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Ridom EpiMRSA

1. Ridom EpiMRSA Version 3 User Guide Copyright 2003 2011 Ridom GmbH All rights reserved For research use only Not for use in diagnostic procedures Information in this document is subject to change without notice Ridom GmbH assumes no responsibility for any errors that may appear in this document This document is believed to be complete and accurate at the time of publication In no event shall the Ridom GmbH be liable for incidental special multiple or consequential damages in connection with or arising from the use of this document Notice to purchaser License Disclaimer Ridom and EpiMRSA are registered trademarks of the Ridom GmbH in Europe U S and certain other countries Java is a registered trademark of Sun Microsystems Inc Microsoft Windows NT Windows 2000 Windows XP Windows Vista and Windows 7 are registered trademarks of the Microsoft Corporation Mac OS X is a registered trademark of the Apple Corporation Linux is a registered trademark of Linus Torvalds Adobe Reader is a registered trademark of the Adobe Corporation ABI is a registered trademark of the Applera Corporation or its subsidiaries in the U S and certain other countries All other trademarks are the sole property of their respective owner Document version 3 0 March 2011 Table of Contents Lol CEOCIUICTION anra EEEE EE EEN E E 7 Sag E n SOR
2. 2 Be sure to plug in the Ridom Hardware Key before starting the program EpiMRSA will first create a profile directory located in your home directory e g using Windows XP this will normally be something like C Documents and settings lt username gt epimrsa This directory will contain your configuration file and the error log file When the login dialog appears for the first time a message will appear and EpiMRSA needs to initialize the default database You can define the path where the database files should be stored and set the password that is needed to log into the database By default the database files will be stored in the profile directory After the new database is initialized the EpIMRSA session will be started WARNING The decryption of the database data is only possible using the EpiMRSA password However this password itself is not stored within the database and cannot be reproduced or reset when forgotten It is therefore vital that the password be memorized well or written down The database cannot be restored without the password For performance reasons an internal database should always be saved on a local hard disk If your profile directory is not on the same computer as the EpiMRSA installation it is recommended to change the path for the database files to a local directory Updating the Software If an update for your EpiMRSA installation is available an information message will appear on each
3. button to display the Export Filter editor dialog Then move field labels from the two lists Available fields and Selected fields The two upper buttons or a double mouse click moves the label selected whereas the two lower buttons move the complete list The selected fields list defines the columns exported and their order in the CSV file 35 EpiMRSA User Guide JU New exporter filter Filter Mame MyExportFilter Column delimiter Create Header row Available fields Selected Fields Strain Sync Comment Strain Laboratory ID Strain PubMed ID Strain Order ID Strain Ma Sync SpaTvpe ID Strain Submitted Strain Isolation date SpaTvpae Comment Care unit City SpaTvpe MLST Care unit Country Spalype Literature UID Methicillin result Spalype Global frequency Person related data Person type Person related data Associated with Person related data Clinical details Person related data Acquisition Person related data Investigation reason Person related data Admission date Person related data Dissmissal date Person related data UserField S l Lt d I m J L TF al Importing CSV Files EpiMRSA can import entries from a comma separated values CSV file Select the CSV file to be imported from the File menu opened with the Import Data File button 5 5 The file will be read and then a preview dialog is opened To import data entries you need to configure an import filter that maps the columns of the file to databas
4. matches the preceding expression or the null string e g GB G matches GG and GBG matches the null string or any number of repetitions of the preceding expression e g GB G matches GG GBG GBBG GBBBG and so on matches one or more repetitions of the preceding expression e g GB G matches GBG GBBG GBBBG and so on can be used for grouping several characters in combination with the operators above e g 12 34 12 matches 12 12 and 12 34 12 m n matches between m and n repetitions of the preceding group e g 12 34 2 3 12 matches 12 34 34 12 and 12 34 34 34 12 O3 D EpiMRSA Version History D EpiMRSA Version History Ridom EpiMRSA version 3 0 released March 2011 revised version for further networks Euregio EpiMRSA version 2 0 released June 2010 improved support for Windows 7 Euregio EpiMRSA version 1 1 released March 2007 introduced the NIS ODG Reports and the Early Warning System Euregio EpiMRSA version 1 0 released November 2006 first release of the software OO E License Ridom GmbH End User License Contract for Software I General a This End User License Contract EULC forms a legally binding contract between you the licensee and Ridom GmbH the licensor for the EpiMRSA software and related media materials and documentation the software product b By opening
5. 6 for calculation of 3 Typing System Concordance 4 Reproducibility 5 Typability and 6 Discriminatory Index Results View The results view displays the calculation results of the selected procedures References for the different procedures are given The results can be saved and printed In addition they can also be exported to the clipboard and used in word processor programs like Microsoft Word Calculation Details Typability The typability is the proportion of strains that are assigned a type by the typing system The formula reads r oN with N the number of isolates assigned a type and N the number of isolates tested The Epidemiological Statistics tool uses N Number of isolates that are not missing N Number of isolates that are not missing and are typable 49 EpiMRSA User Guide See Hunter Gaston 1988 Struelens 1996 Reproducibility Reproducibility is the ability of a typing system to assign the same type to a Strain tested on independent separate assays The formula reads R N with N the number of isolates assigned the same type on repeat testing and N the number of isolates tested The Epidemiological Statistics tool uses the following data N Number of isolates that are not missing N includes non typable values N Number of isolates that are not missing and have the same value The value is the same if both isolates are non typable See H
6. can be displayed the report only contains the entries displayed Internal and External Strain Entry Reports If a spa type is assigned to a strain and the sequence editing is reliable the report for the entry can be created There are two different types of entry reports internal and external to cover different user scenarios A report is generated by clicking the amp button and the pull down menu of the button can be used to configure the report Internal Report This type of report contains nearly all the information stored for an entry It has a plain table layout and the internal comment is appended to the report The internal report is mostly used for communicating results within an institution External Report This document can be used as an official spa typing report and can be partially customized The sender of the report and a signature text can be included in the report configuration and this information will appear in all external reports In addition a specific report comment and a receiver address can be defined for each entry Furthermore a custom logo can be placed in the report for more details it is referred to chapter 13 Report History Every entry report internal or external created is stored encrypted in the report archive and is added to the history of the entry report Clicking the history button in the Strain Browser tool bar displays the report history for an entry The entry history window open
7. clustered if cost is less ar equal 5i Data 2 Choose Marked DB strains gt Choose Strains From File Use Taxa label Spa type PFGE tvpe T Use All Strains OOF spa S930 2002 253 f i032 zi Pat Use Mo Strains TM oor spa anera 2002 ious MY oorspaatosztzoo2 eos ooo o d Export Data MY jUzspaktsii 2002 eoa V oor spa o2 3058 202 eoa o o V jo spa a ta amp 208 es V oor_spawiosz 200 eaa o V oor spa tza e003 eoa o M oor spama zoos ito O oor spa mazo 20 ea Sooo M oor spa meza zoos ea A porspazei200 5 L r 1 5 555 RR J N Use the button Choose Marked DB strains to select all marked strains in the database strains can 41 EpiMRSA User Guide be marked in the StrainBrowser Additionally six data fields of the strain entries can be included MLST PFGE SCCmec coa phage type and the user field in the strain type section Alternatively use the button Choose Strains from File to import the strain data from a CSV file comma separated values containing taxa labels spa types and optionally other fields An import dialog shows a preview of the imported data Be sure to set the correct field delimiter normally or Click on the header of the columns to customize the mapping of the imported data BURP Clustering Max ST Data Clustering Show Gr
8. id tooa Jung one ce ien inie 007 spa id t034 be 4f Edi Entry Data Eingabe circ 23 007 spa id 1490 Wi Delete Entry Entf Clinic 16 007 spa id t032 eun Hb Strath clinic 21 Ward 10 oor spad kisos fun E toos unz di Create Entry Report poor spad i032 Qui SX Mark As Not Reportable E 907 spa id 253 Jun 30 206 peron mos E 107 spad i863 Jun28 2006 person AbsHkhFuBl Cincz wardi _ Ll 007 spa id t151 Jun29 2006 person Trachealsekret Clinic 18 Selected Strains 1 Found Strains 607 Marked Strains 0 14 3 Getting Started Creating Strain Reports If a strain entry is assigned a spa type an entry report can be created Select the entry in the Strain Browser and click the button to create a report for it The report can be viewed by opening the entry history with the button Retrieving Spa Types from the SpaServer When EpiMRSA is started it automatically checks if your spa type data is up to date by requesting the SpaServer Click on the button to manually invoke the download of current spa types and spa alignment data from the SpaServer Note If you are accessing the Internet through a proxy server you first need to set the proxy parameters in the EpiMRSA configuration dialog If you don t have an Internet connection at all you can receive the up to date spa type information by email 15 4 Entering Entry Data 4 Entering Entry Data Stra
