Department Of Microbiology Microbiology Handbook

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Department of MicrobiologyMicrobiology Handbook - Version: 4.9. Index: Microbiology 34. Printed: 01-Jul-2020 09:57Microbiology HandbookDate of Issue – 4th February 2019Microbiology Handbook - Version: 4.9. Index: Microbiology 34. Printed: 01-Jul-2020 09:57Authorised on: 01-Jul-2020. Authorised by: Sital Patel. SOP Unique Reference: 403-93931632. Due for review on: 04-Feb-2021Author(s): Rebecca Prince, Sital Patel, Stephen Farley, Stephen JonesPage 1 of 45

Walsall Healthcare NHS TrustUser HandbookDepartment of MicrobiologyPolicy (Microbiology)REVIEW INTERVALEvery 2 yearsAUTHORDr. SG JonesMr. S FarleyDr AJ PlantLOCATION OF COPIES1. iPassport2. Pathology web page3. Walsall Healthcare IntranetMicrobiology Handbook - Version: 4.9. Index: Microbiology 34. Printed: 01-Jul-2020 09:57Document Review HistoryReviewed by: GradeDateSignD SpillerHead BMS12/10/10DSNext ReviewDate12/10/11S FarleyBMS 202/08/11SF02/08/12S FarleyJ RudgeD SpillerDr SG JonesDr U KumaraDr SG JonesBMS 2BMS 2Head stHead BMSBMS 2BMS 2BMS 2BMS 2BMS 2BMS 17SGJ03/201804/02/19SP02/2021Mr S FarleyMrs J RudgeMrs R PrinceMiss S PatelDr. SG JonesDr SG JonesDr AJ PlantMr S FarleyMrs J RudgeMiss S PatelHead BMSSenior BMSSenior BMSMicrobiology Handbook - Version: 4.9. Index: Microbiology 34. Printed: 01-Jul-2020 09:57ISO Standard: 5.4.2Authorised on: 01-Jul-2020. Authorised by: Sital Patel. SOP Unique Reference: 403-93931632. Due for review on: 04-Feb-2021Author(s): Rebecca Prince, Sital Patel, Stephen Farley, Stephen JonesPage 2 of 45

Walsall Healthcare NHS TrustUser HandbookDepartment of MicrobiologyPolicy (Microbiology)Microbiology Handbook - Version: 4.9. Index: Microbiology 34. Printed: 01-Jul-2020 09:57CONTENTS1Amendment procedure . 42Overview of Services . 53Key contact numbers. 64Location of Department . 65Laboratory Opening Hours. 76Emergency (on-call) requests . 76.1Guidelines for On-call requests . 77Laboratory Supplies . 78Ordering Tests . 89Additional requests . 99.1Time limits for Additional requests . 910High Risk Specimens . 911Transport of Specimens. 1011.1 COVID – 19 . 1111.2 Outside Normal Working Hours. 1112Protection of personal information . 1113Complaints procedure . 1114Uncertainty of measurement . 1115Chain of evidence . 1216Travel Abroad . 1316.1 Related documents: . 1317Needle stick Incidents . 1318Specimen Collection . 1418.1 Patients guide to taking specimens. . 1418.2 Pernasal swab collection. 17Microbiology Handbook - Version: 4.9. Index: Microbiology 34. Printed: 01-Jul-2020 09:57ISO Standard: 5.4.2Authorised on: 01-Jul-2020. Authorised by: Sital Patel. SOP Unique Reference: 403-93931632. Due for review on: 04-Feb-2021Author(s): Rebecca Prince, Sital Patel, Stephen Farley, Stephen JonesPage 3 of 45

