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Enhanced tuberculosis surveillance strain typing module

1. No of ae Isolates London 13 North East 1 Yorkshire and The Humber Total 18 CaseldName D 0 8 SexAgePostcodeHospital HPU Region North East and Central London 196933 HPU London 187527 OYAL LONDON HOSPITAL ag Se T azt and Ce i ond 189574 UEEN S HOSPITAL ROMFORD oe Bo ii 132414 UPAL VEIRA BERAR Morth East HPU North East NEWCASTLE Specimen date 14 09 2012 1082010 12 07 2010 29 06 2010 Case manager Jacqui Carless Jacqui Carless Jacqui Carless Judith Campbell Note cases imported to ETS from the London TB Register LTBR always have Jacqui Carless listed as case manager within ETS and STM Jacqui Carless is the Regional TB Co ordinator for London LTBR case managers are not ETS users so cannot be listed as case managers within the system If you need to contact a London case manager regarding a patient please email LTBR Support phe gov uk or phone 0207 811 7214 the LTBR team with the patient s ETS ID to obtain the contact details of the relevant case manager Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 27 Appendix 1 Other uses of STM The STM can be used to assist in TB data provision processes In particular for Multi Displicinary Teams cohort reviews and sending information to clinics 1 Open the required cluster report as described in the main body of this document 2 Download the report and open in excel 3 In ex
2. Logged in as ehamblion L09 Out Create Template Generate Cluster Reports TRAINING North West Region Oct 2 2013 11 08AM 3 TRAINING Northern Ireland Oct 2 2013 11 09AM View Cluster Reports aa blah arr New Cluster Reports Enter Cluster Details Enter Lab Field Mapping details of any contact tracing undertaken as a result of the investigation Public Health England nt Reports Ad ation Strain typing Help Enter Cluster Details Report Name e Download pap SitePrec recompile 2 0 7 e ServicePrecompile 2 0 7 er data Collection form TRAINING South 2 2013 11 09AM Filter by Cluster Number Cluster Number v A1001 Notes Selectac uster number or other filter options above to load data into the fields below for the selected VNTR cluster Cluster details Cluster Status Awaiting Preliminary Review z Patients in this cluster are also under investigation nationally Save Cluster Details Cluster status change log No status change log found Notes on cluster No cluster notes found Notes Add notes 29 Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 Appendix 2 Searching for a strain type using ETS It is possible to search by strain type using the main ETS search although this is only recommended for clinic users who do not have access to the STM search 86 Public Health England Home page Case management Reports
3. button should be clicked to allow newly generated reports to appear View Cluster Reports Date From DateTo E E Cluster Report Name Report Delivered Regenerated At Report F NMRL National 141013 Oct 14 2013 10 02AM No Mew F NMRL Sussex Sep 24 2013 12 14PM No View F NMRL South West Sep 24 2013 11 52AM No View T NMRL East midlands Sep 24 2013 11 40AM No View Regenerate Report The dates to and from can be used to select cluster reports generated within a specific time period The date boxes should be left blank to see all cluster reports Cluster reports are shown in chronological order with the most recently re generated report at the top The cluster report name is the template name followed by the date and time of the first generation Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 3 1 Cluster report contents To view a report click View in the Report column NMRL Sussex HPU Sep 24 2013 12 14PM Show clusters with new data ClusterNo Caseld Name D O B Postcode SpecimenDate VNTR Profile Resistant To Lab details A1001 155369 a 28 02 2013 614662432622333263313 61 View A1004 131693 22 09 2010 614642432622334263313461 Mew A1004 136870 2 08 07 2011 614642432622334263313461 View A1004 136870 15 07 2011 614 42432622334263313461 View A1004 137394 08 08 2011 614642432622334263313461 PYR View A1018 133047 02 12 2010 46464
4. 6 These data can then be matched with a list of ETS IDs that are part of a cohort review to determine which of the cases that are part of the cohort review are in a cluster for example in Stata Access or by using the vlookup function in Excel 7 You can also use the spreadsheet to analyse the cluster data The excel download contains all the data for the entire report not just the cluster You can see all the data for the cases 28 Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 including the data collected on cluster questionnaires There is also a download button for epidemiological links that you can click to download that data To look at more detailed information on cluster investigations for reporting at cohort review Once you have determined which clustered cases are part of a cohort review by undertaking the above information on the investigation of the cluster can be interrogated 1 Goto the STM Enter Cluster Details tab 2 Look up the cluster you require by using the filter by Cluster Number function 3 Information is then available on the following factors which could then be reported e cases in the cluster in the Cluster Data section e whether questionnaires have been sent and received e notes on the cluster e it s status e g whether under active investigation or not e details on any epidemiological links found 2 Search
5. Administration Strain typing Hep Home page Enter search criteria below to find a case New case Case ID Local patient ID Forename Surname Search for case Treatment outcome result due Case transfers Date of birth Year of diagnosis Strain type Laboratory isolate matching Fe Please select v 31464243262233426231346 Questionnaires due Case manager Region residence HPU residence Hospital Logged in as jdavidson 39 Please select v Please select v Please select Please select v OAE ee e ee ee _ es dania Search options i Return only cases have access to Return only cases do not have access to Search ETS Using ETS to search by strain type return details of notified cases which have a laboratory record containing the strain type Note Using ETS search by strain typing and viewing the case record will not currently tell you if the case is in a cluster or provide the cluster number If from searching by strain type more than one case is returned then it would be known if this case was in a cluster For a user to find the strain type for a specific case use the ETS search by Case ID or Date of birth for example select the case from the search return and navigate to the Laboratory Results page Once on the Laboratory Results page click on a laboratory record and look at the Strain Type field Ethnicity amp Origin Laboratory Results nical Details Resu
6. Last 5 years Last 10 years ALL Select the Geographical level by choosing National Region or HPU If Region or HPU are selected then it is necessary to use the Specific geographical area dropdown to choose the breakdown required To view all isolates with or without an ETS match in a selected time period choose Specimen date and then the time period from the Date Period drop down list By selecting ALL the date period restriction will not apply and all isolates will appear for the chosen geographical area To view only isolates with an ETS match select Notification date Once all desirable criteria are selected click on the Search button The Summary report will show the total number of isolates for all areas and the list of Possible match es found contains all the isolates with ETS IDs and their location In addition isolates which you have permissions to view will have names and date of birth displayed along with the ability to click on the ETS ID which navigates to the ETS record Searching at a National level will produce a summary table of the number of cases by Region Searching at a Regional level will produce a summary table of cases by HPU Searching at the HPU level will produce a summary table of cases found by hospital 26 Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 Summary report by regions