9. in System 1 and a type in System 1 and in different type in System System 2 2 Ac D The ratio C Total Sum is the Typing System Concordance See Robinson et al 1998 References Hunter P R and Gaston M A 1988 Numerical index of the discriminatory ability of typing systems an application of Simpson s index of diversity J Clin Microbiol 26 2465 2466 Struelens M J 1996 Consensus guidelines for appropriate use and evaluation of microbial epidemiologic typing systems Clin Microbiol Infect 2 2 11 Simpson E H 1949 Measurement of diversity Nature 163 688 Grundmann H Hori S and Tanner G 2001 Determining confidence intervals when measuring genetic diversity and the discriminatory abilities of typing methods for microorganisms J Clin Microbiol 39 4190 4192 Robinson D A Hollingshead S K Musser J M Parkinson A J Briles D E and Crain M J 1998 The IS1167 insertion sequence is a phylogenetically informative marker among isolates of serotype 6B Streptococcus pneumoniae J Mol Evol 47 222 229 ol EpiMRSA User Guide 52 C Regular Expressions C Regular Expressions Using Regular Expressions in Repeat Motif Search Use the repeat motif search to find substrings in the repeat successions of the known spa types The search supports both Ridom and Kreiswirth nomenclature Additionally the search term may contain standard regular expressions Examples
10. list search for strains The search criteria for this search are defined by place time case specifications and spa types The last used search criteria are memorized The result of the Line List search is shown in an external dialog window The data of the found strains can be exported to PDF or into a comma separated values file CSV 22 6 Readmission 6 Readmission Readmission Check This function can be used to detect the readmission of previously colonized or infected patients by comparing a list of readmissions with the EpiMRSA database The list must be a CSV comma separated values file containing a row per person e g exported from a laboratory information system It must contain a column with the Person ID and may contain any further columns In order to compare the list with the database both must use the same unique keys for the Person ID field Use the Tools menu function Readmission Check and open the CSV file After confirming the file dialog the data of the CSV file will be shown in the import dialog Be sure to select the right Field delimiter to split the data into the correct number of columns E Readmission Check Import Person ID list for Readmission Alert Input File Mi readmission demo csv Care unit all care units ina MRSA only Person ID column Click on column header Field delimiter First row contains header Last name Birthday Admission date Doez 0 24 05 1996 10 06 2006 Doe s
11. nen UM NEUEN DERI Sa pEL AES 41 MEP OCUICHON eR T P 41 Pele TUS POM IVS coast Boas Que Ma E o Bre eM see mo A bine MM Scu Im x EE 41 Conven NomenclaU G scouts do derriere donde edente drehen eurer Ee dtes E dae edens 44 Repeat Mott oeart Daniae etd EE at td tU Vastu d ER nasum Ed pM stet ee aaa 44 Spa type and Repeat Alignments e eeeeeeeeeeeeeeeee eese esee essa a nautae teta attese eese e eaae sess asas aeta eee 44 Spay Gs DONS rs pe sete safes seo desee pu aveo SD ec esi oe eee eee eee 44 14 Epidemiological SEatiSLICS spei REN M EORR PEDEM MR bIteP d at MN 47 Tlatroce LOB nidos E ed nio tua Edna nt a ray er uoo DR ee 47 waren m A CRT s 47 MAP OLE Data rom a SV PTC seite en S vU VERI dediti te UH S rerE nan Mb asins 48 Iniport IDate trom Clipboard d beu iesue toov EEE bon i eue eteasesyetewed lynne 48 Data VIEW io D HUMEUR MEME M IM M M MEI Dd EE 48 Procedures Selection VIeW estime DUE EN nt tetas iso eee ee 48 PRES UNITS VLG pasisian 49 Calculation CLAUS sssr EAA 49 PRESET UC seriei E E E aN Eu ed PPS Oban 51 C Regular EXDIeSSIOFIS iun vexo asinan edite ota a ox xD ue vr d S oU d EUER UE 53 D EDIMRSA VersIOnD HISEOLY csscsxmasteniVientaip bas EERENS OR OR RP 55 Bel C treat HH 57 End User License Contract TOT Softwa s deu Reese Coe iura a a 57 1 Introduction 1 Introduction Overview Staphyloco
12. replaced by this contract In addition the General Terms and Conditions of Business of Ridom GmbH also apply o9
13. soon E E Fassa atate ia S ETSI PSOE p cease Ene TA AE pe Hope sU eePE RU M UE 15 Retrieving Spa Types from the SpaServer eese snas anna 15 AENEID ENUY Dal deurrie R O 17 W DITE O oes a E E T E E E das RR en R n dd HUE UE 17 macine Be UT ee 19 5 Working with the Strain BroOWSEL cccececeeceeeeeeeeeeeeeeeeeeeeaeegeeaseeeeaneeneaes 21 The Strain Browser WINGO W ve cius2 dasicsctsdaceselerarinedanocewn adeucsahedeeattalebensveddadentnsabeddeahsioavtelesateveldbevelesadeaced 21 SCA oe Or STan BRETT TEE T OO TO ET 21 Piederned Sear IBS ceci esu EERE HI PGURD Id E E E bU UD E EIU OBEN HDI E E EE 22 lid b E 27 GROANS S O M 23 I cialis on FIC K oorr E E N E E E EE 23 2e eg 25 siccis MACE REDOT REO EN 25 Internal and External Strain Entry Reports eeeeeeeeeeee eese e eese eene nee tht hase sess asa sat oaa 25 Rano os Nic C9 TT 25 MEE SASN R EDO leoir E TEN E E 26 OCP Rat aA wre cae EENAA AA AAE EAE EA AE OAA AEA 28 SEY NaN a yS O araar E E E A S 29 Baro M aU INO 5 y e E E E EEA E ETEEN 29 Feel ye WAV E MINS OB E E A A OD 29 CU I esse EE E E E EE T E E EE T E E E ET SS 30 Configuring the Connection Pararmeters ccccccccc
14. without errors in all applications and combinations The subject of this contract is therefore only software which is in principle usable in the sense of the program descriptions and user manual Ridom GmbH supplies without charge within 30 days from the date of purchase replacements for defective data media for the case that the software product is fundamentally unusable in the sense of the description supplied with it or refunds the purchase price to the licensee against return of the defective software product If Ridom GmbH is not in a position to fulfill the warranty both sides have the right to rescind the contract with the purchase price being refunded to the licensee Statements contained in brochures advertisements and similar documents represent only descriptions and do not contain any assurance of properties or guarantees The assurance of properties requires an express written agreement This also applies for price quotations and for statements on the release of additions and extensions Limitation of Liability The licensee bears the responsibility for the selection and for the consequences of use of the software product together with the results thereby intended or achieved The software product is expressly intended only for research purposes and not for the preparation of diagnoses and particularly not for in vitro diagnosis IVD Liability for damages of any kind included without restriction are damages from loss of p
15. you are unable to connect to the Internet directly Register at http www ridom de epimrsa spatypes to receive new spa types by email This emails will have an attached XML file which can be imported with the button to update the spa type data of your local database Updates The automatic checks for available software updates and for new spa type data when EpiMRSA starts can be activated here Receiving Information Messages and Software Updates On occasion the user will receive an html message from the server when the spa type download has been performed This message may include general information or it may be a link to download an important EpiMRSA software update Message Archive The last 10 SpaServer messages can be read in the message archive accessible through the menu Help Message Archive Three types of messages are stored here e messages concerning the results of spa type retrievings e update messages from the server e messages containing information from the server e Spa type group alert messages 31 10 Database Statistics 10 Database Statistics Viewing the EpiMRSA Statistics Click on the lil button to open an internal window that shows the statistics of your local EpDIMRSA database This window has four tabs Database Statistics Shows a summary of contents and a table with all spa types in the database listed according to their local frequency Database Spa types Shows the repeat successio
16. 07 spa_koe BURP Result 004 24 Jul 2003 persan nose person v 07 spa kt6 URF Result 004 24 Jul 2003 erson v B0 spa wi2 URP Result 004 24 Jul 2003 erson kin ve kin erson URP Result 004 10 Aug 2003 person e URP Result 004 erson URF Result 004 10 Aug 2003 person nose person URP Result 004 10 Aug 2003 rson URF Result O04 10 Aug 2003 rson URP Result 004 10 Aug 2003 person genital person URP Result 004 10 Aug 2003 person fluid stomach person URF Result 004 10 Aug 2003 person wound person v 15333 toos URF Result 005 10 Aug 2003 rsan 005 BURP Result 005 10 Aug 2003 rson EM mss oos BURP Result 005 10 Aug 2003 person foral person A ms o URP Result 005 erson A beos koos BURP Result UOS 15 Aug 2003 person fperson A pu spa wi7 BURP Result 008 erson BURP Result 008 erson A oos spa sta koos BURP Result 006 15 Aug 2000 person unknown person wj pos d EURF Result 008 10 Aug 2003 erson URP Result 008 10 Aug 2003 persom person wj psi pn Ii URF Result 008 10 Aug 2003 person blood person Selected Strains 0 Found Strains 42 Marked Strains 42 Strains in DB 612 45 14 Epidemiological Statistics 14 Epidemiological Statistics These features are only available if the Expert Mode is selected in configuration Introduction Epidemiological typing has many different applicat
17. 09 2003 and e that the susceptibility results are given in one of the following three forms not done empty empty resistant R intermediate I susceptible S JU Import CSV Data File C54 Import Filter Import Filter Mee v Filter me E B Delimiter Header row Strain La SpaTvpe ID 3 Strain Iso y a Strain Labor 5paType ID Strain Order Strain m Strain Recei Stra Grinin Jstrain 5neri IMeFhicillin re D15 328 tono hw i3 5ep 1996 jpe Map to Strain B D16 QP5RW t no p Jz003 fpe MaptoSpaType gt O16_050R toos p33ukz003 pe Map to Person related data gt 007 spa a9 t040 r May 2002 Pe Map to Person D15 335 roos mo JM Deci996 pe nt Map tac t O07 spa w t034 pereo bpe nt gt gt tible osas 8l OoOO oraa pe Mep to Clinic O5 338 koo O 72003 pe Mapto ward Gi6 n32 H d 7 Aaa 2H pe ap to susceptibility O16 091 099 M Hux2003 e Remove mapping meo i33 MoO pema pe Di6 079 t8 MoO eaa pe PT ypeSroup TP 0l6 073 84 peaga pe SP aT ypeGroup Name meos tS Aug 2003 pe SpalypeGroup Comment Grece fois ea pese P e meos 097 MoO ema person meo n MO o peaa person 016 093 kos MO peaa person P Og ivF emee pen Od i a a Ca c E PRNNR a a a a a cR CNN To resolve any
18. 1 10214 12 06 2006 007 sp id SI8 2005 Aug 31 2008 24 09 1915 PIOI3 14 05 2006 007 spe id 1332 2006 un 2006 Doe24 0e385 oe314 corresponding strain data 31 10 1915 P10341 12 07 2006 07 spa id 1391 2006 jJul 2006 09 06 11 01 1937 P10232 25 06 2006 007 spa id 954 2005 Sep 30 2005 11 08 1948 P10023 28 06 2006 007 spa id 1061 2005 Dec 8 2005 10 07 i 20 03 1935 P10280 19 07 2006 007 spa id 1253 2006 Apr 18 2006 Doe356 14 03 1924 P10316 05 08 2006 007 spa id 1335 2006 Jun 13 2006 Doe352 04 11 1919 P10312 07 08 2006 007 spa id 1331 2006 Jun 6 2006 Copy to Clipboard Use the check boxes above the result table to add further columns containing values from the according database strains Finally the result table can be exported to a CSV file or copied to the clipboard 24 Creating Reports Creating Reports EpiMRSA creates reports in PDF file format and therefore the Adobe Reader needs to be installed in order to view or print these documents Strain Table Reports Clicking the 4 button in the tool bar of the Strain Browser creates a report of the table displayed This report due to layout restrictions contains only the first five columns by default However the pull down menu of the button can be used to change the number of columns displayed or to directly select the report columns required Note Even when more strain entries are found in a search than
