreased. In diseased fish, the serum levels of total protein, albumin, globulin, and alkaline phosphatase decreased significantly, and those of aspartate aminotransferase, alanine aminotransferase, and complement C3 increased significantly. There were obvious pathological changes in several tissues of the diseased fish. H-701 was sensitive to antibiotics such as florfenicol, enrofloxacin, and doxycycline. This study not only demonstrated that V. metschnikovii was the cause of death of a large number of hybrid sturgeon but also revealed its potential risk in hybrid sturgeon aquaculture. The results provide a basis for the diagnosis and prevention of this disease.

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Extraintestinal pathogenic Escherichia coli (ExPEC) is a leading cause of human and animal infections worldwide. The utilization of selective and differential media to facilitate the isolation and identification of E. coli from complex samples, such as water, food, sediment, and gut tissue, is common in epidemiological studies. During a surveillance study, we identified an E. coli strain isolated from human blood culture that displayed atypical light cream-colored colonies in chromogenic agar and was unable to produce ß-glucuronidase and ß-galactosidase in biochemical tests. Genomic analysis showed that the strain belongs to sequence type 59 (ST59) and phylogroup F. The evaluation in silico of 104 available sequenced lineages of ST59 complex showed that most of them belong to serotype O1:K1:H7, are ß-glucuronidase negative, and harbor a virulent genotype associated with the presence of important virulence markers such as pap, kpsE, chuA, fyuA, and yfcV. Most of them were isolated from extraintestinal human infections in diverse countries worldwide and could be clustered/subgrouped based on papAF allele analysis. Considering that all analyzed strains harbor a virulent genotype and most do not exhibit biochemical behavior typical of E. coli, we report that they could be misclassified or underestimated, especially in epidemiological studies where the screening criteria rely only on typical biochemical phenotypes, as happens when chromogenic media are used. IMPORTANCE The use of selective and differential media guides presumptive bacterial identification based on specific metabolic traits that are specific to each bacterial species. When a bacterial specimen displays an unusual phenotype in these media, this characteristic may lead to bacterial misidentification or a significant delay in its identification, putting a patient at risk depending on the infection type. In the present work, we describe a virulent E. coli sequence type (ST59) that does not produce beta-glucuronidase (GUS negative), production of which is the metabolic trait widely used for E. coli presumptive identification in diverse differential media. The recognition of this unusual metabolic trait may help in the proper identification of ST59 isolates, the identification of their reservoir, and the evaluation of the frequency of these pathogens in places where automatic identification methods are not available.

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We report a case of melioidosis in China and offer a comparison of 5 commercial detection systems for Burkholderia pseudomallei. The organism was misidentified by the VITEK 2 Compact, Phoenix, VITEK mass spectrometry, and API 20NE systems but was eventually identified by the Bruker Biotyper system and 16S rRNA sequencing.

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Mycoplasma bovis (M. bovis) is one of the important pathogens which may cause bovine respiratory disease syndrome (BRDS), and results in huge economic losses for yaks (Bos gaurus) breeding industry. However, there is limited information about M. bovis in yaks. In our study, 145 nasal mucus samples from yaks with pneumonia were collected to clarify. Bacteriological determination was carried out through biochemical identification and Polymerase Chain Reaction (PCR) detection. And ten strains of Mycoplasma bovis (M. bovis) were found from collected samples. Then, the growth curve of isolated strains was determined by the change of optical density (OD630), pH value and Color Change Cnit (CCU). K-B disk method was also used for antimicrobial susceptibility testing. Results of colony morphology and biochemical testing were consistent with the biological characters of M. bovis. The nucleotide sequences of uvrC specific gene and 16S rRNA gene among the 10 strains were highly homologous. The growth curve assay showed that the isolates cultured in PPLO medium were in lag phase for 24 h, entered stable period in 42 h, and entered decline phase after 78 h. The isolates were found resistant to macrolides, aminoglycosides and lincomycin at various degrees, but they were sensitive or moderately sensitive to doxycycline and kanamycin under antimicrobial susceptibility analysis. In conclusion, the results provided certain reference for the follow-up research and guiding for the treatment of M. bovis in yaks.