7. Public Health England Enhanced Tuberculosis Surveillance Strain Typing Module User Guide TB Section CIDSC November 2013 This user manual was produced by CIDSC TB Section Maeve Lalor TB Cluster Investigator Jennifer Davidson TB Laboratory Surveillance Scientist and Laura Anderson TB Surveillance Senior Scientist Please contact CIDSC if you have queries regarding this manual or if you experience technical problems using the STM With thanks to Esther Hamblion TB Cluster Investigator for comments and producing the user manual Appendix 1 and with thanks to Andy Burkitt TB Cluster Investigator and Natasha Ratna Information Assistant for providing comments on this user manual If you require assistance in cluster investigation please contact one of the cluster investigators maeve lalor phe gov uk 020 8327 7154 esther hamblion phe gov uk 020 7811 7228 jennifer davidson phe gov uk 020 8327 7610 andy burkitt phe gov uk 0844 225 3550 Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 Contents introduction TO Strain typing module ccccccceeseccccesscceceesececeesececeeeeececsuecesseeeceeseesecessuaecessugeceeseneeeetas 3 Heh OCT ONS ET ice reared ced hates fa Seaton ange seaiest E pent cele aaa ane 4 Getting stant e Uenon A oe ee UG eel Bee a eee ei a A ols Svea 4 el EAS Ie Ml ates icca ace on ca cue lecacsecoeceecGaeto iets othe can E N EN 5 2 Genere cluster HE DOI LS n S
8. a case may need to be deleted if the isolate has been confirmed as a contaminant Ifa case has one missing loci they may cluster with more than one cluster but if there is reason to believe that a case should not be part of one of the clusters it is assigned to then the delete function can be used 1 1 Viewing and recording cluster details To view a specific cluster use the Filter by dropdowns and select Cluster number or VNTR Profile Cluster Status can be selected from the Filter by drop down list to see all clusters with a given status Note If you filter by VNTR profile you will miss cases isolates with one missing loci who have been assigned to the cluster It is therefore recommended that you filter by cluster number if looking at a specific cluster Filter by Cluster Number Cluster Number ka Please select Please select Hotes Select a cluster number for other y for the selected VNTR cluster Cluster Data y clusters with new data Download Report Accept Vntr Changes Delete a _ 5 Name gion asi mEn VNTR i oe e Questionnaire A1016 2 18022011 6445646 24a 246 O21 02013 A1016 s 05 10 2011 GH5E2432622333243312451 0210 2013 ATTIS 132375 n 2A102010 464647452622 3321AG3232T 1 h AM 02310 2013 View A1018 139063 m 17 11 2011 454542432622332 1 Ads a2 iT 1 02310 2013 View A1018 139063 p m 21711 2011 454542432522 321AG3232T 1 0210 2013 View A1018
9. cases In addition the STM can be used to search for cases in a cluster by cluster number or strain type The cluster report contains isolates which have been identified as being part of a strain typing cluster based on 24 loci Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeats MIRU VNTR typing see TB Strain Typing and Cluster Investigation Handbook for further details The allocation of isolates to a geographical area is based on the source laboratory of the isolate This means that occasionally the isolate belonging to a patient will not be assigned to the cluster report for the patient s Health Protection Team HPT of residence and manual editing of reports may be required The STM has been designed primarily for use by HPT users who have responsibility for monitoring and investigating TB clusters There is also the function for regional and national ETS users to view cluster reports at the relevant geographical level Clinic level users do not have access to the STM tab itself but can access questionnaires sent to them through ETS by the cluster questionnaire alert on the ETS homepage Laboratory users are able to see cluster reports containing isolates typed at their laboratory while HPT and regional users are able to see isolates for cases within the geography relevant to their access from all reference laboratories Cluster reports created by the laboratories are only seen by the laboratory that created
10. the case notification is found click on the result and navigate to the laboratory results page Laboratory records which have been received and uploaded into ETS received routinely from the reference laboratories and are not yet matched to the notification will appear under the Mycobnet matched results section Review if these laboratory results should be linked to the notification and tick the Accept box in the bottom right hand corner to manually match the isolates The case will now be linked to the laboratory record in the STM report 46 Public Health England Home page Id 192183 Case notification date 17 06 2011 Legacy Migration Id 2011 200381511 Denotify Case Demographics Patient Occupation Ethnicity amp Origin Laboratory Results Clinical Details Results Laboratory Results Risk Factors Delete selected re Treatment Planned Category Specimen Status Specimen date Species Source Delete Report Details Microscopy Sputum Negative 25 05 2011 ETS Treatment Outcome Mycobacterial Culture Sputum induced Positive 25 05 2011 Mycobacterium tuberculosis ETS g Report Summary Microscopy Sputum induced Negative 25 05 2011 ETS F Logged in as jdavidson Leg Out Note s Laboratory result matches are automatic and should be checked and confirmed by the case manager e Download paper data collection form SitePrecompile 2 0 14 Servic ec e 2 3 a aaa Add a new sputum smear result Specimen Type Speci
11. 0240 2013 West Midlands West HPU Oct 2013 12 27PM 0210 2013 West Midlands East HPU Oct 2013 11 20AM 02 10 2013 To open a cluster report click on the report name Opening the report shows the records of all cases isolates that are clustered within the geography of the report under the Cluster Data title Clusters are ordered alphanumerical by cluster number At the top of the report there are several functions available Cluster Data Show all clusters Accept Vntr Changes Delete Cluster Case Case Specimen Resistant Date No id Name D O B Postcode Manager HPU Region Date VNTR To Added Questionnaire C1212 130706 kay South East 23 07 2010 3223525525173322424233384 22 10 2013 View 5 E West Midlands C1212 1353438 va 16 05 2011 322352552517332242423384 22 10 2013 View T E Birmingham and Midlands Solihull a Thames Valley C1212 136296 HPU South East 19 05 2011 322352552517332242423384 22 10 2013 View gt E C1212 C1348 London 06 04 2010 422552442518323541421384 22 10 2013 C1348 London 31 05 2011 422552442518323541421384 22 10 2013 C1348 Show clusters with new data Download Report Accept Vint Changes Delete Click on the Show clusters with new data to display only clusters that have cases with specimen dates in the last three months Click on the Download Report button to create an excel line listing of the report The excel spreadsheet includes the fields shown in the STM report
12. 140674 n JO0XJ2012 454542432622 3271A8323271 50 02310 2013 View Once a cluster has been selected from the dropdown list this will display an information specific to the cluster The page includes several sections which are explained in points 1 10 below page 1 Cluster details which is used to assign a cluster status which will be logged in the Cluster status change log The default cluster status is Awaiting Preliminary Review see TB Strain Typing and Cluster Investigation Handbook for status definitions Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 18 Cluster details Cluster Status Cluster status change log Awaiting Preliminary Review Awaiting Prelimina Review Se Date Username Cluster Status No Action Required I 18 10 2013 etempest Active Investigation Active Investigation Re opened for Active Investigation Watchful Waiting Closed e 2 Notes on cluster can be used to record the following information on a cluster o asummary of the cases in the cluster after risk assessment o any information already known that may be relevant to the investigation e g active investigation not required at present as epidemiological links already well known o HPZone number o Actions taken during the investigation e g Cluster questionnaires sent out screenings undertaken o Any information obtained during the course of the investigation that cannot b