19. 21 09 1935 10 08 2006 Doez43 28 09 1941 Dosis 24 09 1915 1406206 Doe743 23 09 1985 05 08 2006 1 Doe3s2 04 11 1918 07 08 2006 ll Perform Check Use the Care unit combo box above the table to limit the search to a certain care unit Select the column that contains the Person IDs by clicking on its header or choosing it in the Person ID The selected column will be highlighted yellow The settings of Care unit Person ID column Field delimiter and First row contains header will be memorized when using the Readmission Check function again Click on the Perform Check button to start the comparing of the Person IDs with the entries stored in the EpiMRSA database If one or more Person IDs were found an alert window appears after the check is completed The input rows whose Person IDs were found in the database are shown in the result table The first columns contain the values from the input CSV file The last column contains the Laboratory IDs of all strains that were isolated from the according person Click on a Laboratory ID to open the 23 EpiMRSA User Guide Doe270 0e243 0e353 Doe261 Last name Readmission Check readmission demo csv amp Found 30 Readmission s Add Columns from Database Isolate ID Person Name C Care unit _ Clinic and Ward Isolation date Export with header Birthday Person ID Admission Isol 24 05 1996 X P10240 10 06 2006 007_spa_id_968_2005 0 28 09 194
20. SB ports it is possible to apply the hardware key to a server computer The hardware key of the server computer can than be used by any other computer in the same local network If this is needed please contact support ridom de for further information Software Requirements e Microsoft Windows 7 Vista XP 2000 e Adobe Reader software must be installed to view or print PDF reports Installing Instructions If you do not agree with the End User License Contract EULC please return the CD and the hardware key immediately back to the Ridom GmbH All other applications need to be closed before installing EpiIMRSA 1 Insert the EpiMRSA Program CD into the drive The installation program usually starts automatically if not open the CD with the Windows Explorer and double click the EpiMRSA 3 x x exe file 2 Confirm the on screen dialog to start the installation 3 Follow the on screen instructions until you ve completed the installation procedure 4 The last step of the installation will be the installation of the hardware key driver The name of the driver is WIBU Box 5 Plug in the Ridom hardware key delivered with the CD and wait until Windows has initialized the new USB device 6 EpiMRSA can now be run by clicking the desktop icon or selecting the entry in the Start Menu Installed Components e Ridom EpiMRSA e Drivers for Ridom hardware key WIBU Box EpiMRSA User Guide Starting EpiMRSA for the First Time 1
21. WEB FOTO 2022250595 5 05989989 9 9980920 E 00949585 40 sS n s E EAS UST pan EE RA UNGMUSSMR S UOPREE 8 Protection of Data PrivaCy CREER m 8 Info O COMAC U ean on a E A EE E A A E A AEE EA E EAE EE EN 8 N ariesiselaoitell 9 SY Se DY GUI G PIG INES ooo eoe ETE E eosPabebp es uEO T AM IHASE 9 Iastaliine TIS GC EOS eueouecesiee reos dezmace viov aeE ane une aie rhe sonde cnim sa tiuceaq ecu ec un E ess uc reise rund uec Meum esee qu E 9 lisse Sa o inDIPTO D MH NEN TET Tm mme 9 Starting EpiMRSA for the First DNO e po 9o Dehu YS Ness p aae pu Rx e Ee E99 De RR NES Nds pepe eene ERE SS uep te EUR ee Rn 10 MCCUE SORE W ANC a onto ud mE mM Er SMS E S 10 MESO UW AIR gt ss Mail m m 10 Inm calis Epi So sites diesen EE A wet se M E dowstdetuS T E ER OEA A 11 3 Getting StArted cc cccccccc ese ee eee eeeeeeeeeeeeeeeeeaeseeaeaeeeeaesaeaeeeeaesteataeeataneaneags 13 bine EDINE S coss sd E EUM MINIME EMEND EIDEM MIN 13 Using the EpDIMRSA Main WindoOw e eeeeeee eene eee nnus annee eh sas s ahhh haa a hase sess sees asas aas a teta sas 13 IS DOSE 25 MO MIC WIG 2ooscoocienise eder Deco E E Ud UTER QUU E Ud Cour UR US 13 Entering tiec Stan DO lanes cree otoentegtingetidagdd ar i E biles toos e utu O Ree Hsu PUER DE PEdUN RUE 13 POS UI 1110 5 EAT D GOOD eeepc egies noe vdpes sue sep iecte E tS v Pipe Idu DE DESDE EON nuu oreD A 14 Gecin SIEGE PCOS
22. a types to examine the alignment or the relation between specific spa types explicitly Spa type Groups Spa types can be arranged in spa type groups These groups are only locally defined they are not synchronized and are only meant for local usage Each spa type may belong to one group only Spa type groups are conceptually independent of the spa type clusters but the BURP Clustering dialog can be used to add the spa types of one or more clusters into a spa type group Select Spa type Groups from the Tools menu to manage defined groups create new groups and edit the following group settings Name A descriptive name for the group Comment Any comment Alert Define if an alert should be given if a new strain with a spa type of this group appears The alert can also be defined by a maximum spa alignment distance to any spa type of this group If an alert is triggered a warning message appears Spa types Can be used to add or remove spa types manually Color Defines the background color for all spa type ID of this group in the Strain Browser If a spa type is grouped the Strain Database Browser shows the color of according group in the spa type column 44 13 BURP Clustering Strain Database Browser amp A PRP OAs Recent Strains 4A Not Submitted S Marked Strains Marked Laboratory SpaTypeID SpaTypeGroupNa Strain Em Strain Origin Strains Strain O
23. ain The oldest strain in the consecutive possible outbreak strains The index strain is taken from the chosen alert when creating an outbreak and can be changed by the user Secondary strains The strains which follow the index strain in the possible outbreak chain The secondary strains are taken from the chosen alert when creating an outbreak and can be changed by the user No of strains The number of primary index and secondary strains Comment A comment for the outbreak 30 9 Retrieving Spa Types from the SpaServer 9 Retrieving Spa Types from the SpaServer Configuring the Connection Parameters Network Connection The communication parameters can be set in the Configuration window Menu Options SpaServer Download Connection Two options are available when communicating with the Ridom SpaServer connection dialog Automatic communication via http This is generally the method of choice when connecting to the server when your computer has a direct connection to the Internet or when you can access WWW sites through a proxy The correct SpaServer URL is already predefined If you need to use a proxy to connect to the Internet it is necessary to set the proxy parameters in the connection configuration If you do not know these parameters ask your network administrator e Manual communication via file export and email For technical or security reasons this is the method of choice when
24. anage In Herkunft des Isolates MRSA Nicht im NIS OGD Report ber cksichtigen Isolat ID Auftrag ID Abnahmedatum E Einsendedatum E MRSA Befund mitgeteilt EJ emm SO mI d gt r Browsing the Strain Data Click the button in the main toolbar to open the Strain Browser window When opened it shows initially a list of all entries that were created or edited in the last 30 days E3 Click the button 4 to search for specific strain entries A dialog window appears in which search criteria can be defined The results of the search will be shown as a new tab in the Strain Browser window If the Isolate ID columns is highlighted red the entry does not contain all data that is necessary for an MRSA NIS report Move the mouse over the red marked field to show a tooltip with further details Strain Database Browser SEBRA H FE 88 8 HE E Recent Strains All Strains Mar Isolate ID Spa type ID Strain Isol Strain Origin Strain Spe Clinic Name Ward Name UU spa Id 14 5 Jun 2U ZUUb person Blutkultur Clinic 13 ward 4 s 1 E E spa id H2 Dun25 2006 person Trachealsekret Cnc 18 warda Bam toaz un26 2008 person abstriechFuB Cinc2 ward2 E Jr spe id koos bun 25 2006 persm hose c2 wadi BH t un27 2006 person ose Cink23 Wadi E jr spe id tist Dunzz2006 person rose cia Wad2 007zspa
25. aph Add to Spa type Groups Export Cost Distance Matrix Export Results 11 Epidemiological Statistics Cluster 1 spa CcC 004 of strains 157 33 of all strains of spa types 30 35 of all spa types C Cluster 2 spa CC 002 of strains 169 35 of all strains of spa types 19 22 of all spa types t001 tOO2 t003 t010 1035 1039 t041 t045 t053 1055 t056 t066 t067 t071 t072 t0r t081 105 106 Show Strains Cluster 3 spa CC 008 of strains 84 17 of all strains of spa types 9 11 of all spa types 1008 1009 1024 1036 1051 1052 1054 t068 tors Show Strains C Cluster 4 spa CC 084 085 of strains 8 2 of all strains of spa types 5 6 of all spa types t083 t084 t085 1091 t094 Show Straine Found 6 groups and 5 singletons 4 spa types were excluded 1 strain contained no spa type When the strain data was selected and is shown in the table click on the Clustering tab to perform the clustering The algorithm tries to find clusters of spa types so that every spa type in a cluster is related to at least one other spa type in the cluster Each spa type is member of one cluster only Spa types that cannot be assigned to a cluster are kept as singletons Two clustering parameters can be configured in the Data tab dialog e Exclude spa types that are shorter than x repeats Because it is impossible to infer the evolutionary history from very short spa ty
26. ccccccecccececcececceeceeecceceeeeeeeeeeeeeeeeseseeseseeenanaes 31 LO DatapaSe o LALI SLIG S vice med m 33 Viewing he EDIMES A Statistics 5 squacaaisaccuagtasnabiarsabcuueg agudedaiaatonseseonaniasactanses asuscuvesiumeataaraunmnents 33 VIEWING the Spaserver Statis liCS esain anann E E AEREA 33 11 Database Backup and Data IMport EXPOlt cece eee eeeee eee eeeeees 35 Packing Up tne DataDas C is5 ie72 care sca teteceenteranins ccsecusen a M EU 35 lmportins a Database Backups bot eR o pev ER e IIR RIS hM RI EU DINE 35 Checking the Integrity f the Databases coscerceve treten yi Precor teret ei Py nece recen tere Por eniis 35 XO UNG DA ee E E EA E O 3D lan pre Edi Seo MM op cp 36 I2 Conrgurng EbDIMBmBSJA sscidt vet verd vetbda prater Gein avian EH ROM dui 39 EDINMIRSACDIG GTGDOGS enden str ri mete e este do In s TE CEE EITO ANTES ITIN SEN OI DrE terme anaes 39 COnrguriie AD Peal A NCO cs etenim estafa pea ad do Fadvot cmlta fase bead vd fatum uat cma Nase bead e ue DE CORE 39 CONMSUTING Spdserver DOSnloBd eec eee tiet aeta Cerise bu RON pd e D ee 39 COHBteurne REDOT radonin RID RTIRSA NU be CENA US DeV GUTES Rune I NDA d UM obi ui CENE en beeen 39 CS OMI OUE ITI SOCHEID obstetricia dietus rout 40 FTC Pal A DNC AON S cecus A a ons rtu OA Econ E dn OP Ue MED Ter uti a 40 PRAY ATCO Oise EN T UE m 40 Ha TSP ASS WONG nce pecie ette dion edente tatum dO ende edes demi edades o eni eu Rud 40 Ls DERIT CUSTER uus esudt laut tulocurdubi mean