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Liquid feed is susceptible to microbiological growth. Yeasts are said to cause sudden death in swine due to intestinal gas formation. As not all animals given high yeast content feed fall ill, growth and gas formation potential at body temperature were investigated as possible causally required properties. The best identification method for these environmental yeasts should be tested beforehand. Yeasts derived from liquid diets without (LD - S) and liquid diets with maize silage (LD + S) were examined biochemically (ID32C-test) and with MALDI-TOF with direct smear (DS) and an extraction method (EX). Growth temperature and gas-forming potential were measured. With MALDI-EX, most yeast isolates were identified: Candida krusei most often in LD - S, and C. lambica most often in LD + S, significantly more than in LD - S. Larger colonies, 58.75% of all yeast isolates, were formed at 25 °C rather than at 37 °C; 17.5% of all isolates did not grow at 37 °C at all. Most C. krusei isolates formed high gas amounts within 24 h, whereas none of the C. lambica, C. holmii and most other isolates did. The gas pressure formed by yeast isolates varied more than tenfold. Only a minority of the yeasts were able to produce gas at temperatures common in the pig gut.

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OBJECTIVES: The objective of this study was to evaluate the efficiency of SB-20 M culture medium to perform differential morphological identification of S. mutans and S. sobrinus compared to biochemical identification and to proteomic identification by the MALDI-TOF mass spectrometry technique. MATERIAL AND METHODS: Unstimulated saliva samples from 266 dental students were seeded on SB-20 M culture medium by the wooden spatula technique. After incubation, S. mutans and S. sobrinus colonies were identified by stereomicroscopy based on their differential morphological characteristics. Following these procedures, 135 colonies with characteristic morphology of S. mutans (89 colonies) and S. sobrinus (46 colonies) were randomly selected, submitted to biochemical identification (biotyping) and proteomic identification by the MALDI-TOF mass spectrometry technique. The results were compared using the Kappa test, with a 5% significance level. RESULTS: All (100%) S. mutans colonies were correctly identified after culture in SB-20 M medium compared to biotyping and proteomic identification. For S. sobrinus, morphological identification in SB-20 M medium was correct for 43 colonies (93.5%) compared to biotyping and proteomic identification. However, there was no statistically significant difference when comparing the capacity to identify S. mutans and S. sobrinus of the three techniques (p < 0.001; K = 0.951). CONCLUSIONS: It was concluded that the SB-20 M culture medium for morphological identification of S. mutans and S. sobrinus was highly reliable, being comparable to the MALDI-TOF mass spectrometry technique. CLINICAL RELEVANCE: The efficiency evaluation of identification methods of S. mutans and S. sobrinus is clinically relevant in order to determine caries risk and activity of patients.

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Specimen collection and processing is an important aspect of clinical microbiology laboratory. The reports are dependent on the quality of the specimen and the time between the collection and processing. Appropriate methodology needs to be followed for the collection, amount, type, labeling, transportation, and processing of the specimens especially for organism like Acinetobacter species. Various biochemical tests are used for identification of various organisms. Such identification depends on the ability of organisms to produce certain enzymes or to utilize certain compound to be identified by biochemical tests.

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Due to their pathogenic potential, identifying Vibrio species from recirculating aquaculture systems (RAS) for Pacific white shrimp (Litopenaeus vannamei) is of great importance to determine the risk for animal's as well as for the consumer's health. The present study compared identification results for a total of 93 Vibrio isolates, including type strains and isolates from shrimp aquaculture. Results from biochemical identifications, 16S rRNA sequencing, sequencing of the uridylate kinase encoding gene pyrH and analysis of the protein spectra assessed by MALDI-TOF MS were compared. The results achieved by these different methods were highly divergent for many of the analysed isolates and for several Vibrio spp difficulties in reliably identifying occurred. These difficulties mainly resulted from missing entries in digital databases, a low number of comparable isolates analysed so far, and high interspecific similarities of biochemical traits and nucleotide sequences between the closely related Vibrio species. Due to the presented data, it can be concluded that for identifying Vibrio spp. from samples in routine diagnostics, it is recommended to use MALDI-TOF MS analysis for a quick and reliable identification of pathogenic Vibrio sp. Nevertheless, editing the database, containing the main spectra of Vibrio is recommended to achieve reliable identification results.