13. 153065 17 09 2012 4646424326223321A83232 1 Mew A1018 155611 eee ___ 11 04 2013 4646424326223321A8323271 View Select Show clusters with new data to see only new clusters with new cases within 3 months from date of regeneration NMRL Sussex HPU Sep 24 2013 12 14PM Show all clusters ClusterNo Caseld Name D O B Postcode Specimen Date VNTR Profile Resistant To Lab details A1001 155369 28 02 2013 614662432622333263313 61 View E B1005 128255 amp 07 04 2010 424352332515333456443382 View B1005 136102 03 06 2011 4 4352332515333456443382 View E B1005 136820 amp 28 06 2011 424352332515333456443382 View i B1005 137443 amp 09 08 2011 424352332515333456443382 View F B1005 141269 amp 16 02 2012 42435233251533345644338 View E B1005 1539383 26 01 2013 424352332515333456443382 View B1005 157220 orig 424352332515333456443382 vew Delete Accept Vntr Changes Download Report Accept Cluster report Save Cluster report Duplicates may be removed from the new data that has been added as previously described Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 4 Search The search page can be used to find isolate information by selecting either Cluster number or Strain type from the search criteria drop down menu O Enter search criteria below Administration Strain typing Create Templ
14. Typing Module User Guide Version 1 22 11 2013 Cluster Data Show clusters with new data Downlosd Report Accept Vntr Changes Delete Cluster Cas tame _ D O B _ Postcode HPU Region SPecimen itp ican Questionnaire No Id Manager Date To Added South West South amama 4c gt Nason C1398 138501 me 19 09 2011 422352531517333542423374 24 09 2013 View L South HPU West ar aS ss C1398 139531 South West South 06 12 2011 42235253151733354242337 24 09 2013 View 30 a South HPU West Sz Summary of cases Id Name Notification SexAge Postcode Birth Ethnicity Year Occupation Symptom TreatmentPrev Drug AlcoholHomeless Prison Sputum Disease Resistant date Country of Onset Start Date DiagnosisUse Use Result to Entry 138501 KENYA Black 1989 14 08 2011 7 10 2011 No No No No No Negative Pulmonary African 139531 SYRIAN Mixed 2006 Unemployed 01 05 20119 12 2011 No lo 10 lo Positive Pulmonary ARAB Other REPUBLIC Close 8 To view ETS details of each case click on the Case ID This accesses the ETS case record To return to the cluster you must go back through the strain typing tab C1006 Citos 140822 c arth a Stephen peilida Moore c1008 C1011 126647 Judith Wells C1011 134941 aces 9 During investigation you may disco South a s 12 01 2012 422342742511334432423254 24 09 2013 S F HPU South saa a 02 04 2012 422342742511334432423254 24 09 2013 View a HPU South West South
15. as well as risk factor and epidemiological information from ETS and the STM cluster questionnaire data 16 Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 http colhpaswdOO5 ETS Site S TM ExportClusterReport aspx lab Microsoft Internet Explorer File Download Do you want to open or save this file Name LabClusterReport xls Type Microsoft Excel Worksheet 2 11KB From colhpaswdoos While files from the Internet can be useful some files can potentially harm Your computer IF you do not trust the source do not open or save this file What s the risk Accept Vntr Changes function highlights changes in strain type profiles of cases within the report Records will appear in red when the strain type for a case in the cluster report has been updated following regeneration of the report Updated records include isolates which had a missing locus when it was first reported but have since had the locus filled The cluster algorithm does not check that the updated isolate should still remain in the cluster so it is necessary to review the VNTR changes If the VNTR is no longer valid as part of the cluster you should select the record s using the tick box at the left hand side and click the Delete If the VNTR is valid as part of the cluster you should acknowledge these changes by selecting the record s using the tick box at the left hand side and then click the Accept Vntr Chan
16. cluster number from the dropdown list before saving the comment using the Add Comments button For each isolate that is deleted duplicate false positive or other a comment should be added outlining the reason for deletion to avoid the loss of important information that may be of importance to clinical or public health staff The ETS ID if available or the name and date of birth of the case should precede the comment Any other comments that may be relevant with respect to the cluster can also be added in the comments section A record of the user who added the comment and the date the comment were added are recorded next to each comment Lab comments Date Username Cluster No Comments 22 10 2013 Inmrn A1001 isolate with ETS ID 111111 Johnny Walsh O1 01 7 was deleted as the isolate is conimed as contaminated Cluster Number A1001 Comments Add Comments Note Deleting a case from the report generated by the lab will not result in the case being deleted from other reports Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 3 3 View lab record details Information contained on the lab record in the cluster report or combined information from all lab records into the merged lab record can be viewed in more detail by selecting view at the side of the entry in the cluster report ETHAM SQ KAN RIF RIFE E B1011 155069 CALL OW0N2013 A495 299251 FS ETR View MycobNet
17. default status of Awaiting Preliminary review To see the list of clusters with a particular status select View next to the status and the list will be displayed by cluster number and VNTR as shown below Cluster Investigation Administration Home page Case management Enler Cision Ikai Cluster No VNTR Profile Search E1695 226321432615324332413272 E1178 324332332615323242443373 c1008 427349642517323442443474 Logged in as AAput Leg Out e Download paper data collection form e SitePrecompile 2 0 8 ServicePrecompile 2 0 8 Public Health England Designed developed and maintained by CFI Software Development Unit To return to the home page click on the strain typing tab 15 Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 In the STM there are two tabs you have access to 1 Enter Cluster Details and Enter Cluster Details 2 Search Sioi Logged in as hhput LeS Out 1 Enter Cluster Details Download paper data collection form SitePrecompile 2 0 3 To view clusters select Enter Cluster Details This will ServicePrecompile 2 0 8 show you a table of cluster reports Open a report by clicking on the report name Enter Cluster Details Report Name Date Created Regenerated At West Midlands Oct 2013 11 11AM 0202013 West Midlands East C HPU Oct 2 2013 12 26PM 02 10 2013 West Midlands North HPU Oct 2013 12 26PM
18. details Forename Surname Date of birth Sex Age M 50 Address Postcode NHS number Hospital Patient No Organism name Source laboratory number Source laboratory Reference laboratory number TO125877 Reference laboratory tuberculosis Comments NTYGH Morth Tyneside General Hospital 492712T New castle Specimen type Strain Type MIRU VHTRI Sputum 4243529329 TIAM Strain type details ETR ETR ETR ETR ETR MIRU MIRU MIRU MIRU MIRU MIRU MIRU MIRU MIRU MIRU MIRU MIRU MIRU MIRU MIRU A B C D E 2 10 16 20 23 24 26 2f 39 40 4 42 47 52 53 4 2 4 3 a 2 3 3 2 a 1 T 3 3 3 4 6 4 4 3 3 2 uf a MTUB21 MTUBS4QUB26QUB11B Antibiotic susceptibility Result Antibiotic Sensitive Amikacin Sensitive Azithromycin Sensitive Capreomycin Sensitive Ciprofloxacin Sensitive Clarithromycin Resistant Ethambutal Resistant leoniazid Resistant Kanamycin Sensitive Linezolid Sensitive Moxifloxacin Sensitive Ofloxacin Sensitive PAS Sensitive Prothionamide Sensitive Pyrazinamide Resistant Rifabutin Resistant Rifampicin Resistant Streptomycin Close Note The results specimen type VNTR profile and susceptibility on the merged record in the cluster report may be different from the results listed in your laboratory system for the ID shown on the merged record 3 4 Accepting VNTR changes Isolates which were first reported with one missing loci but have since had the locus filled will appear in red The cluster algorithm does
