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Multicenter Evaluation Supports Accuracy of the Beckman Coulter Gram-Negative Identification Panel ECCMID 2016 with Improved Database for Clinically Significant Bacteria Hindler J1, Lewinksi, M, Schreckenberger P2, Beck C3, Nothaft D3, Bobolis J3, Carpenter D3, Mann L, Madriaga OM3, Wong T3, Smoot L3 1UCLA David Geffen School of Medicine, Los Angeles, CA, 2Loyola University Medical Center, Maywood, IL, and 3Beckman Coulter Microbiology, West Sacramento, CA INTRODUCTION METHODS (Continued) RESULTS (Continued) Incorrect Results (Table 3) A multicenter study was performed to evaluate the performance of the • MicroScan Dried Gram-negative Identification panels were assessed at Fermenter Results (Table 2) There were 8 incorrect results out of a total of 609 clinical and stock MicroScan Gram-negative Identification (NID) panels’ updated organism 16-18 hours. If any of the following criteria were met, reagents were Fermenters were identified correctly 99.2% (417/420) and only 3 isolates. database and revised performance matrix on the WalkAway system and the added to the VP, IND, NIT, and TDA tests and the results reported: isolates generated an incorrect identification. autoSCAN-4 instrument. • GLU, SUC, or SOR were positive Table 2. Fermenter Total Performance Table 3. Total Isolates Incorrectly Identified • ARG and OF/G were positive Reference Identification NID Panel Identification The Gram-negative organism database was revised and includes an • ARG and CET were positive B. cepacia complex 85.92% additional 39 new taxa – 22 fermentative and 17 non-fermentative • LYS or ORN were positive Achromobacter species R. pickettii 10.23% Correct ID (with organisms – along with updated nomenclature. A multicenter study was Correct ID Incorrect ID B. gladioli 3.85% • FD64 and OF/G were positive (oxidase-negative isolates only) additional tests) performed to evaluate the accuracy of the updated NID database and • Panels which could not be read at 16-18 hours were rechecked at 21 Organism Total Cupriavidus spp. 64.36% performance matrix. Achromobacter xylosoxidans A. faecalis 18.48% hours. If the criteria above were met, reagents were added and the P. aeruginosa 17.16% results reported. N % N % N % D. acidovorans 36.44% • Panels for which the criteria did not apply at 21 hours were re- S. putrefaciens 22.83% METHODS incubated an additional 24 hours, after which reagents were added and Aeromonas caviae complex ^ 1 1 100 0 0.0 0 0.0 Achromobacter xylosoxidans B. bronchiseptica 22.83% the results reported. Cupriavidus spp. 13.37% Aeromonas hydrophila complex 1 1 100 0 0.0 0 0.0 Myroides spp. 4.54% Study Design Data Analysis (Tables 1 and 2) • Data analysis included the following calculations for clinical and frozen A. lwoffii group 93.35% Clinical and Stock Isolate Testing Aeromonas veronii complex ^ 1 1 100 0 0.0 0 0.0 Achromobacter xylosoxidans P. oryzihabitans 5.67% • MicroScan Dried Gram-negative Identification panels were tested at stock isolates included in the study: Citrobacter amalonaticus 5 5 100 0 0.0 0 0.0 A. baumannii/haemolyticus 0.97% two sites. • Number and percent species correct ID Citrobacter braakii ^ 4 4 100 0 0.0 0 0.0 Enterobacter aerogenes Very Rare Biotype • A total of 609 clinical and frozen stock isolates: • Number and percent species correct ID, with additional tests (e.g., E. amnigenus 1 97.71% egg yolk agar, motility, growth at 42°C, production of H2S) Citrobacter freundii ^ 15 14 93.3 1 6.7 0 0.0 C. sedlakii 1.12% • 420 fermentative Gram-negative isolates (Fermenters) Enterobacter cloacae complex • 189 non-fermentative Gram-negative isolates (Non-Fermenters) • Number and percent species incorrect ID (or Very Rare Biotype) Citrobacter koseri 14 14 100 0 0.0 0 0.0 E. cloacae 1.03% E. cancerogenous 0.14% • Reference testing was performed following the sites’ current protocols. Cronobacter sakazakii 1 1 100 0 0.0 0 0.0 Enterobacter hormaechei E. cloacae 99.99% Sequencing of 16S rDNA and MALDI-TOF analysis were included for Citrobacter werkmanii ^ 3 3 100 0 0.0 0 0.0 Pseudomonas putida group P. aeruginosa 99.99% discrepant isolates. RESULTS Enterobacter aerogenes 25 23 92.0 1 4.0 1+ 4.0 Panels Quality Control Enterobacter amnigenus 1 1 1 100 0 0.0 0 0.0 • MicroScan Dried Gram-negative Identification panels contained Non-Fermenter Results (Table 1) All Quality Control (QC) strains tested were within specification. modified conventional and chromogenic tests for the identification of Non-Fermenters were identified correctly 97.4% (184/189) and only 5 Enterobacter amnigenus 2 1 1 100 0 0.0 0 0.0 isolates generated an incorrect identification. fermentative and non-fermentative Gram-negative bacilli. Enterobacter cloacae 36 35 97.2 0 0.0 1 2.8 Additional New Taxa (Table 4) Quality Control Table 1. Non-Fermenter Total Performance Escherichia coli 78 76 97.4 2 2.6 0 0.0 There were 39 new taxa added to the Gram-negative ID database: • Quality Control (QC) testing was performed prior to the beginning of Correct ID (with Enterobacter gergoviae 1 1 100 0 0.0 0 0.0 Correct ID Incorrect ID Table 4. New Taxa Added to Gram-Negative ID Database the study using all QC strains and specifications listed in MicroScan Organism Total additional tests) Enterobacter hormaechei ^ 1 0 0.0 0 0.0 1 100 Instructions for Use. N % N % N % New Non-Fermenters New Fermenters Edwardsiella tarda 1 1 100 0 0.0 0 0.0 Achromobacter piechaudii Aeromonas caviae complex 2 Enterobacter hormaechei • Weekly QC testing was performed using the primary QC strains. Alcaligenes faecalis 1 0 0.0 1 100 0 0.0 Hafnia alvei 1 1 100 0 0.0 0 0.0 Achromobacter denitrificans Aeromonas veronii complex 2 Escherichia albertii • The QC strains are below: Achromobacter 21 13 61.9 5 23.8 3 14.3 Acinetobacter junii Citrobacter braakii 3 Leminorella grimontia 4 xylosoxidans/denitrificans Klebsiella oxytoca 27 26 96.3 1 3.7 0 0.0 Primary Strains Acinetobacter ursingii Citrobacter farmer 3 Leminorella richardii 4 Acinetobacter Klebsiella pneumoniae 60 59 98.3 1 1.7 0 0.0 Bordetella trematum Citrobacter freundii 3 Mannheimia haemolytica ATCC 25922 Escherichia coli baumannii/haemolyticus 22 21 95.5 1 4.5 0 0.0 Morganella morganii 15 14 93.3 1 6.7 0 0.0 Brevundimonas diminuta 1 Citrobacter gilleni 3 Serratia ficaria ATCC 49131 Klebsiella oxytoca complex Brevundimonas vesicularis 1 Citrobacter murliniae 3 Vibrio metschnikovii Acinetobacter lwoffi group ^ 6 6 100 0 0.0 0 0.0 Pantoea agglomerans 2 2 100 0 0.0 0 0.0 ATCC 49128 Pseudomonas putida Burkholderia gladioli Citrobacter rodentium Vibrio furnissii Burkholderia cepacia Providencia alcalifaciens 1 1 100 0 0.0 0 0.0 ATCC 27853 Pseudomonas aeruginosa 1 1 100 0 0.0 0 0.0 Comamonas testosteroni 1 Citrobacter sedlakii 3 Yersinia frederiksenii 5 complex Additional Strains Proteus mirabilis 56 54 96.4 2 3.6 0 0.0 Pseudomonas alcaligenes 1 Citrobacter werkmanii 3 Yersinia intermedia 5 Bordetella trematum ^ 1 1 100 0 0.0 0 0.0 ATCC 49132 Proteus vulgaris Pasteurella multocida 3 3 100 0 0.0 0 0.0 Pseudomonas pseudoalcaligenes 1 Citrobacter youngae 3 Yersinia kristensenii 5 Chryseomonas indologenes 4 2 50.0 2 50.0 0 0.0 Pseudomonas mendocina ATCC 29213 Staphylococcus aureus Providencia rettgeri 3 3 100 0 0.0 0 0.0 1 – Previously included in Pseudomonas species group Cupriavidus species 1 1 100 