27. ccus aureus S aureus is the cause of the most hospital acquired infections worldwide Thereby infections are particularly susceptible to being caused by Methicillin resistant S aureus MRSA for which there are only few if any possibilities of antibiotic therapy It has been clearly demonstrated by various authors that Methicillin resistance is directly associated with increased mortality and morbidity with S aureus infections In the last 10 years an increase in the MRSA rate from 2 to approx 25 was observed in Germany In the Netherlands and Scandinavia a stable rate under 3 has been recorded for years Particularly for the Netherlands adhering to a consequent search and destroy policy MRSA felt off to very low rates and is now under control In the Netherlands the main focus will be on isolating and controlling CA MRSA that are a possible danger for the open population outside hospitals The main aim of the project is the creation of a network of the major health care providers in the region and the achieving of a lower MRSA rate a reduction of the number of MRSA infections and thus a shorter stay in hospital as a result A basic requirement for this is the active education of the region s population by the EUREGIO network A transborder quality group from hospitals public health authorities and laboratories is therefore planned over the course of three years The network aims to consolidate those already locally established resources e
28. d H51 Jun 27 2006 D07 spa id toos Jun 279 356 anesan loin inici z L 007 spa id t1490 T Delete Entry Entf Clinic 16 c L _ 007 spa id t034 xs E Edit Entry Data Eingabe Idini23 L 07 spaid ee View Entry History Strg H L 007_spa_id_ t1505 Jun 2i HF t009 EA Create Entry Report Clinic 21 L 007 spa id kosz AX Mark As Not Reportable L 007 spa id 253 Jun 20 2006 Iclinic 14 L 007 spa id kaos Jun 28 2006 person Abstrich Fu 1 1 oo7 spa id E151 Dun 29 2006 person Trachealsekret Clinic 18 Selected Strains 1 Found Strains 607 Marked Strains O Strains in DE 607 The first column in each row can be used to mark the corresponding strain The marks are kept persistent in the database They are useful to mark a subset of strains for clustering or exporting Use the toolbar buttons z to mark all or selected strains from the current tab to unmark all or selected strains from the current tab and to unmark all strains in the database Searching for Strain Entries Click the 4 button to define new search criteria This opens a dialog for selection of the search criteria Each row contains a field name an operator and a value Additional rows can be added by selecting the and checkbox The available operators depend on the type of field i e date number and text Person data howeve
29. d for any task or function not covered by the other fields The label of a user field can be changed and this change will apply to all other entries Additional user fields are found under the other tabs Care Unit Clinic and Ward Fields The field Care Unit e g a hospital nursing home or doctor s practice is a mandatory field for each strain entry The fields Clinic and Ward are subunits of the Care Unit and are optional A unit Care Unit Clinic or Ward can be selected in the pull down box or newly created with the button The Ef button can be used to edit an already existing unit It should be noted that this will change the data for all strain entries referencing this unit The following relationships exist between Care Unit Clinic and Ward e A Care Unit may contain one or more Clinics and one or more Wards e A Clinic may have one or more Wards e A Clinic can belong to only one Care Unit e Each Ward belongs to one Clinic or one Care Unit 17 EpiMRSA User Guide Strain Type Tab This form is used to gather typing test results for the strains isolated The first row defines the current spa type assigned to this strain If a strain is not typable using spa gene sequencing e g when the strain does not harbor the Protein A gene NT non typable can be selected The MRSA MSSA field is directly linked to the MRSA check box in the Source tab and to the methicillin row in the Susceptibility tab Susceptibility Tab T
30. d to rent the software product to lease it or to lend it g Without prejudice to its other rights Ridom GmbH is entitled to terminate this EULC insofar as the licensee contravenes the provisions of this EULC In such a case the licensee is obliged to return all copies of the 07 EpiMRSA User Guide h i software and all its components to Ridom GmbH or to destroy them After installing a copy of the software product in compliance with this EULC the original medium on which the software product was supplied by Ridom GmbH may only be kept for security or archiving purposes If the original copy is necessary in order to use the software product on the computer a copy of the software product may be made only for security or archiving purposes Insofar as not expressly permitted in this EULC the licensee may not in any other case make copies of the software product or of the printed material which accompanies the software product Ridom GmbH reserves all rights not expressly granted The individual provisions of this license agreement can only be changed by Ridom GmbH The written form is required for this without any exception IV Warranty and Assurances a b a b c d e f g The software product is supplied in accordance with the current development status Ridom GmbH draws attention to the fact that is not possible in the current state of technology to create computer software such that it works
31. d until the login password is entered The program can also be locked manually by selecting Lock Program in the Options menu External Applications When using BURP Clustering EpiMRSA can call the external applications MEGA and SplitsTree if they are installed on the computer The paths for these application is normally found automatically but they can be changed here Advanced Memory Usage Define the maximum memory RAM that may be used for EpiMRSA can be configured here For large databases it is recommended to increase this value depending on the available memory on your computer Default Field Values Define default values for newly created isolates Early Warning System Define the settings for the early warning system Noskomial Imported Cases Define the expected distance between admission and isolaion date for nosocomial imported cases Expert Mode Can be enabled to show the features of the tool menu e g BURP cluster algorithms BURP Disable auomatic initialising of BURP functions if Expert Mode is enabled Changing Password To change the database password select Change Password in the Option menu Note that this process may take some time because in the case of many stored reports all the PDF files must be encrypted with the new password 40 13 BURP Clustering 13 BURP Clustering These features are only available if the Expert Mode is selected in configuration Introduction This chapter de
32. e fields To define a new filter for an input data style Click the button to create a new import filter Choose a descriptive name for this import filter 2 3 Set the correct delimiter so that all columns appear in the preview 4 D Mark the Header row checkbox if the files contain a column name header Map each column to be imported to a database field To do this click on the column header using the right mouse key and choose the field from the pop up menu The red column number will be replaced by the field name If all columns to be imported are mapped to a database field click on the Test button to check if the actual data can be imported without problems with the previously defined filter This test will check that each database field is mapped to one column only The only exception is the Strain Internal Comment field This field can be used to collect data from several columns not otherwise mapped to a specific database field that the mandatory database fields Isolate ID Isolation date Care Unit name city and country are mapped to columns and that these columns contain data in all rows e that person data imported include information for the mandatory fields First name Last name and Date of Birth 36 11 Database Backup and Data Import Export e that each Laboratory ID in the file is unique and does not already exist in the database e that the date conforms to the format dd MM yyyy e g 24
33. e first row should be used for selecting column names If this applies and two or more columns have the same name numbers are attached to the names to make them unique Data View Each row contains one isolate and each column contains a specific attribute The attribute names are unique this means that two columns cannot have the same name The table columns can be reordered by dragging them with the left mouse button Table columns can be selected by clicking their column head Multiple columns can be selected by pressing the Ctrl key while clicking the column head To edit the table double click a cell The Tab key can be used to traverse the table s cells while editing The Table menu contains functions for modifying and sorting of the table It is also possible to sort the table by double clicking a column head with the left mouse button The head of the sorted column appears blue It is possible to merge two or more columns with the Merge Columns button A new column is created with a name made out of the names of the merged columns and the new column is filled with the concatenated values of these columns Be careful with cells containing non typable values Check that the merged cells contain the correct data for your usage Procedures Selection View The figure below shows the view that is used for selecting the procedures See next chapter for calculation details The panels allows the input of values for missing or not non typabl
34. e values The default for missing is an empty text the default for non typable values is NT Change this if your dataset uses other values It is possible to select multiple lines in the lists by using the Ctrl key while clicking with the mouse button Typing system concordance and reproducibility can only be calculated for 2 attributes at once 48 14 Epidemiological Statistics FXEpiGompare File Edit Table Help o Back 2 Procedures Hint Use ctrl key to select multiple elements String For non typable NT String For missing data empty cells amp C Show Summary for C Show Typability for Strain Strain PFGE PFGE coa lin I coa lin I coa lin II coa lin II coa type coa type spa lin Kreisw spa lin Kreisw spa type Kreisw spa type Kreisw MLEE lin MLEE lin MLEE type MLEE type C Show Discriminatory Index for Strain PFGE 1 coa lin I C Show Reproducibility for coa lin II coa type Strain E Strain and spa lin Kreisw spa type Kreisw MLEE lin MLEE type 0 81 Koreen microarray groups 0 5 Koreen microarray lineages 0 31 Koreen microarray lineages 0 81 Muenster microarray Show Typing System Concordance for Strain Eland Strain Procedures View The upper panel 1 contains the text for non typable and missing isolates Selecting attributes in 2 displays a summary statistic for this attribute Select 3