19. people with a history of prison a incluing 3 who are currently in prison The Majority of cases are of White ethnicity and born in the UK v To investigate transmission of disease could you please provide the follow ing information and ask extra questions in relation to information given above e g did the patient visit or have visitors from these areas Please provide postcodes of places visited frequent contacts where possible Thank you very much for your co operation Patient specific questions Has this patient ever spent time in Pentonville prison If so what were the dates a Has the patient ever attended Florence Nightingale Rehab in Lisson Grove If so when Has the patient ever socialised in the Red Lion Pub in Camden If so how often and during which dates There is no onset of symptoms date completed on ETS please could you find out when his v Save Save downlosd Submit Go back The questionnaire can then be sent through ETS to the assigned case manager by clicking the Submit button The questionnaire will then appear as an alert on the case manager s ETS homepage Treatment outcome 9 twelve month treatment outcome reports due View e 2twenty four month treatment outcome reports due View e 2 thirty sm month treatment outcome reports due View Case transfers inbound transfers pending e 0 outbound transfers pending e QO rejected outbound transfers pending Laboratory isola
20. 1001 128461 North HPU Midlands 24 02 2010 614662432622333263313661 22 10 2013 View East Midlands East A1001 127566 South HPU Nedlands 26 02 2010 614662432622333263313661 22 10 2013 View West Midlands East West Birmingham and Midlands Solihull Bedfordshire gt 04 03 2010 614662432622333263313661 22 10 2013 gt gt S and East of f 127637 Hertfordshire England 10 03 2010 61466243262233326331 661 22 10 2013 View 63 HPU gt prg This will open the questionnaire in a separate window The patient details are pre filled at the top There is an option to enter detail on the size of the cluster the location of the cases and any other 22 Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 relevant information including patient specific questions Once any additions have been made to the top section of the form select Save at the bottom of the questionnaire Cluster investigation questionnaire Cluster No A1001 Case ld 128461 Case Manager jgratton Forename HT Hospital DERBY CITY GENERAL HOSPITAL HPU East Midlands North HPU Region East Midlands Source Lab DRI MIRUVNTR 614662432622333263313661 Mycobactertotogy p ringham reference unit Dear Colleague There are currently 15 TB cases in this cluster The other cases are in the follow ing HPUs Regions Tow ns Cities London Finsubry Park area Brighton and Birmingham Cluster characteristics of interest There are 5
21. 16 05 2012 4223525425 15333322423384 View C c1599 156649 17 05 2013 422352542515333322423384 View C1623 132195 22 10 2010 42235254251 133542423384 View 12345678910 Delete Accept Vntr Changes Download Report Save Cluster report 3 5 Saving and downloading a cluster report All changes or additions that have been made to the report can be saved by selecting Save Cluster report The report can be downloaded as an excel file by selecting Download report You will then be given the option to save it on your computer or to open it and print File Edit wiew Faworites Tools Help E http colhpaswdOO5S EIS Site S TM ExportClusterReport aspx lab Microsoft Internet Explorer File Download Do you want to open or save this file Note There is also a button development is planned Name LabClusterReport xls Type Microsoft Excel Worksheet 11KB From colhpaswedo0s While files from the Internet can be useful some files can potentially ham pour computer IF you do not trust the source do not open or save this file What s the nisk Accept Cluster Report This is not currently in use further 11 Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 3 6 Regenerating cluster reports Cluster reports should be regenerated by selecting the cluster report in View Cluster reports and using the Regenerate Report button Several reports can be
22. 24326223321A8323271 ISO Mew _ A1018 138629 26 07 2011 4646424326223321A83232 1 STR Mew A1018 138494 01 11 2011 4646424326223321A8323271 Mew A1018 141262 21 03 2012 4646424326223321A8323271 View A1018 142693 19 04 2012 4646424326223321A8323271 Mew A1018 153065 17 09 2012 4646424326223321A83232 1 Mew A1018 155611 11 04 2013 4646424326223321A8323271 Mew A1025 138245 02 09 2011 464642432622332148323271 Mew A1025 138245 06 10 2011 464642432622332148323271 View The isolates shown in the cluster reports are from the data that is routinely uploaded into ETS from each laboratory Each cluster of two or more cases within the specified time period and geographical location is shown along with the cluster name as assigned in the cluster naming tool http www hpa bioinformatics org uk TBCluster tbhome php A summary of each case isolate is shown in the cluster report Isolates with specimen dates in the 3 months prior to the date the report was re generated are highlighted in yellow The case isolate information shown in the report is derived from deduplication and merging of records with identical name and date of birth for specimen dates within a year of each other This allows for the cluster report to show the most complete strain type and the most complete resistant drug resistance profile Merged records are indicated by a blue symbol next to the name field Cluster Ho Case ld Name C 41368 137419 A1358 1
23. 37103 Note Please be aware that clusters can span more than one page Isolates may be matched to ETS cases automatically through the system if they have identical personal identifiers or they can be matched manually by ETS users Isolates matched to ETS cases will have an ETS ID shown in the report Click this ID to access the ETS case record Note All laboratories will have read only access to ETS case records To navigate back to the strain typing tab from a case record click on the strain typing tab and then on the View cluster reports Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 3 2 Comments and deleting cases from clusters Where the deduplication and merging of records is not possible due to difference in names and dates of birth duplicates may be deleted from reports To delete a case the box next to the case should be selected and the Delete button should be clicked For duplicates it is of benefit for the record with the most relevant information should be kept Laboratory details will need to be examined in order to determine which isolate should be kept To view further laboratory details on each case click on View in the Lab details column Isolates which are confirmed as false positives may also be deleted as outlined above There is a function for the laboratory staff to add comments to the report Comments are linked to clusters by selecting the appropriate
24. SO 12 A1018 Thames Valley HPU SouthEast _06 06 2011 46464243262233 1A8323271 4 To look between a particular date range e g for cohort review filter by notification date 5 To look at cases that are part of clusters by hospital e g to send monthly reports to a clinic scroll along to the hospital column and select only the hospital that require the information XW 7 7s East Oct 22013 11 09AM C sO x Home Insert Page Layout Formulas Data Review View a gt i B amp J ri AutoSum Calibri 9 U W EF Wrap Tert General 7 x a Z a Fill 7 27 itage Paste fD vy iiiv p A BE a Merge amp Center 7 v 9 0 0 onal Format Cell Insert pon Eagna Sort amp Find amp F Urinary 2 For i Be nee tting as Table Styles Clear Filter Select Voltage man P Font 4 Alignment 4 Number Styles Cells Editing H1 v fe HPU AF AG AH Al AJ AK AL AM r PrisonMoreThan5YearsA v PrisonAbroadMoreThanSYearsAg SputumResu v DiseaseSites v Hospital ReferenceL v ReferenceLabl v ClusterStatus vf 67 Po Negative Pulmonary EAST SURREY HOSPITAL NMRL H111460003 159 Po Puimonary EAST SURREY HOSPITAL NMRL H124060069 190 Po Putimonary BAST SURREY HOSPITAL NMRL H124060069 242 Po Putmontary EAST SURREY HOSPITAL NMRL 1124060069 405 Pt Pulmonay EAST SURREY HOSPITAL NMRL H120320003 432 PCE Puo SEAST SURREY HOSPITAL NMRL H122640008 500 Psi Pulmonary EAST SURREY HOSPITAL NMRL H102180521