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INTRODUCTION: During the manufacturing of sterile drugs, it is of the utmost importance to meet the minimum requirements for asepsis recommended by the legislations on good manufacturing practices-based efficient environmental monitoring. AIMS AND METHODS: The availability of relatively simple to use matrix-assisted laser desorption ionization-time of flight mass spectromtomy (MALDI-TOF MS) devices in the last years has changed the laboratory workflows for the microbial identification, mainly in the clinical area. Thus, the objective of this work was to evaluate the suitability of the MALDI-TOF MS technique for the identification of bacteria isolated from the environment of clean rooms used in some stages of the production of a viral vaccine. Eighteen known bacterial species commonly isolated from clean rooms studied were identified by MALDI-TOF technique and by a biochemical technique (BBL Crystal® System). RESULTS: Performance of MALDI-TOF MS was better than biochemical technique for correct species identifications (88.89% and 38.89%, respectively) and produced less unreliable identification (5.55% and 22.22%). CONCLUSION: MALDI-TOF MS can be implemented for routine identification of bacteria in a pharmaceutical quality control laboratory, but as a database-dependent system, maybe some isolated not identified by this technique must be additionally studied and, if appropriate, added to an in-house database.

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BACKGROUND: Burkholderia pseudomallei is a Gram-negative saprophytic soil bacterium that causes melioidosis, a potentially fatal disease endemic in wet tropical areas. The currently available biochemical identification systems can misidentify some strains of B. pseudomallei. The aim of the present study was to identify the biochemical features of B. pseudomallei, which can affect its correct identification by Vitek 2 system. MATERIALS AND METHODS: The biochemical patterns of 40 B. pseudomallei strains were obtained using Vitek 2 GN cards. The average contribution of biochemical tests in overall dissimilarities between correctly and incorrectly identified strains was assessed using nonmetric multidimensional scaling. RESULTS: It was found (R statistic of 0.836, P = 0.001) that a combination of negative N-acetyl galactosaminidase, ß-N-acetyl glucosaminidase, phosphatase, and positive D-cellobiase (dCEL), tyrosine arylamidase (TyrA), and L-proline arylamidase (ProA) tests leads to low discrimination of B. pseudomallei, whereas a set of positive dCEL and negative N-acetyl galactosaminidase, TyrA, and ProA determines the wrong identification of B. pseudomallei as Burkholderia cepacia complex. CONCLUSION: The further expansion of the Vitek 2 identification keys is needed for correct identification of atypical or regionally distributed biochemical profiles of B. pseudomallei.

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The intestinal pathogen Escherichia coli serotype O104:H4 (ECO104) can cause bloody diarrhea and haemolytic uremic syndrome. The ECO104 O antigen has the unique repeating unit structure [4Galα1-4Neu5,7,9Ac3α2-3Galß1-3GalNAcß1-], which includes the mammalian sialyl-T antigen as an internal structure. Previously, we identified WbwC from ECO104 as the ß3Gal-transferase that synthesizes the T antigen, and showed that α3-sialyl-transferase WbwA transfers sialic acid to the T antigen. Here we identify the wbwB gene product as a unique α1,4-Gal-transferase WbwB that transfers Gal from UDP-Gal to the terminal sialic acid residue of Neu5Acα2-3Galß1-3GalNAcα-diphosphate-lipid acceptor. NMR analysis of the WbwB enzyme reaction product indicated that Galα1-4Neu5Acα2-3Galß1-3GalNAcα-diphosphate-lipid was synthesized. WbwB from ECO104 has a unique acceptor specificity for terminal sialic acid as well as the diphosphate group in the acceptor. The characterization studies showed that WbwB does not require divalent metal ion as a cofactor. Mutagenesis identified Lys243 within an RKR motif and both Glu315 and Glu323 of the fourth EX7E motif as essential for the activity. WbwB is the final glycosyltransferase in the biosynthesis pathway of the ECO104 antigen repeating unit. This work contributes to knowledge of the biosynthesis of bacterial virulence factors.