35. earch without any criteria values will display all person entries existing in the database e The button disables enables the write protection and is therefore used to make the current person data editable Editing the person data will have an effect on the person data of all strain entries referencing that person e The button is used to create a new person entry and to assign it to the strain entry This will not delete the person entry referenced by the strain previously Person entries are automatically deleted when no longer referenced by a strain entry Management Tab This tab can be used to describe the isolation management for this isolate and according information like contact persons of the patient Report Tab This tab is used to customize the external report for this entry Select the check box Do not report if it is planned not to generate a report 18 4 Entering Entry Data By default the receiver address for an external report is the Care Unit that was assigned to this strain Alternatively a different receiver address can be entered here The text entered into the comment field of the report will be shown in every external report created for this strain By clicking in this field with the right mouse key it is possible to insert a time stamp Ctrl T or define Ctrl M and use text macros Ctrl 1 Ctrl 9 Comments Tab This tab can be used to enter free text comments The comment for internal documentation wi
36. ears and after initialization is complete the screen shows a login form you are asked to enter the database password By default EpiMRSA uses an internal database If you want to use an external database server the database configuration can be changed with the manage button Using the EpIMRSA Main Window After entering the correct password and clicking the Login button the main window will appear showing from top to bottom the following components e Menu bar f Datei Datenbank Optionen Fenster Hilfe e Tool bar E SOng ca e EpiMRSA desktop e Status bar Permanent windows such as those for the Strain Browser are opened inside this main window on the EpiMRSA desktop Keyboard Shortcuts Frequent occurring actions can be conveniently invoked by keyboard shortcuts e g Ctrl N opens a new entry form A shortcut is always composed of the key Ctrl and another key To pop up right mouse button menus Entering the Strain Data Click on the New Strain button to create a new entry in the database The Entry Data Editor appears containing 7 different tabs for grouping the various classes of information Be sure to fill in the mandatory fields Isolate ID Isolation date Care unit and Origin and click the Save button A new strain entry together with the sequences will be created and saved in your database 13 EpiMRSA User Guide Herkunft des Isolates Isolat Typisierung Empfindlichkeit Fall bezogene Daten M
37. efore after importing a database backup you need to enter the password that was used when the backup file was created Checking the Integrity of the Database Select Check Database Integrity in the Database menu to test the database This test checks for empty datasets unreferenced foreign keys and illegal repeat sequences This feature should normally return a no problems found message Exporting Data EpiMRSA can export strain entries into comma separated values CSV files This commonly used file format can be imported by most spreadsheet applications There are two ways to invoke the CSV export e Select Export Database Content in the File menu to export all entries the main tool bar button has the same function or e click the button in the Strain Browser tool bar or Linie List result to export the entries that are found in the currently selected search result tab When starting the export procedure a file dialog with a Filter pane is opened in which an export filters must be chosen or newly created The export filter defines e the data fields that will be exported sequence data cannot be exported e the delimiter for the fields normally use or e if a header line with the field names should also be exported If the export procedure is called in the Strain Browser or the Line List result then the currently shown table columns are use as the default export filter To create a new export filter click the
38. f the software MEGA 3 x or SplitsTree 4 x are installed on your computer you can use the buttons in this dialog to the start these programs with the selected matrix as input data Export Distance Matrix Mega Format Create distance matrix For clustered spa Evpes Use data From all spa CCs and singletons m Distance The database s maximum pairwise cost is 31 The maximum pairwise cost of your data is 28 t075 and ED 323 The latter should correspond to a similarity of 0 097 Scale 1 identical and O total independent Taxa Labels Include spa type in taxa label Include spa Cc in taxa label Use only one isolate Far each spa type External Programs Open matrix with Use the button Epidemiological Statistics to perform some statistics on th clustered data see chapter 8 for details 43 EpiMRSA User Guide Convert Nomenclature Use the Convert Nomenclature function to convert a repeat succession from Ridom to Kreiswirth nomenclature and vice versa Repeat Motif Search Use the Repeat Motif Search menu entry to find substrings in the repeat successions of known Spa types The search supports both Ridom and Kreiswirth nomenclatures Additionally the search term may contain standard regular expressions For a more detailed description of using regular expressions see appendix F Spa type and Repeat Alignments Use Tools menu functions Spa type Alignment Repeat Alignment and Related Sp
39. g laboratories hygiene specialists etc and will be coordinated by the two headquarters M nster and Enschede in order to organize the containment of MRSA more effectively The basis of all efforts for the fight against MRSA comprises 1 Rational antibiotic therapy in order to reduce the selective pressure 2 Prevention Real implementation of the hygiene measures according to guidelines Isolation of potential MRSA carriers 3 Surveillance Early laboratory diagnostic identification of carriers in order to avoid nosocomial transmission as soon as possible Molecular classification of the MRSA isolates in order to recognize transmission chains and to gain an overview of the dynamics of the spread and persistence in the patient 4 Therapy and decontamination of the infected and or colonized persons during and after hospitalization 5 Education of the population as well as further training of personnel in the health care service Cited from http www mrsa net eu The Ridom EpiMRSA software is an integral part of the strategy for prevention surveillance and decontamination of MRSA EpiMRSA User Guide Software Features Database e The personal data encrypted and relevant epidemiological information can be stored locally in the database system incorporated in the EpIMRSA software e Information from the database can easily be exported in comma separated spreadsheet format The same format can also be imported e The integ
40. gross negligence Equally claims which are based on mandatory legal regulations for product liability remain undisturbed Ridom GmbH is not responsible for and makes no warranty for the products running without interruption or without error The liability of Ridom GmbH for damage and loss of any kind whatsoever and regardless of the legal basis on which the claim or grievance is based is limited to the extent permissible under the law to the amount which the licensee actually paid for the software product that caused the damage or loss 58 h E License The obligation to warranty lapses completely if the licensee alters the software without authorisation from the licensor VI Place of Judgment and Applicable Law a b d Place of fulfillment for all obligations arising from the contract relationship is for both contract partners M nster the base of Ridom GmbH This applies even if the residence of the customer is unknown or is outside Germany Exclusive place of judgment for all disputes arising from this contract is also M nster if the licensee is a merchant a publicly incorporated company or a special fund under public law or is without a place of judgment in Germany insofar as no other place of judgment is compulsorily prescribed by law For the following claims of Ridom GmbH on the basis of this license contract regardless of what kind the law of the Federal Republic of Germany applies exclusively wit
41. h exclusion of the provisions for uniform UN sales law for the sale of chattels Insofar as not otherwise agreed German law is also applicable to contract relationships with foreign customers VII Final Provisions a b c d Should any provision of this EULC be or become ineffective or contestable for any reason its content is not otherwise disturbed thereby Rather it is to be performed in accordance with the intent Instead of the ineffective or contestable provision an appropriate regulation is to apply which as far as legally permissible comes as close as possible to that which the parties who concluded the contract intended or would have intended in accordance with the sense and purpose of this contract if they had considered the point when concluding this contract The same applies in the event of a lacuna in this contract This also applies even if the ineffectiveness of a provision rests in any way on a measure of the performance and the time period or date prescribed in the contract A legally permissible measure of the performance or time date or period which comes as close as possible to that which was intended shall then be deemed to be agreed This EULC replaces all written or oral declarations of intent of those concluding the contract which were given in connection with the contract negotiations even insofar as these declarations may differ from the contents of the present contract Equally any previous EULC is
42. he bottom of each column 19 5 Working with the Strain Browser 5 Working with the Strain Browser The Strain Browser Window Clicking the icon in the main tool bar opens the Strain Database Browser Since this is an external dialog window only one window can be opened at any one time This window contains a tool bar a tabbed pane and a status bar Each tab contains a table in which each row in the table represents one strain entry in the database The rows can be sorted in ascending or descending order by clicking on the column headers with the left mouse button Click on the header with the right mouse button to hide the column or to add another field to the table The first column is always the Isolate ID The adjacent columns show other database fields definable by the user If the Isolate ID columns is highlighted red the strain entry does not contain all data that is necessary for an MRSA NIS report Move the mouse over the red marked field to show a tooltip with further details 7 Strain Database Browser g EER BS DR amp BHESR x Icx E Recent Strains Er all Strains Mar Isolate ID Spa tvpe ID Strain Isl Strain Origin Strain Spe UU spa Id E1375 Jun zl zb person a E nor spa id M32 Dun26 2008 person Trachealsekret Ciric 18 E tos2 bun26 2006 person abstichFu5 Ciric 2 E oor spaid boos n2 2006 person hose dinca E c C t032 Jun 27 2006 nic 23 E Q7 spa i