25. See ae m ee i cae 27042012 422342647517323442443474 24 09 2013 View S North West ani HPU South TA cm t WES South am OVOV2010 422352642515333s42423374 2409 2013 View a South West HPU South West South n 5 PEN rs i er 20032011 4229526475 15999s42405974 24 09 2013 View Cc North West HPU ver epidemiological links between cases in the cluster with someone who does not have a strain type but who is a contact that you wish to add to the cluster To add a case to cluster enter the ETS ID into the Case Id box in the section of Add case to cluster and click on Search to check for any lab results that are available for the case Finally click Add the case will appear in the cluster with the date added in the Date Added column Added cases with no laboratory results will have no specimen date or VNTR so it will be easy to recognise added cases 10 Links can be formed between cases by selecting the cases from the two drop down lists under Epidemiological links The certainty of the link can be added as Known epidemiological link No epidemiological link or Possible epidemiological link The Type of contact and Contact Setting can be added along with the Postcode of Setting To add the link click on Add link 21 Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 The link with th
26. anually matched to the notification Cluster Data Show clusters with new data Download Report Accept Vni Changes Delete Cluster Case mpenn qn Cae yapt SPECIMEN 5 Resistant Date per _ No id Name D O B Postcode anager HPU Region Date WHTR To Added Questionnaire North A1001 ogon London 28 06 2010 614662432622333263313 61 25 11 2013 HPU North East and A1001 Central London 02 07 2010 614962492622333263313 61 25 11 2013 E London HPU North A1001 West London 02 08 2010 614662432627333263313 61 25 11 2013 E os London E HPU North A1001 191804 Jacqui West London 07 04 2011 614662432622333263313 61 25 11 2013 View aT ore Caress London HPU South A1001 194457 Jacqui West London 11 01 2012 614662432622333263313661 25 11 2013 View a e Caress London HPU North East and Central London 30 01 2012 614662432622333263313661 25 11 2013 View 7 Te London HPU South Jacqui West London 30 05 2012 614662432622333263313661 25 11 2013 View a Caress London re HPU North East and A1001 a Central London 12 09 2012 614662432622333263313661 25 11 2013 a London HOII Jacqui Aigo 194479 Caress A1001 195776 Case managers who use ETS are notified of unmatched isolates so that they can manually match isolates However not all case managers are ETS users e g London case managers and there are always outstanding isolates that require matching STM users may find it useful to manually match cases for cases in clus
27. ate Search criteria Search value Generate Cluster Reports Please select View Cluster Reports search a Please select Cluster number Logged in as Jneweastia Log Out e SitePrecompile 2 0 8 e ServicePrecompile 2 0 8 Public Heath England Designed developed and maintained by CFI Software Development Unit After selecting to search by either Cluster number or Strain type geographical date and time parameters must be selected Geographical level Specific geographical area Date options Date Period National Specimen date Last 6 months hall Region Notification date Last 6 months HPU Last 12 months Last 2 years Peete eee eee eee eee eee eee eee ELE Last 5 years Last 10 years Select the Geographical level by choosing National Region or HPU If Region or HPU are selected then it is necessary to use the Specific geographical area dropdown to choose the breakdown required To view all isolates with or without an ETS match in a selected time period choose Specimen date and then the time period from the Date Period drop down list By selecting ALL the date period restriction will not apply and all isolates will appear for the chosen geographical area To view only isolates with an ETS match select Notification date Once all desirable criteria are selected click on the Search button The Summary report will show t
28. cel apply filters xT ewe East Oct 2 2013 1109 b Home Insert Page Layout Formulas Data Review View A o ep es Pas E nuan i E Autos r calibri lo J a EA EF wrap Text General 557 i Emm ox i a T Fy Ba E Fin Z Paste B AT i Pi v A Ary EEE BE A Merge amp Center h 9 lt 0 00 Conditional Format Cell Insert Delete Format Sortt amp Find amp ig F r A7 EE 3 i ees Formatting as Table Styles X A v 2 Clear Filter Select Voltage Clipboard G Font P Alignment Number P Styles Cells Editing Al M fe Cluster No a gt 4 B c D E H mi J K oa Cluster No IlCase Id Surname Forename DOB Specimen Date VNTR Profile Resistant To E A1001 Valley HPU r 17 09 2012 614 62432622333263313661 A1001 Sussex Surrey HPU South East _28 02 2013 614662432622333263313 61 E A1001 Sussex Surrey HPU ne 25 07 2013 614662432622333263313661 5 A1002 Thames Valley HPU 11 05 2012 614862432622333263313661 6 A1002 Thames Valley HPU South East 17 09 2012 614 62432622333263313661 7 A1004 Sussex Surrey HPU South East 22 09 2010 614642432622334263313461 8 A1004 Sussex Surrey HPU South East 08 07 2011 614642432622334263313461 9 A1004 Sussex Surrey HPU South East 15 07 2011 614 42432622334263313461 10 A1004 Sussex Surrey HPU Seay 08 08 2011 614642432622334263313461 PYR 11 A1018 Sussex Surrey HPU 02 12 2010 4646424326223321A8323271 I
29. d years 10 Time period for recent isolates months 120 Note If an error is made during template creation the template can be deleted by clicking in the box beside the template name and selecting Delete Once a cluster report has been generated based on the template it cannot be deleted Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 2 Generate cluster reports This is used the first time you need to generate a cluster report using the templates you have created Generate Cluster Reports Name Level Geographical Area Min Isolates Years Recent Isolates Months Max Isolates Show 15 Loci C NMRL National National 2 10 2 120 5000 No NMRL East midlands Regional EastMidlands 2 10 2 120 5000 No NMRL South West Regional South West 2 10 2 120 5000 No NMRL Sussex HPU Sussex Surrey HPU 2 10 2 120 5000 No Generate cluster report To generate a cluster report tick the box beside the cluster report name and select Generate cluster report More than one template can be selected at the same time Note If the number of templates span more than one page the Generate cluster report button must be selected on each page 3 View cluster reports Reports can be viewed in the View Cluster Reports tab Please be patient as the generation of cluster reports can take several minutes to complete depending on the size of the report The Refresh
30. e entered into the questionnaires e g investigated whether new cases since 2012 have ever been to The Red Lion pub where outbreak investigation was conducted in 2010 they have not so no further investigation of the The Red Lion pub is required at present o Reason for changes in cluster status 3 Actions recommended by Cluster investigator e g Additional screening of hostel should be considered as two cases reside in the same hostel this information should be recorded by the HPT if discussion or advice is sought from cluster investigators It should be noted that this text box should be completed by those leading the cluster investigation at local level Note It is necessary to click the relevant Add button to save these notes and actions Notes on cluster No cluster notes found Hotes Add notes Actions recommended by cluster investigator No actions recommended found Actions recommended Add actions recommended 4 A summary table of settings relevant to the cluster is populated automatically by data from the competed cluster questionnaires Note This is not a summary of the risk factor information that is recorded on ETS which can be viewed in the cluster data This is a summary of the information from the questionnaire data 19 Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 Summary 5 Contact tracing figures and re