0 0.0 0 0.0 Paracoccus yeei ATCC 49138 Shewanella putrefaciens 2 – Previously included in Aeromonas hydrophila complex Plesiomonas shigelloides 1 1 100 0 0.0 0 0.0 Ralstonia mannitolilytica ATCC 49127 Stenotrophomonas maltophilia Myroides species 1 1 100 0 0.0 0 0.0 3 – Previously included in Citrobacter freundii complex Providencia stuartii 16 16 100 0 0.0 0 0.0 Roseomonas species Pseudomonas aeruginosa 89 87 97.8 2 2.2 0 0.0 4 – Previously included as Leminorella species Shewanella algae Proteus vulgaris 4 4 100 0 0.0 0 0.0 5 – Previously included in Yersinia enterocolitica group Panel Inoculation, Incubation, and Reading Pseudomonas stutzeri 2 2 100 0 0.0 0 0.0 Wautersiella falsenii • All isolates were subcultured to trypticase soy agar (TSA) with 5% Pseudomonas Salmonella Typhi 2 2 100 0 0.0 0 0.0 12 11 91.7 0 0.0 1 8.3 sheep blood or MacConkey agar and incubated for 18-24 hours at 35- fluorescens/putida Salmonella enterica 6 6 100 0 0.0 0 0.0 Rhizobium radiobacter 1 1 100 0 0.0 0 0.0 37ºC prior to testing. Isolates from frozen stocks were subcultured Serratia fonticola 1 1 100 0 0.0 0 0.0 CONCLUSION Stenotrophomonas twice before testing. 23 23 100 0 0.0 0 0.0 Serratia liquefaciens 1 1 100 0 0.0 0 0.0 • Inoculum suspensions for each strain were prepared with the direct maltophilia Serratia marcescens standardization (turbidity standard) method for MicroScan Dried Gram- Sphingomonas paucimobilis 1 1 100 0 0.0 0 0.0 30 30 100 0 0.0 0 0.0 The results of this evaluation with fresh clinical isolates show that the negative Identification panels. Acinetobacter species * 1 1 100 0 0.0 0 0.0 Serratia odorifera 1 1 100 0 0.0 0 0.0 MicroScan Dried Gram-negative Identification panel with an updated • Following inoculation, MicroScan Dried Gram-negative Identification Pseudomonas species * 1 1 100 0 0.0 0 0.0 Pantoea species * 1 1 100 0 0.0 0 0.0 database and performance matrix provides accurate identification results for clinically important Gram-negative bacteria.
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  • Metaproteomics Characterization of the Alphaproteobacteria

    Metaproteomics Characterization of the Alphaproteobacteria

    Avian Pathology ISSN: 0307-9457 (Print) 1465-3338 (Online) Journal homepage: https://www.tandfonline.com/loi/cavp20 Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssus gallinae (De Geer, 1778) José Francisco Lima-Barbero, Sandra Díaz-Sanchez, Olivier Sparagano, Robert D. Finn, José de la Fuente & Margarita Villar To cite this article: José Francisco Lima-Barbero, Sandra Díaz-Sanchez, Olivier Sparagano, Robert D. Finn, José de la Fuente & Margarita Villar (2019) Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssusgallinae (De Geer, 1778), Avian Pathology, 48:sup1, S52-S59, DOI: 10.1080/03079457.2019.1635679 To link to this article: https://doi.org/10.1080/03079457.2019.1635679 © 2019 The Author(s). Published by Informa View supplementary material UK Limited, trading as Taylor & Francis Group Accepted author version posted online: 03 Submit your article to this journal Jul 2019. Published online: 02 Aug 2019. Article views: 694 View related articles View Crossmark data Citing articles: 3 View citing articles Full Terms & Conditions of access and use can be found at https://www.tandfonline.com/action/journalInformation?journalCode=cavp20 AVIAN PATHOLOGY 2019, VOL. 48, NO. S1, S52–S59 https://doi.org/10.1080/03079457.2019.1635679 ORIGINAL ARTICLE Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssus gallinae (De Geer, 1778) José Francisco Lima-Barbero a,b, Sandra Díaz-Sanchez a, Olivier Sparagano c, Robert D. Finn d, José de la Fuente a,e and Margarita Villar a aSaBio.