43. his tab shows a table in which the susceptibility to various substances can be defined If the result for methicillin is set to resistant the Penicillin row is also set to resistant automatically New substances can be added to the list and will appear in all other strain entries The user defined substances can be renamed Note User defined substances cannot be deleted but are removed automatically if not used in an entry Person Tab The Person tab is only available if the origin of the strain is set to person The upper part of the form shows input fields for person related data and person data can be entered in the lower part The values in these fields are stored encrypted in the database as indicated by the padlock symbol and these fields are NEVER synchronized When entering a newly created strain entry or a strain entry for which person data has not yet been entered the Ef button is selected by default The person data can be directly entered into the fields and a new person entity will be created for this strain When editing a strain entry for which person data has already been entered the person data fields are shown write protected The state of the person data fields can be changed by using the three buttons below e The 4 button is used to assign to the strain a person already entered in the database A search dialog will open in which the search criteria birthday last name and first name can be entered A s
44. in Data Editor Clicking the New Strain button amp of the main tool bar opens the Strain Data Editor Since this is an external dialog window there can be only one entry open at any one time The window shows all the data of an entry organized in 7 different tabs e Strain Source strain specimen data e Strain Type typing data e Susceptibility susceptibility data e Case person and person related information e Management isolation management and patient contacts e Report entry report and optional report receiver information e Comments internal and public comment information Database entry shortcuts Ctrl C and Ctrl V copies and pastes field content The right arrow functions as a quick search for the field content and with the down arrow you can move in the list of possible field entries Strain Source Tab Defines the strain and specimen data Mandatory fields are Laboratory ID Isolation date or alternatively Receipt date Care unit Clinic and Origin These mandatory input fields are highlighted until they are filled If a new strain entry is created from sequence files the laboratory ID and the isolation date are filled with default values The default for the laboratory ID is taken from the sequence name and the isolation date default is the last modified date of the sequence file Using the User Fields The last two rows in the Strain Source form are User Fields They have no predefined meaning and can therefore be use
45. ions Those include surveillance of infectious diseases outbreak control and others Often two ore more different typing methods are available There are several criteria for evaluating the power of typing methods and for comparing different methods The underlying mathematical formulas are often quite simple but the handling of the data can get demanding for large data sets The Epidemiological Statics tool can calculate various criteria for data of different typing techniques It combines easy calculation with ease of data handling F EpiGompure File Edit Table Help e 1 sa 1 Da Procedures 3 Results coa lin I spa lin Kreisw spa type K Commands ne CO PO epika Hoo OS OD BB MANUS New Table Open CSV File Export Data to CSV File Print Table 2 Copy Complete Table Replace Table with Clipboard Content o a oO a oO e o 3 2 Insert Column Rename Column e e T or o D o t 1 Insert Row Tr Sl Sort Table a OPW KP OP OPO OPW OPO OO WO OO OD aD OO a ele 3L oO o Data View The buttons for switching views are below the menu bar 1 The command pane 2 offers the currently available commands The currently edited cell is indicated 3 A blue table head as shown in 4 marks the cur
46. ll only appear on internal reports It will not be shown on external reports and will not be transferred during synchronization The text entered into the Report Comment field will be shown in every external report created for this strain By clicking in this field with the right mouse key a time stamp Ctrl T can be inserted or defined Ctrl M and use text macros Ctrl 1 Ctrl 9 The fields Public Comment and PubMed ID may be used for descriptions and literature references that should be accessible to all via the SpaServer Here also it is possible to use macros by clicking in this field Ctrl M and Ctrl 1 Ctrl 9 with the right mouse key Note The content of the Public Comment and PubMed ID fields will be transferred during synchronization and will be published on the SpaServer website Managing Care Units Care Units Clinics and Wards can be created and edited in the Strain Source tab of the Strain Entry Editor However there is a specific dialog window providing a convenient way to create edit and delete these units Selecting Manage Care Units in the Database menu opens a dialog window with three columns the left of which shows all the Care units in the database Selecting a Care unit in the list shows all Clinics in this Care unit in middle column and or in the right column all Wards associated with it In the same way selecting a Clinic shows all Wards in the clinic The editor for the currently selected units is located at t
47. log are not checked at all Each ward can have one or more functional relations to other clinics of the same hospital The functional relations can be defined when editing the data of the ward Detection Possible Outbreak Strains Level Ward Possible outbreak strains must be in the strain s ward or in any clinic that is linked with the strain s ward by a functional relation or in any ward that is linked with the strain s clinic by a functional relation Clinic Possible outbreak strains must be in the strain s clinic or in any clinic that is linked with a ward of the strain s clinic by a functional relation or in any clinic that has a ward that is linked with the strain s clinic by a functional relation Care unit Possible outbreak strains must be in the strain s care unit hospital Finally it can be defined if all strains of a possible outbreak must have the same spa type If the strains must have the same spa type then an alternative trigger setting can be defined for local high frequency spa types The defined minimum frequency is counted in the specified time interval and care unit as the number of MRSA strains with the specific spa type in relation to all MRSA strains Early Warning Alert When a Strain entry is saved and the Early Warning settings are fulfilled a new alert is triggered The oldest strain of the possible outbreak strains is used as index strain and the following strains are defined as
48. ns of all spa types in the database Database Repeats Shows the nucleotide sequences of all repeats in the database BURP Alignments Shows the missing spa type alignments which have to be downloaded global spa types or calculated local spa types Note The four documents can be saved as HTML or converted to PDF Viewing the SpaServer Statistics If the network connection was configured for use of the http protocol it is possible to retrieve the current content summary of the SpaServer To display the summary of all spa types and repeats in an internal window select View SpaServer Statistics in the Database menu This page can be saved locally as HTML If synchronization by email was chosen it is necessary to direct the WWW browser to the URL http www ridom de spaserver in order to view the most recent SpaServer Statistics 33 11 Database Backup and Data Import Export 11 Database Backup and Data Import Export Backing Up the Database Select a Make Database Backup in the File menu to create a copy of the local EpiMRSA database for safekeeping The backup is stored as a zip archive file Importing a Database Backup Select Import Backup File in the File menu to import a saved backup Importing a backup will completely overwrite the current databases Therefore you are asked to create a backup of the current data before importing a backup Note Changing the database password has no effect on older backups Ther
49. on intellectual property This EULC does not grant the licensee the right to use such content If this software product includes documentation which is only provided in electronic form the licensee may print a copy of this electronic documentation He is not entitled to reproduce the printed material accompanying the software product III Scope of License a The licensee is entitled to install the software product the demonstration version or an earlier version on several computers workstations portable PCs or another digital electronic device b The licensee is only allowed to use to access and to execute or in another way to interact with the software with the hardware key Dongle C If this software product is a license package the licensee is entitled to use additional copies of the computer software part of the software product up to the number of copies which are contractually established as licensed COpies d The software product is licensed as a unitary product The licensee is not entitled to separate its components for use on more than one computer e The licensee is not entitled to reverse develop to decompile or to disassemble the software product unless and then only insofar as the applicable law regardless of this limitation expressly permits this f The licensee is not entitled to resell the software product or in any other way to transfer the software product for a counter value The licensee is not entitle
50. one day within the year i e start date within year or end date within year or start date before year and end date after year Start date for imported Admission date for Nosocomial Isolation data alternatively Receipt date End date Discharge date Last day a case is not counted beside 31 of December Inpatient MRSA isolation case days Includes all inpatient MRSA cases that have at least one day within the year i e start date within year or end date within year or start date before and end date after year Start date Isolation start date End date Isolation end date alternatively Discharge date Last day a case is not counted Number of strains with MRSA MSSA MRSA and Person type inpatient and if imported Admission date within year else if nosocomial Isolation date alternatively Receipt date within year Special If a case starts at 31 of December it is assigned to the following year beside 31 of December Inpatient case days manual input Inpatient cases manual input MRSA Rates Once per NIS category and once for the care unit as a whole NIS categories intensive medicine internal medicine surgery other operative discipline other conservative discipline not classified Clinics Wards are listed separately Field Name Field Value Total no of MRSA cases per 1000 case days 1000 inpatient MRSA cases inpatient case days Total no of no