31. e relationship will then appear underneath If the link needs to be deleted e g link added in error select the right hand box and click on Remove Relation Epidemiological links Create a link Type of contact Contact Setting Postcode of Setting Please select w Flease select w Epidemiological Link Comments Add link 1 2 Cluster questionnaires aes There are three symbols beside the View questionnaire lin these are all greyed out when no actions have been taken with the case s questionnaire o The first symbol 4l indicates when the questionnaire has been saved o The second symbol ie a circle goes green which indicates the questionnaire has been completed information has been entered into the patient question fields in the questionnaire Not all fields need to be completed for it to be assigned completed symbol o The third symbol 2 shows the questionnaire has been submitted through ETS to the case manager It is only possible to view questionnaires for cases which have ETS IDs If no ETS ID is shown the case is either not notified or the isolate has not been matched to the case To view a cluster questionnaire click on View on the right hand side of the case Cluster Data Show clusters with new data Downlosd Report Accept Vntr Changes Delete Cluster Case Case Specimen Resistant Date s No id Name D O B Postcode Manager HPU Region Date VNTR To Added Questionnaire East Midlands East A
32. eographical level Select National Region or HPU from the drop down list By selecting national as the geographical area you can see all the isolates typed in your laboratory regardless of geographical location Specific geographical area Select a specific Region or HPU from the drop down list Show 15 loci The option is included if users wish to create additional reports which include historical data with 15 loci for retrospective investigation or research purposes Note This will not be selected for routine cluster reports generated by CIDSC Colindale to be sent to HPTs Max isolates This is the maximum number of isolates with an indistinguishable strain type that will appear in a cluster report Recommended entry is 50 000 Min isolates This is the minimum number of isolates with an indistinguishable strain type that will appear in a cluster report Recommended entry is 2 This is to ensure all clusters with at least 2 isolates will be reported Min number of recent isolates This is the minimum number of isolates with an indistinguishable strain type within a selected recent time period which will appear in a cluster report Recommended entry is 2 Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 Max time period years This is the number of years of data that will be returned in the report Isolates returned are those with indistingu
33. ges button Two clusters see below have updated strain types to review The isolate for Case ID 156896 previously had a missing locus and was valid to appear in two clusters Since it was first reported the missing locus was typed therefore the updated results appear in red see below In the first cluster B1005 the updated isolate is no longer valid strain type is different than cluster strain type and should be deleted In the second cluster B1134 case 156896 is still valid within this cluster and should be accepted Show all clusters Download Report Accept Vint Changes Delete Cluster Case Case Specimen Resistant Date No id Name D O B Postcode Manager HPU Region Date VATR To Added Questionnaire North Yorkshire Yorkshire and Humber and The 07 06 2011 424352332515333456443382 05 12 2012 View HPU Humber North Yorkshire Yorkshire and Humber and The 02 08 2012 42435233251533345 443382 26 03 2013 View HPU Humber North Yorkshire Yorkshire B1005 137400 B1005 and Humber andThe 26 10 2012 424352332515333456443382 2710212013 HPU Humber _ Yorkshire B1005 155954 West Yorkshire and The 24 05 2013 424352332515333456443382 23 09 2013 View Hi Humber North Yorkshire Y orkshire and Humber and The 27 02 2013 424352332515333456443372 04 09 2013 View HPU Humber B1134 154504 17 Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 In addition
34. he total number of isolates for all laboratories while the list of Possible match es found contains all the isolates from your own laboratory Searching at a National level will produce a summary table of the number of cases by Region Searching at a Regional level will produce a summary table of cases by HPU Searching at the HPU level will produce a summary table of cases found by hospital 13 Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 Possible match es found Summary report by regions Regions Isolates 3 East of England 1 London 11 North East T North West 1 South East 3 Wales 1 West Midlands 5 Yorkshire and the Humber 17 Total 49 Note The Summary numbers by region include all isolates in the cluster nationally The detailed list below shows isolates from your reference laboratory but do not show isolates from other reference laboratories CaseldName 0 0 8 SexAgePostcodeHospital HPU 147637 LEEDS GENERAL INFIRMARY West Yorkshire HPU 139199 HULL ROYAL INFIRMARY aas Yorkshire and Humber 154332 HULL ROYAL INFIRMARY pas SS e ii Region Yorkshire and The Humber Yorkshire and The Humber Yorkshire and The Humber Specimen date 1602012 0a 2 2011 ew 12 2012 If the isolate displayed in the list matches an ETS case you can view the ETS case record by clicking on the ETS ID Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Ve
35. ic Health England Designed developed and maintained by CFI Software Development Unit There are four tabs you have access to 1 Create Template Create Template Generate Cluster Reports 2 Generate Cluster Reports View Cluster Reports Search 3 View Cluster Reports and Logged in as newcastle leg Out SitePrecompile 2 0 3 ServicePrecompile 2 0 3 4 Search Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 1 Create Template Create cluster template Template name Geographical level Specific geographical area Show 15 Loci Please select ha d Max no of isolates Min no of isolates Min no of recent isolates 2 2 No of missing loci permitted Max time period years Time period for recent isolates months 0 2 6 Seve template A cluster template can be created with specific criteria which can be used to generate the cluster report for your laboratory Flexibility exists to change the criteria set in the template to allow for laboratories to analyse their own data over a specified time period or in a particular geographical area e g all clusters in London over the last 10 years Template name This is the name that will be given to the cluster report The template name must be in the following format laboratory abbreviation NMRL BMH NCL CRD geographical location of template North East London For example NMRL London NCL North East G
36. ishable strain types with specimen dates within the number of years specified Recommended entry is 10 Time period for recent isolates months This is the specimen time period for classifying what a recent isolate is Recommended entry is 120 months i e showing all clusters with no restriction See note Note There is other functionality within the report which highlights isolates with specimen dates in the last 3 months We therefore recommend users not to restrict the clusters that are returned in the report No of missing loci permitted This specifies the maximum number of missing loci present in isolates to be included in clusters Selecting O will produce clusters only with complete 24 MIRU VNTR profiles Recommended entry is 1 Note A standard template which captures all clusters with a minimum of 2 isolates without any time restriction will be generated by CIDSC Colindale for distribution to HPTs The recommendation is that each laboratory sets up a template for each HPU region and a national report with the same standard template to be able to view isolates processed by your laboratory Additional templates can be created as determined by your needs or interests Standard Template Template name NCL North East Geographical level Region Specific geographical area North East Max isolates 50 000 Min isolates 2 Min number of recent isolates 2 No of missing loci permitted 1 Max time perio