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BACKGROUND: Enterococci are indigenous flora of the gastro-intestinal tracts of animals and humans. Recently, interest in two major species, E. faecium and E. faecalis, has heightened because of their ability to cause serious infections and their intrinsic resistance to antimicrobials. This study was aimed at determining the prevalence of E. faecium and E. faecalis in human faecal samples and evaluating the susceptibility of the isolates to antibiotics. MATERIALS AND METHODS: One hundred faecal samples were collected from apparently healthy individuals and analysed using conventionalbacteriological methods. The susceptibility profile of the isolates to nine antibiotics were determined using disk diffusion method. RESULTS: Seventy-three (73) Enterococcus were phenotypically identified and 65 of the isolates were differentiated into 36 (55.4%) E. faecium and 29 (44.6%) E. faecalis. Eight (8) isolates could not be identified by the conventional biochemical methods employed. No dual colonization by the E. faecalis and E. faecium was observed and isolation rate was not dependent on sex of the participants. All the isolates were resistant to ceftriaxone, cefuroxime and ceftizoxime. Enterococcus faecium exhibited resistance toerythromycin (88.9%), gentamicin (77.8%), amoxicillin-clavulanate (63.9%), ofloxacin (44.4%), teicoplanin (19.4%) and vancomycin (16.7%). Enterococcus faecalis showed the least resistance to vancomycin (13.8%) and teicoplanin (27.7%). Remarkable multiple antibiotic resistances to the classes of antibiotic tested were observed among the two species. CONCLUSION: The high carriage rate of antibiotic resistant E. faecium and E. faecalis in this study provides information on the local antibiotic patterns of our enterococci isolates thereby suggesting that they could present as important reservoir and vehicle for dissemination of resistant genes in our community.

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Objective To compare the difference of simple-rapid identification method and automatic biochemical identification method in the identification of Escherichia coli .Methods The strains of Escherichia coli isolated from clinical samples were identi-fied by the simple-rapid method and automatic biochemical method .The consistency of result and the time of two methods were compared .Results Among 492 suspected strains ,248 strains were identified as Escherichia coli by simple-rapid method ,and other 244 strains were not .Meanwhile ,231 strains of these 248 Escherichia coli strains and 7 strains of 244 non Escherichia coli strains were identified as Escherichia coli by automatic biochemical method .The positive and negative predictive value of simple-rapid method were 93 .1% (231/248) and 97 .1% (237/244) .2 .5-7 .0 h [average(4 .12 ± 1 .08) h] were used to identify Escherichia coli by automatic biochemical method while0 .5-2 .0 h[average(1 .08 ± 0 .45) h] were used by simple-rapid method ,the difference was statistically significant(t= -40 .252 ,P<0 .001) .Conclusion The result of simple-rapid method is close to that of automatic bio-chemical identification method on Escherichia coli ,and simple-rapid method used less time .

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Objective To compare the difference of simple-rapid identification method and automatic biochemical identification method in the identification of Escherichia coli .Methods The strains of Escherichia coli isolated from clinical samples were identi-fied by the simple-rapid method and automatic biochemical method .The consistency of result and the time of two methods were compared .Results Among 492 suspected strains ,248 strains were identified as Escherichia coli by simple-rapid method ,and other 244 strains were not .Meanwhile ,231 strains of these 248 Escherichia coli strains and 7 strains of 244 non Escherichia coli strains were identified as Escherichia coli by automatic biochemical method .The positive and negative predictive value of simple-rapid method were 93 .1% (231/248) and 97 .1% (237/244) .2 .5-7 .0 h [average(4 .12 ± 1 .08) h] were used to identify Escherichia coli by automatic biochemical method while0 .5-2 .0 h[average(1 .08 ± 0 .45) h] were used by simple-rapid method ,the difference was statistically significant(t= -40 .252 ,P<0 .001) .Conclusion The result of simple-rapid method is close to that of automatic bio-chemical identification method on Escherichia coli ,and simple-rapid method used less time .