51. pes it is recommended to use here a value of at least 4 default value is 5 e Spa types are clustered if cost is less or equal x Defines the dimension of clusters If a greater value is chosen the clusters are going to be bigger and a less number of clusters will be formed default value is 6 Use the button Show Graph to calculate the BURP graph s for the selected cluster s BURP graphs are an eBURST like Feil et al 2004 graphical representation of the relation between spa types The founder of each cluster is colored blue subfounders are colored yellow If the visualize strain count button is selected the size of the spa type node represents the number of clustered strains which belong to this spa type The actual costs between different spa types can be visualized by using the other two buttons The graph can be moved by clicking and dragging with the mouse and it can be zoomed using the mouse wheel The graph can be saved in various formats The gif format is the recommended bitmap format If you plan to further edit the graph the vector graphic format svg is recommended e g use the freeware editor Inkscape for further processing 42 CA spa CC 007 of strains 168 3555 of all strains of spa oles E 9 2 tua 13 BURP Clustering Use the button Export Cost Distance Matrix to translate and export the distances of the strains in the selected cluster s for the use in phylogeny software I
52. problems detected the cells in the table can be edited manually If the test runs successfully the actual import of the data is achieved with a click on the Import button nk 37 12 Configuring EpIMRSA 12 Configuring EDIMRSA EpiMRSA Preferences Select Preferences in the Option menu to display the configuration dialog In the left pane of the dialog are shown the main groupings Appearance SpaServer Download Reports Security External Applications and Advanced If one of these main groupings is opened browsing down to an entry will show the appropriate form of this configuration property in the right panel Configuring Appearance The Colors Fonts and the Look amp Feel of the application can be defined here The Live window dragging should be disabled on slow systems to prevent redrawing when moving the internal windows The Localization options can be set to define the date format for displays and reports and the printer page format Configuring SpaServer Download This grouping is used to define the connection parameters and the automatic search for spa types and software updates Further details can be found in chapter 9 Configuring Reports Entry Report e Enable disable the option if a report created is always to be printed e Sets a default PDF encryption password for exporting a report e Sets the report style internal contains most fields of an entry this style is normally used for internal comm
53. r are stored encrypted in the database and can only be searched as equal or not equal 21 EpiMRSA User Guide Clicking the Find button starts a search and a new tab appears in the Strain Browser showing the Strain entries that match the given search criteria Clicking on the tab header using the right mouse key modifies the search criteria or renames the tab Note If the number of strains found in a search is too large for browsing the table shows only the most recent 2000 entries The total number of entries found in the search is shown in parenthesis in the status bar However exporting from this table by clicking the in button exports all strain entries In contrast the summary report created by clicking the button that is created from such a table contains only the strains that were also shown in the table Predefined Searches The tool bar offers shortcuts for often used searches Clicking on the pull down arrow of the M button shows the list of predefined search criteria 2 Recent Strains searching all strains which were modified in the last 30 days To change the length of this time period right click on the tab label of a search result table to open its context menu and use the function Modify Search 4 Strains for which no reports were created yet Strains which are currently marked by a check in the first column AI strains in the database Line List Use the main menu item Ed Line List to start a line
54. rently sorted column Switching Views The panel below the menu bar is used for switching different views There are three views Data which contains a table for the used data Procedures which allows selection of calculation procedures and Results where the calculation results are displayed Click on the text in the panel or use the Back and Forward buttons to switch the views 47 EpiMRSA User Guide Import Data from a CSV File Use the button in the command pane to open a CSV file Several import options can be set for CSV files whether the CSV file contains a header in the first line or not 66 99 the delimiter can be set In most cases this will be or Take a look at the preview table to find out if the delimiter is chosen correctly and each column in the table needs an unique name Columns that have a name assigned are displayed in white If a column has no name assigned it is displayed in a light red colour Click on a column and select a name in the context menu You can specify a name by selecting the pop up menu entry Enter Column Name Import Data from Clipboard It is also possible to import a table from the clipboard This feature supports Microsoft Excel clipboard format This means that you can select a table or parts of it in Excel copy it to the clipboard and paste it into the program Press the button H to replace the table with the current clipboard content You will be asked if th
55. rity of the database is checked regularly and the contents can be backed up to prevent data leakage Report Generator e Reports can be created with various configurations using EpiMRSA e These reports are stored internally as read only tamper proof and encrypted PDF files e MRSA NIS Reports and OGD Reports can be created for use in MRSA surveillance Spa type up to date service e EpiMRSA automatically searches for new spa types on the SpaServer and retrieves them Protection of Data Privacy All personal data are saved encrypted in the database using a password based cipher with a 128bit key How to Contact Us You can contact with requests for support e by email support ridom de e by the built in support dialog of EpiMRSA in the Help menu 2 Installing EpIMRSA 2 Installing EDIMRSA System Requirements Hardware Requirements e 1GBRAM e Hard disk with at least 200 MB available space depending on database size e One free USB port for the hardware key Dongle Hardware Key Dongle EpiMRSA may be installed on different computers without registration or activation codes However the Ridom hardware key Dongle that was delivered together with the software must be plugged to the computer when working with the EpiMRSA The installation program includes a specific device driver made available by the manufacturer of the key device WIBU Systems If the computer where EpiMRSA is installed has no accessible U
56. rofit loss of business information or from any other financial loss which arises as a result of the use of this product or of the inability to use this product is expressly excluded Insofar as not expressly stipulated in this EULC Ridom GmbH makes no warranties either expressly or implicitly including implicit warranties with respect to merchantability or suitability for a specific purpose All implicit warranties which may possibly be imposed by law are restricted to the greatest extent permitted by law to the provisions contained in this EULC For damage or loss which involve death or physical injury Ridom GmbH is in no case liable for aggravated compensation for damages or penalty compensation for damages for any specific indirect coincidental damage or loss or consequential loss or damage arising therefrom this applies particularly but not exclusively for loss of use loss of data loss of profit and for loss of savings and business This applies regardless of the basis of the claim or grievance such as for example infringement of the warranty of the provisions of the contract of the contract from law and arising from an offence including strict liability and negligence or other legal grounds and even if notification is given of the possibility of such damages or if such a possibility was reasonably foreseeable This exclusion according to origin does not apply for damage which is caused by Ridom GmbH through malicious intent or
57. s and in the first tab all reports for the selected strain are listed The windows tool bar provides functions for viewing printing exporting and deleting a selected report A PDF report that is exported can be optionally encrypted by a default or custom password Clicking the 2 button marks the report selected as forwarded sent this action only sets a marking flag for internal use however the entry can be no longer be deleted 25 EpiMRSA User Guide MRSA NIS Report The MRSA NIS Nosocomial Infection Surveillance report can be used to calculate and report epidemiological data per care unit and year The fields and the layout of the MRSA NIS report are based on the German surveillance protocol MRSA KISS Krankenhaus Infektions Surveillance System des Nationalen Referenzzentrums fiir Surveillance von nosokomialen Infektionen http www nrz hygiene de surveillance mrsa htm The intra hospital transfers that can be defined in the tab Management of the Strain data editor are not used in current implementation of the MRSA NIS report Each case is always counted for its first clinic ward as defined in the tab Strain Source Care Unit Data Once per Care Unit Field Name Field Value Year manual input Number of S aureus Total manual input roe Infection manual input Blood culture manual input Case adjusted manual input yes no Number of nose Number manual input wale Per 100 ca
58. scribes the basic principles of the BURP Based Upon Repeat Patterns algorithm for spa type aligning and clustering and its usage within the software For a detailed description of the ESDI spa type alignment see Sammeth M Weniger T Harmsen D and Stoye J Alignment of tandem repeats with excision duplication substitution and indels edsi in R Casadio and G Myers Eds WABI 2005 LNBI 3692 pp 276 290 When starting EpiMRSA the spa type alignments must be loaded before the BURP functions can be used This initialization process is shown by a small dialog window in the lower right corner of the main window and normally takes a few seconds The spa type alignments for global spa types are calculated on the SpaServer after a new spa type was submitted They can be downloaded automatically using the normal synchronization process Spa type alignments for local spa types must be calculated locally This calculation process starts automatically when a new local spa type is saved to the database The calculation of local spa types can be enabled in the preferences dialog and is disabled by default BURP Clustering Press the button in the toolbar of the main window or select BURP Clustering in the Tools menu to open the BURP dialog window for clustering strains There are two ways to choose the strain data a BURP Clustering Data Clustering Parameters Exclude spa types that are shorter than 5 repeats Spa types are