37. lts Laboratory Results Risk Factors Treatment Planned Category Report Details Treatment Outcome Mycobacterial Culture Report Summary Mycobacterial Culture Mycobacterial Culture Logged in as jdavidson LOS Out T ee ya r Mycobacterial Culture Details of MycobNet data Forename Surname Date of birth Sex Address Patient ID CTW Wd ee Sem Reference Source Reference Source laboratory number laboratory laboratory laboratory WBIRM number ee WBIRM Saar Birmingham 4 11 0604790 A g Strain Type MIRU VNTR 614642432622334262313461 Specimen Click on the strain type to search ff YPC for other cases with same strain Other tissues type 30 Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 Appendix 3 Matching laboratory records to notifications The Cluster Data table in the Enter Cluster Details tab shows name date of birth and postcode from the laboratory record The HPU and region are derived from the local laboratory on the laboratory record The Case Id column in the Cluster Data table shows if a laboratory record is linked to an ETS record i e if there is no id then the laboratory record is not linked to a case Note laboratory records match automatically within ETS to case notifications if the personal identifiers are identical If there are differences in personal identifiers laboratory records will have to be m
38. men Date Status Please Select i Please Select Add new culture or other results Test Type Specimen Type Specimen Date Please Select v Please Select k Status Please Select v Add MycobNet matched results The following reference laboratory results may relate to this patient Only positive cultures are listed Click on each record to view further details Please select all the records that you are certain relate to this patient and click the Accept selected records button Further results may appear here later Accept selected r Name Date of birth Age Sex Specimen date Reference laboratory Accept a a aa a i 32 Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013
39. not check that the updated isolate should still remain in the cluster so it is necessary to review the VNTR changes If the VNTR is no longer valid as part of the cluster you should select the record s using the tick box at the left hand side and click Delete If the VNTR is valid as part of the cluster you should acknowledge these changes by selecting the record s using the tick box at the left hand side and then click the Accept Vntr Changes button Two clusters shown below have updated VNTRs to review In the first C1575 the two updated isolates are valid and should be accepted while cluster C1580 is no longer a valid cluster and both isolates should be deleted 10 Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 C1575 129670 17 03 2010 42235254251 333542423384 View C1575 140292 26 01 2012 422352542517333542423384 ISO View C1575 141759 28 03 2012 4223525425 1 3335424233384 View E 1575 157024 30 05 2013 422352542517333542423384 View C c1580 138636 24 01 2011 422352642517334422223374 View _ 1580 147520 17 08 2012 422352642517334422223364 View C1587 147145 21 07 2012 422352572517333541423424 View C1587 147145 21 07 2012 422352572517333541423424 View C1587 154107 09 08 2012 422352572517333541423424 View E C1587 154107 12 08 2012 422352572517333541423424 View C1599 142614
40. orucial dake dnenatnuts E E AA N 7 5 VIEW cluster repons ersan a N wi dasetdsmosbic ve sauuncassaness wanuosaatanieecuneauouianeanetc eo 7 7 Wats sie a te wecere ar CreTen Te emer are Ve TI ter Mee terre rng Gee Med tr A Meme yee eer ere ey RA 13 FIP Tsai REGION al USE S ycgecenass coat cosh cance eacedeceuvte A ince van tetera eae 15 Gerines tar EUA aise ae aac ats ease t easiness Raga swanademae tanec ae E A ce anancoss 15 1 Enter Cluster Detall lt skcerstapieethlotetsdigias awehslasious bona tliaia ak oeier tak wien aes 16 Do E11 a ENT EE EE E EE un bones Dotson TAA aes san T E AE EE A EE E ETA 26 Appendix 1 Other USES OF SUV era N a E 28 Appendix 2 Searching for a Strain type USING ET Soens a e ERRA i 30 Appendix 3 Matching laboratory records to NotifiCations cccccescccccssecccesececeesececseeeceeseusecesauneess 31 2 Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 Introduction to strain typing module The strain typing module STM is an integrated part of the Enhanced Tuberculosis Surveillance ETS system The module is designed to identify strain typing clusters and assist with cluster investigation Users can review clinical and risk factor data relevant to cases in a cluster to inform investigation Questionnaires within the system can be used to collect additional information on cases and information on cluster investigation can be recorded for example epidemiological links between
41. rsion 1 22 11 2013 14 HPT and Regional users The reports used by HPT and regional users are different to those used by laboratory users The reports generated by laboratories only contain isolates from the specific laboratories while the reports generated by CIDSC for HPT and regional users contain isolates from the given area for all laboratories that the isolates have been sent to Getting started Log in 1 Goto ETS website https webservices hpa nhs uk ETS Site 2 Login with user name and password 3 You will be brought to the home page of ETS Click on the Strain Typing tab Administration Strain typing Case management Alerts Enter Cluster Detail e 22 clusters with status awaiting preliminary review View Search e 3 clusters with status active investigation View 1 clusters with status re opened for active investigation View Logged in as AAput Log Out e 0 clusters with status active investigation e Download paper data collection form 1 clusters with status no action required View SitePrecompile 2 0 8 clusters with status closed View e ServicePrecompile 2 0 3 Public Health England Designed developed and maintained by CFI Software Development Unit HPT and Regional users will see an Alerts page which will display the number of clusters with each status set by those investigating the cluster e g the number of clusters under investigation All clusters are given the
42. selected at the same time After selecting the Regenerate Report button the reports will temporarily disappear from the list but will reappear again once they have been regenerated New cases will be added to the existing clusters from the previous report as well as any new clusters that have appeared since the previous report New cases are highlighted in yellow when the specimen date is within the last three months from the date the cluster report was re generated The date when the cluster report was regenerated is shown in the Regenerated At column NMRL Sussex HPU Sep 24 2013 12 14PM Show clusters with new data Cluster No Caseld Name D O B Postcode SpecimenDate VNTR Profile Resistant To Lab details A1001 155369 28 02 2013 614662432622333263313 61 Mew moot 157060 25107 2013 614662432622333263313661 Mew A1004 131693 22 09 2010 614642432622334263313461 View A1004 136870 08 07 2011 614642432622334263313461 View F A1004 136870 15 07 2011 614 42432622334263313461 View A1004 137394 08 08 2011 614642432622334263313461 PYR View A1018 133047 02 12 2010 464642432622332 1A8323271 ISO View A1018 138629 26 07 2011 464642432622332 14A83232 1 STR View _ A1018 138494 01 11 2011 464642432622332 1A8323271 View A1018 141262 21 03 2012 464642432622332 14A8323271 View C A1013 142693 19 04 2012 464642432622332 1A8323271 View M A1018