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BACKGROUND: Microbiological criteria applied to powdered infant formula (PIF) require the absence of all Cronobacter spp. Consequently, misidentification of isolates from finished products can lead to significant financial losses for manufacturers and could increase the risk of neonatal infection. Biochemical identification of suspect isolates using commercially available test panels is recommended for use by PIF manufacturers by both the US FDA and ISO standard methods for Cronobacter species; however, phenotyping can be unreliable, particularly for a genus such as Cronobacter where the taxonomy has been subject to frequent changes. This study compared the predicted identification by commonly used phenotyping kits (API20E and ID32E) for over 240 strains of Cronobacter from diverse sources, which had been identified using DNA sequence analysis. In 2015, the databases associated with the API20E and ID32E biochemical test panels were updated, including the recognition of the Cronobacter genus. Thus, the identifications from multiple versions the databases were compared to each other and to identifications based on DNA sequencing methods. RESULTS: Using previous versions of the API20E database, 90.0 % of strains (216/240) resulted in a match for the species identification; however, version 5.0 produced matches for only 82.3 % of strains (237/288). Similarly, the update to version 4.0 in the ID32E database caused the percentage of matches to drop from 88.9 % (240/270) to 43.2 % (139/322). A smaller study showed that the Vitek GN system identified all 14 strains, belonging all seven Cronobacter species, as members of the 'C. sakazakii group,' but also attributed three strains of Franconibacter helveticus and F. pulveris to this group. In silco analysis of a PCR-based method targeting ompA predicted that amplification would only occur with Cronobacter species and this method may be a feasible alternative to biochemical phenotyping. CONCLUSIONS: These results indicate that commercially available biochemical test panels are not sufficiently reliable for speciation of Cronobacter isolates. Although DNA-sequence based methods would be the more reliable approach; however, this is not currently feasible for many food microbiology laboratories. Instead, a previously published PCR-based method targeting ompA is suggested as an alternative for identification of Cronobacter species based on in silico analysis.

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Clinical yeast isolates belonging to Candida pelliculosa, Candida utilis and Candida fabianii are difficult to distinguish in a routine mycology laboratory using common biochemical tests. The aims of this study were to determine the prevalence of C. pelliculosa, C. utilis and C. fabianii in clinical samples and to compare their minimum inhibitory concentrations (MICs) to systemic antifungals. Two hundred and forty-eight clinical yeast isolates obtained from eight large hospitals in the Czech Republic were included in this study. Identification was performed biochemically using ID 32C kit and by MALDI-TOF MS. MICs were determined using colorimetric broth dilution Sensititre YeastOne panels. From a total number of 248 isolates, 175 were identified as C. pelliculosa and 73 as C. utilis using the biochemical kit. In contrast, MALDI-TOF MS identified 222 isolates as C. fabianii, 20 as C. pelliculosa and 6 as C. utilis. The highest mean MICs were found in C. fabianii and, regardless of the studied species, in isolates from blood cultures and central venous catheters. MALDI-TOF MS revealed C. fabianii to be most prevalent in clinical samples as compared with the other studied species. Higher MIC values in C. fabianii support the importance of correct identification of this species.

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OBJECTIVE: To establish a evaluation method of microbial identification technology by comparing four different microbial identification methods. METHODS: A total of 50 tests by API microbial identification system, VITEK 2 compact system, Riboprinter system, and MicroSeq ID DNA sequencing system were performed against 19 standard strains and 10 wild strains. The accuracy and reproducibility of these methods were evaluated. RESULTS: All the four identification technologies could be used to identify specified micro-organisms, but they had difference in other strains. Molecular biotechnology was better than biochemical identification in accuracy and reproducibility. CONCLUSION: The users should establish suitable acceptance criteria for accuracy and reproducibility, taking into account method capability.

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The Bruker Biotyper MALDI-TOF MS (Biotyper) system, with a modified 30 minute formic acid extraction method, was evaluated by its ability to identify 216 clinical Staphylococcus isolates from the CDC reference collection comprising 23 species previously identified by conventional biochemical tests. 16S rDNA sequence analysis was used to resolve discrepancies. Of these, 209 (96.8%) isolates were correctly identified: 177 (84.7%) isolates had scores ≥2.0, while 32 (15.3%) had scores between 1.70 and 1.99. The Biotyper identification was inconsistent with the biochemical identification for seven (3.2%) isolates, but the Biotyper identifications were confirmed by 16S rDNA analysis. The distribution of low scores was strongly species-dependent, e.g. only 5% of Staphylococcus epidermidis and 4.8% of Staphylococcus aureus isolates scored below 2.0, while 100% of Staphylococcus cohnii, 75% of Staphylococcus sciuri, and 60% of Staphylococcus caprae produced low but accurate Biotyper scores. Our results demonstrate that the Biotyper can reliably identify Staphylococcus species with greater accuracy than conventional biochemicals. Broadening of the reference database by inclusion of additional examples of under-represented species could further optimize Biotyper results.

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