59. secondary strains An alert is only triggered if no other alert already exists that has the same index strain the same secondary strains and the same trigger settings Each triggered alert is automatically stored in the database Use the menu item Database Early Warning System to view and control the alerts The icon of the menu item shows if there are new 29 EpiMRSA User Guide alerts to clarify Early Warning Alert Data Timestamp The date and time when the alert was triggered State The state can be to clarify false alert or true alert Each new alert has the state to clarify it must be manually set to true or false If the EWS contains alerts with the state to clarify the EWS menu item shows the red flashing light Index strain The oldest strain that was found in the consecutive possible outbreak strains Secondary strains The strains which follow the index strain in the possible outbreak strains No of strains The number of index and secondary strains Comment A comment for the alert Outbreaks If an Early Warning Alert seems to be true the user can manually define an outbreak Outbreaks are never created automatically they can only be defined by the user Outbreak Data Timestamp The date and time when the outbreak was created Primary strain The primary strain of the outbreak Must be selected by the user Index str
60. ses 100 nose swabs inpatient cases Patient adjusted manual input yes no Established screening regime manual input yes no Number of beds manual input Number of ICU beds manual input MRSA rate of all S aureus Isolates manual input MRSA Cases Once per NIS category and once for the care unit as a whole NIS categories intensive medicine internal medicine surgery other operative discipline other conservative discipline not classified Clinics Wards are listed separately Field Name Field Value Inpatient MRSA cases Number of strains with MRSA MSSA MRSA and Person type inpatient and if imported Admission date within year else if nosocomial Isolation date alternatively Receipt date within year Special If a case starts at 31 of December it is assigned to the following year Imported Colonization like all cases but only if Case type imported and Associated with MRSA cases colonization Infection like all cases but only if Case type imported and Associated with infection 26 Creating Reports Nosocomial Colonization MRSA cases like all cases but only if Case type nosocomial and Associated with colonization Infection like all cases but only if Case type nosocomial and Associated with infection Inpatient MRSA case days Includes all inpatient MRSA cases that have at least
61. socomial MRSA cases per 1000 case days 1000 nosocomial cases inpatient case days Total no of imported MRSA cases per 100 cases 100 imported cases inpatient cases Total no of MRSA case days per 100 case days 100 inpatient MRSA case days inpatient case days Total no of nosocomial MRSA cases per 1000 MRSA 1000 nosocomial cases inpatient MRSA case days case days 27 EpiMRSA User Guide MRSA Patients Once per NIS category and once for the care unit as a whole NIS categories intensive medicine internal medicine surgery other operative discipline other conservative discipline not classified Clinics Wards are listed separately Field Name Field Value Inpatient MRSA cases Number of strains with MRSA MSSA MRSA and Person type inpatient and if imported Admission date within year else if nosocomial Isolation date alternatively Receipt date within year Special If a case starts at 31 of December it is assigned to the following year MRSA Patients Number of patients of inpatient MRSA cases Inpatient MRSA cases without person data are counted as individual patient MRSA readmissions Number of readmitted MRSA cases of MRSA patients Additional blocked bed days Sum of additional blocked beds of all inpatient MRSA cases Decontamination status Sum of each decontamination status for inpatient MRSA not initiated cdd not done aborted
62. start of the program if configured Using the menu Help Software Update Online Update an update can be searched and download from the Ridom web server The update will be installed after exiting the program Note If you are accessing the Internet through a proxy server you first need to set the proxy parameters in the EpiMRSA configuration dialog If a direct Internet connection is not possible or wished the update can be downloaded manually from http www ridom de EpiMRSA support and installed through the menu Help Software Update Import Update File EpiMRSA Help User Guide this document invoke context sensitive online help by pushing the F1 key Quick Reference Card overview of menu toolbar functions and key shortcuts Help Info dialog for version and system information Bug Report dialog send feedback messages such as bug reports and feature requests 10 2 Installing EDIMRSA Uninstalling EDIMRSA To remove EpiMRSA from your computer select the Uninstall EpiMRSA icon from the Start Menu When uninstalling the software only the application directory will be removed from your system The profile and the database directory will not be deleted automatically If you want to reinstall EpiMRSA be sure to reboot your computer first This is strongly recommended to prevent problems with the hardware key driver 11 3 Getting Started 3 Getting Started Running EpiMRSA When running EpiMRSA a splash screen app
63. the CD packaging and or by using the hardware key Dongle to make a downloaded demonstration version useable you declare your agreement to be bound by this EULC C If you do not agree to these conditions you are not entitled to use the software package and must return this unused i e with undamaged seal on the CD container and without delay at the latest within 10 days from receipt in order to receive a complete refund of usage charges paid for the software d The person who concludes this EULC assures and makes warranty that he is entitled to declare a legally binding contract on behalf of his employer as the licensee e The software product is licensed not sold II Copyright a The software product distributed by Ridom GmbH is protected both by copyright laws and international copyright treaties and also by other laws and agreements concerning intellectual property b Ownership and copyright of the software product including but not restricted to images photographs animations video audio text and applets which are included in the software product the accompanying printed material and each copy of the software product are the property of Ridom GmbH All rights and intellectual property rights in and to content which can be accessed with the aid of this software product are the property of the respective owners of the content and may be protected by applicable intellectual property rights laws and other laws and agreements
64. unication within an institution external creates a report that presents the spa typing result in an improved and tidier style suitable for external communication purposes External Entry Report External reports can be configured with the following e The Design template defines the layouts of the report It can be chosen from the available predefined layouts Further customized design templates can be ordered at support ridom de e The Logo image is shown on the header of the report The given image must be a JPG PNG or GIF file e The Report sender address is printed on the right of the page header e The Signature can be used to print name at the bottom of the report for a possible handwritten signature Summary Report Defines the default number of columns that are to be written to a summary report created from the Strain Browser Because of restrictions in the layout more than six columns are not recommended 39 EpiMRSA User Guide PDF Viewer EpiMRSA requires the Adobe Reader software to be installed in order to display and print the PDF report files The path to the executable Adobe Reader software should in most cases be filled in here automatically If this is not the case the user must enter the path here to view and print PDF files Configuring Security Can be used to enable an inactivity lock If the program window stays inactive no mouse or keyboard action for a specified period of time the program is locke
65. unsuccessful provisionally successful successful in progress OGD Report The German version of EpiMRSA can create in addition an OGD ffentlicher Gesundheitsdienst report This surveillance report was drafted in cooperation with Euregio MRSA net http www mrsa net org and is also based on the MRSA KISS protocol Krankenhaus Infektions Surveillance System des Nationalen Referenzzentrums f r Surveillance von nosokomialen Infektionen http www nrz hygiene de surveillance mrsa htm An explicit description of the OGD report is available under the Help menu of the German version of EpiMRSA 28 8 Early Warning System 8 Early Warning System Early Warning System The Early Warning System EWS of EpiMRSA can be used to detect possible MRSA outbreaks in a care unit clinic or ward Each time a newly created or modified strain is saved to the database the EWS checks for potential outbreaks The settings for the EWS can be defined in the EpiMRSA preferences or in the alert overview The EWS searches for strains that fulfill the defined criteria and triggers an alert if the defined minimum count is reached This search is done sequentially finding all strains of a possible outbreak chain with the maximum allowed distance between two consecutive strains The place for these strains is defined by the selected detection level for this hospital Hospitals which are not listed in the settings dia
66. unter Gaston 1988 Struelens 1996 Discriminatory Index Discriminatory index is calculated with the following formula 1 s paten is Hn ex where N is the total number of strains in the sample population s is the total number of types described and n is the number of strains belonging to the jth type A 9596 Confidence Interval CI can be calculated for D with the following formula CI D 24 o D 21 o with Paty m m and mat The Epidemiological Statistics tool uses all isolates that have no missing data and are typable for calculation of discriminatory index and 95 confidence interval Isolates with missing data or isolates that are non typable are ignored in this calculation See Simpson 1949 Hunter Gaston 1988 Grundmann et al 2001 50 14 Epidemiological Statistics Typing System Concordance Use typing system concordance to compare the results of different typing systems For calculation pairs x y x y lIsolates of all isolates are created All pairs are arranged in a 2x2 table according to their type in both typing systems System 1 System 1 System 2 A B of pairs x y for which of pairs x y for which x and y have the same x and y have the same type in System 1 andin type in System 2 anda System 2 different type in System 1 System 2 C D of pairs x y for which of pairs x y for which x and y have the same x and y have a different type

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