Library Stats Sheet: Gram-negative

Transcription

1 Library Stats Sheet: Gram-negative Not for Use in Diagnostic Procedures. DiversiLab Kit: Bacterial (cat.# ) DiversiLab Library Name: DL Gram-negative Library Application: Strain-typing for all Gram-negative organisms and characterization of Gram-Negative organisms at the genus/species level.* Reference Methods: Phenotyping, sequencing Library Contents Overview Total Number of Samples represented: 563 Number of genera represented: 75 Number of species represented: 176 Cutoff for species match: Indistinguishable See complete sample list on pages 4-5. Sample ID Genus Species Subspecies Alternate ID Class 1 Viewable Report Fields Sample ID Genus species subspecies ATCC number Salmonella serotype** General Information: The Gram-negative library is comprised of samples amplified using the DiversiLab Bacterial fingerprinting kit. This kit must be used to process samples for comparison to the library and this should be the selected kit inside the DiversiLab software. The culture collection largely used to populate this library is derived from geographically-diverse clinical and industrial sources. On the clinical side, the collection houses isolates with various antimicrobial resistance mechanisms of interest. From the industrial community, isolates are included from agri-food sources as well as from the environment. Because of the large number of samples contained in the Gram-negative library, the library should be created in a specific way for a quicker report processing speed and analysis. During report creation, the following options should be selected. Figure 1 illustrates how to select these settings in the DiversiLab Software. Type Classification, allows use of the Top Match feature Viewable Report Fields Sample ID, Genus, Species, other fields listed above optional Color-coding Genus (or Species if more specific information is required) Collapse (%) 85-90%, allows dendrogram to condense to manageable size * For the highest level of discrimination of a particular organism, use of the genus-specific kit is recommended when available. The use of the Bacterial fingerprinting kit is not recommended for Mycobacteria or fungi. ** The number of Salmonella serotypes in this library is limited. For more thorough characterization of Salmonella serotypes, use of the Salmonella fingerprinting kit and Salmonella library is recommended. Note: The Library should be used as a guide.

2 Bacterial Figure 1. Recommended settings for report creation After you have created the report as shown above, report processing may take some time depending on the number of samples that you are comparing due to the large nature of the report. Please be patient. When first looking at the report, it is recommended to: 1. Check the top match section of the report: if the query sample has 97% similarity to a library entry using either method, there is likely a match. To confirm, examine graph overlays for indistinguishable fingerprints. The interactive screen will not display when the dendrogram is larger than 300 samples. Figure 2. The top match (left) shows that the unknown query sample at key 28 shows only top matches to Escherichia coli. The overlay confirms that the fingerprints are very close (right).

3 2. If the top match has <97% similarity, examine the dendrogram. If the query sample falls in a discreet cluster of fingerprints (85% similarity cutoff or greater) of all the same species, the query is likely a member of that species. Figure 3. The top match (left) shows that the unknown query sample at key 256 shows three top matches to A. baumannii, but all are lower than 97%. The dendrogram shows that this sample clusters solely with A. baumannii; however, none show indistinguishable fingerprints (right). In general, the library shows clustering at the genus/species level. Oftentimes, a specific genus will show a large cluster in which multiple species are contained. However, each species has a distinct fingerprint. It is important to note that dendrograms created in the DiversiLab software show the similarity between sample fingerprints; they do not indicate phylogenetic similarity between samples. Since rep-pcr can discriminate at the subspecies level 1, there may be multiple fingerprint patterns (strains) for an individual species. Therefore the following are possible: 1. There may be multiple clusters for a single species represented in the library. 2. The query sample fingerprint may not have a match in the library, even though the particular species is represented. 1. Olive, D. M. and P. Bean Principles and applications of methods for DNA-based typing of microbial organisms. J. Clin. Microbiol. 37(6):