43. sults related to the cluster can be recorded in a table The Save button must be clicked for the information to be stored Contact tracing prior to cluster investigation No of contacts No screened for mantoux No screened for IGRA No screened chest X ray No with latent infection No diagnosed with active disease No of contacts that did not attend screening Contact tracing as a result of cluster investigation No of contacts screened No of active cases No of latent cases Seve No positive with mantoux No positive IGRA No positive chest X ray 6 Cluster Data displays the cases isolates in the cluster The functions detailed in section 1 Enter Cluster Details can also be performed when looking at a specific cluster Cluster Data Caster Case Mame DOB Postcode HPU No Id Manager South West 1 128391 ao North HPU South West C1688 148447 1 oo North HPU Show clusters with new data Downlosd Report Accept Vntr Changes Delete s Specimen Resistant Date x Region Date VNTR To Added Questionnaire a 17 02 2010 42234274251133443242325 24 09 2013 View 30 coy 02 11 2012 422342742511334432423253 24 09 2013 View 3 7 To view the Summary of cases which shows the risk factors for each case with an ETS ID in the cluster click the cluster number in the Cluster Data table and a new table will be presented below the cluster data 20 Enhanced Tuberculosis Surveillance Strain
44. ted with the information derived from specific key fields and a proportion of cases in the cluster with a specific characteristic is automatically calculated and displayed Note This is not a summary of the risk factor information that is recorded on ETS which can be viewed in the cluster data This is a summary of the information from the questionnaire data Hotes Select a VNTR profile above to load data into the fields below for the selected VNTR cluster Summary 25 Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 2 Search The search page can be used to find isolate information by selecting either Cluster number or Strain type from the search criteria drop down menu Public Health England Enter search criteria below Case management Administration Enter Cluster Details Search criteria Search value Search Please select Please select eop spent ose aeieeiaii Logged in az hhput Lea Out Cluster number Strain type Download paper data collection form SitePrecompile 2 0 13 i a oa i ee emilee FE AP After selecting to search by either Cluster number or Strain type geographical date and time parameters must be selected Geographical level Specific geographical area Date options Date Period National Specimen date Last 6 months O Region Notification date Last 6 months Last 12 months HPU Last 2 years
45. ters under investigation To link a laboratory record to a case in the STM cluster report it is necessary to do this through ETS To check if the case has been notified use the ETS search page and search using the name and or date of birth from the laboratory record Note it may be necessary to search using the name and date of birth separately in order to find the case record as there must be difference s in the personal identifiers on the case notification and the laboratory record as the match has not occurred automatically within the system 31 Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 R Public Health England Strain ping Y Hes Home page Enter search criteria below to find a case New caze Case ID Local patient ID Forename Surname Treatment outcome result due Administration Date of birth Year of diagnosis Strain type Please select Case transfers Laboratory isolate matching Questionnaires due Case manager Region residence HPU residence Hospital Logged in as jdavidson 49s Out Please select Please select w Please select w Please select Download paper data collection form E e SitePrecompile 2 0 14 Search options ServicePrecompile 2 0 13 Return only cases hawe access to O Return only cases do not hawe access to Search ETS If the case notification is not found then it is likely that this case has not been notified If
46. tes e 190 unmatched laboratory isolates available for matching View Questionnaires due e 1 Strain typing questionnaire due View 32 M bovis questionnaires waiting View 23 Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 The questionnaire can also be downloaded as a word document by selecting Download http colhpaswd005 E1TS Site S M QuestionnaireDownload aspx Microsoft Internet Explorer provided by Health Protect Fie Edit View Favorites Tools Help File Download Do you want to open or save this file Name Questionnaire doc Type Microsoft Office Word 97 2003 Document 168KB From colhpasiwdO05 harm your computer IF you do not trust the source do not open or 0 While files from the Internet can be useful some files can potentially save this file What s the risk You can then save it and send it to clinics by email or open and print for example if the case manager is not an ETS user In particular this will affect London HPTs who will need to send questionnaires by email or fax Questionnaire NORTH MANCHESTER GENERALHOSPITAL Greater Manchester Patient Forename North West 422352541517 333542 Patient DOB MIRU VNTR 423384 Mycobacteriology l Dear Colleague There are currently 2 TB cases in this cluster The other cases are in the following HPUs Regions Towns Cities London Cluster characteristics of interest Alcohol use To in
47. the report Reports for local geographical areas are created and regenerated weekly by the CIDSC TB Section Please note at the time of the STM release November 2013 ETS functions within the boundaries that were in existence under the Health Protection Agency Plans to update this to Public Health England PHE boundaries are underway Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 Laboratory Users Laboratory users can create and utilise reports within the STM to see geographical reports of isolates submitted to their laboratory which cluster with other isolates submitted to their laboratory The STM cluster reports can also be used to link and view to clinical data relevant to the case as entered on ETS The STM search page can be used to identify if strain types are present elsewhere in the UK or have been identified by other laboratories Getting started Log in 1 Goto the ETS website https webservices hpa nhs uk ETS Site 2 Login with user name and password Please log in User Name For any problem related to Tuberculosis surveillance please contact the regional TB surveillance co ordinators Password 3 You will be brought to the home page of ETS Click on the Strain Typing tab Strain typing i Help Lab Newcastle s home page Administration Home page Logged in as Jnewcastle log Out SitePrecompile 2 0 38 ServicePrecompile 2 0 3 Publ
48. vestigate transmission of disease could you please provide the following information and ask extra questions in relation to the information given above on this cluster e g did the patient visit or have visitors from these areas Please provide postcodes of places visited frequent contacts where possible Please return this form to Laura Anderson Thank you very much for your help and co operation Patient specific questions Did the patient attend Brownlee Mosque 24 Enhanced Tuberculosis Surveillance Strain Typing Module User Guide Version 1 22 11 2013 The questionnaire can be entered on the STM in by the case manager person investigating the cluster if returned in paper format using the drop down lists and the free text boxes Please save any changes to the questionnaire by selecting Save To return to the cluster select Go Back Did patient regularly attend the following in the 2 year before diagnosis Please provide name address and dates Childcare Education Y A l es k C J Nursery Primary School F College sixth form v Workplace No i e s Place of worship Yes v 4S F Church F Synagogue Mosque v Regular place of socialising Please select Ss Detention e g prison Please select vi 4 Treatment Rehab Centre Please select v A s Once data is completed in questionnaires the summary table at the top of the report will be popula

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