4 Genus species # Genus species # Genus species # Achromobacter xylosoxidans 9 Elizabethkingia meningoseptica 12 bivia 2 Prevotella baumannii 5 aerogenes 6 oralis 3 calcoaceticus 1 amnigenus 7 mirabilis 1 genomospecies 3 3 asburiae 5 Proteus penneri 5 genomospecies TU13 2 Enterobacter cancerogenus 4 vulgaris 2 Acinetobacter haemolyticus 2 cloacae 3 alcalifaciens 3 johnsonii 1 gergoviae 1 Providencia rustigianii 1 junii 5 hormaechei 2 stuartii 3 radioresistens 2 coli 23 aeruginosa 1 ursingii 5 fergusonii 3 alcaligenes 1 Escherichia punctata 1 hermannii 1 luteola 7 hydrophila 1 vulneris 1 Pseudomonas oryzihabitans 4 Aeromonas salmonicida 4 Ewingella americana 2 pseudoalcaligenes 1 sobria 1 Fluoribacter dumoffii 1 putida 1 veronii 3 Fusobacterium necrophorum 1 stutzeri 5 actinomycetemcomitans 2 Grimontia hollisae 4 Rahnella aquatilis 3 Aggregatibacter aphrophilus 5 haemolyticus 3 Ralstonia pickettii 2 segnis 1 influenzae 3 Raoultella planticola 2 Haemophilus Agrobacterium genomospecies 4 1 parahaemolyticus 1 Rhizobium radiobacter 2 Alcaligenes faecalis 5 parainfluenzae 3 Salmonella enterica 54 caccae 2 Hafnia alvei 2 ficaria 1 fragilis 3 Kingella denitrificans 1 fonticola 2 ovatus 3 Klebsiella pneumoniae 7 grimesii 2 Bacteroides stercoris 4 ascorbata 1 liquefaciens 2 thetaiotaomicron 4 Kluyvera cryocrescens 3 Serratia marcescens 1 uniformis 4 intermedia 3 odorifera 1 ureolyticus 3 Leclercia adecarboxylata 3 plymuthica 2 vulgatus 4 adelaidensis 1 proteamaculans 2 bronchiseptica 7 bozemanae 1 rubidaea 2 Bordetella parapertussis 1 longbeachae 1 algae 1 Legionella Shewanella Brevundimonas diminuta 1 micdadei 2 putrefaciens 3 Budvicia aquatica 4 pneumophila 5 boydii 2 Burkholderia cepacia 2 quinlivanii 1 Shigella dysenteriae 2 gladioli 2 Mannheimia haemolytica 4 flexneri 2

5 2008 biomérieux, Inc. BBI multivorans 3 Moellerella wisconsensis 3 Shigella sonnei 1 Burkholderia stabilis 2 catarrhalis 1 multivorum 1 vietnamiensis 1 lacunata 3 spiritivorum 2 Moraxella Sphingobacterium Buttiauxella agrestis 5 nonliquefaciens 3 thalpophilum 4 coli 1 osloensis 2 multivorum 1 Campylobacter fetus 2 Morganella morganii 7 Sphingomonas paucimobilis 1 jejuni 5 odoratimimus 2 Stenotrophomonas maltophilia 1 Myroides ochracea 1 odoratus 2 Suttonella indologenes 2 Capnocytophaga sputigena 2 animaloris 1 Veillonella parvula 1 Cedecea davisae 4 cinerea 3 alginolyticus 3 Chromobacterium violaceum 3 elongata 4 cholerae 5 Chryseobacterium gleum 1 Neisseria gonorrhoeae 4 fluvialis 4 indologenes 6 lactamica 4 Vibrio metschnikovii 2 amalonaticus 4 meningitidis 4 mimicus 2 braakii 2 zoodegmatis 4 parahaemolyticus 4 Citrobacter freundii 6 Ochrobactrum anthropi 2 vulnificus 5 koseri 5 Oligella urethralis 2 Weeksella virosa 1 sedlakii 5 Pantoea agglomerans 1 aldovae 2 Comamonas testosteroni 1 Parabacteroides distasonis 4 enterocolitica 4 Cronobacter sakazakii 1 aerogenes 3 frederiksenii 2 Yersinia Cupriavidus pauculus 5 Pasteurella canis 3 intermedia 3 Delftia acidovorans 5 multocida 4 kristensenii 4 Edwardsiella hoshinae 5 Photobacterium damselae 3 ruckeri 1 tarda 2 Plesiomonas shigelloides 3 Yokenella regensburgei 2 Eikenella corrodens 3