Walsall Healthcare NHS TrustUser HandbookDepartment of MicrobiologyMicrobiology Handbook - Version: 4.9. Index: Microbiology 34. Printed: 01-Jul-2020 09:5718.3Policy (Microbiology)Testing for COVID-19 . 1819Sample Requirement . 1920Update on service during Covid-19 pandemic . 2521Diagnostic Tests Available . 2521.1 Referred Virology tests . 2521.2 Referred Tests . 2621.3 In-House Serology (including antigen detection) . 2921.4 Blood Cultures . 3021.5 CSFs. 3121.6 Antibiotic Assays . 3121.7 M.R.S.A. Screen swabs . 3321.8 Carbapenem resistant organism screening . 3321.9 Vancomycin resistant Enterococci screening . 3321.10 Faeces MC&S . 3421.11 Mycology . 3421.12 Sputum & Other Respiratory Tract Specimens . 3421.13 Urine Examination . 3421.14 Uro-Genital Swabs . 3521.15 Chlamydia and gonorrhoea Molecular Testing . 3521.16 Wound Swabs, Aspirates & Pus Specimens. 3621.17 COVID – 19 . 3622Laboratory results . 3623Reference ranges . 3624Turnaround times . 3725Rejection of Specimens Submitted to the Laboratory. . 3726Specimen quality . 3927Reference Laboratories . 4028Appendix 1 LABORATORY CHAIN OF EVIDENCE FORM. 451 Amendment procedureAny amendments to this document must only be made with the prior agreement of theLaboratory Manager and/or the Quality Manager. The Quality Manager will ensure that thedetails of all amendments are recorded in the amendment record below. When it isnecessary to make minor amendments to the document, create a new version of thedocument on iPassport and make the relevant changes. Record the amendment(s) on thetable below and authorise the document stating a minor revision has been made. Allamendments must be circulated to all staff. The previous version will be stored on iPassport.Microbiology Handbook - Version: 4.9. Index: Microbiology 34. Printed: 01-Jul-2020 09:57ISO Standard: 5.4.2Authorised on: 01-Jul-2020. Authorised by: Sital Patel. SOP Unique Reference: 403-93931632. Due for review on: 04-Feb-2021Author(s): Rebecca Prince, Sital Patel, Stephen Farley, Stephen JonesPage 4 of 45

Walsall Healthcare NHS TrustUser HandbookDepartment of MicrobiologyMicrobiology Handbook - Version: 4.9. Index: Microbiology 34. Printed: 01-Jul-2020 09:57No.DatePolicy (Microbiology)1PageNo.08/03/2019 5Section(s) involved and amendment DetailsAuthorisedByUKAS SP208/04/2019 40308/04/2019 11408/04/2019 1254508/04/2019 29608/04/2019 10708/04/2019 31806/06/2019 39902/10/2019 25, 281002/10/2019 291108/10/2019 Var1209/10/2019 Var1325/03/2020 391403/04/2020 Var26 Stools for Norovirus PCR must be sent to the S Patellab within 2 daysCOVID-19 addedJ Rudge1501/07/2020 VarAmendments to COVID-19 testingAmended section 2 and link toaccreditation certificate added27 Measles and Mumps IgM is referred to PHEHeartlands14 Information regarding measurement ofuncertainty in the lab15 Information regarding chain of evidenceincluded28 Laboratory chain of evidence form included21.3.1 Helicobacter pylori stool Ag is now an inhouse test11 clarification on what can be sent via thepneumatic tube system21.5 Clarification CSF samples should be sent tomicrobiology urgently as microscopy and cultureshould be done within 2 hours of collection26 clarification of 3 day age limit for fluids21.1, 21.2.1 – clarification of what samples tosend for serology testing21.3.1 – update to Legionella Urine AntigenTestingTspot change to ref lab and collectionrequirements. IGRA test removedH.simplex type specific serology addedSPSPSPSPSPSPSPSPSPJ RudgeJ RudgeS Patel2 Overview of ServicesThe Microbiology Department provides a high quality, cost effective service to the WalsallHealthcare NHS Trust, including GP surgeries.Qualified and experienced medical and technical personnel staff the department.This guide gives information on how to use the Clinical Microbiology Department, a separateguide is provided on the rational use of Antimicrobials; see also the Trust Infection ControlPolicies. It is important that all medical and nursing staff familiarise themselves with theseguidelines, to optimise use of these services.The department is subject to external accreditation by UKAS (United Kingdom accreditationservice) to ISO15189 – accreditation number is 9101Our accreditation is limited to those activities described on our UKAS schedule ntent/uploads/schedule otappearing in the schedule are Not UKAS accredited. These tests however, are performed bythe same trained and competent staff.Microbiology Handbook - Version: 4.9. Index: Microbiology 34. Printed: 01-Jul-2020 09:57ISO Standard: 5.4.2Authorised on: 01-Jul-2020. Authorised by: Sital Patel. SOP Unique Reference: 403-93931632. Due for review on: 04-Feb-2021Author(s): Rebecca Prince, Sital Patel, Stephen Farley, Stephen JonesPage 5 of 45

Walsall Healthcare NHS TrustUser HandbookDepartment of MicrobiologyPolicy (Microbiology)The laboratory is recognised for training by the Institute of Biomedical Sciences.All work is performed with due care for the health and safety of staff and visitors and withproper regard for the environment. The laboratory complies with comprehensive safetyprocedures and Control of Substances Hazardous to Health (COSHH) regulations.Advice on the microbiological investigation of patients with infection, and their treatment, canbe obtained from the Clinical Microbiologists who provide a 24-hour service. To seek advicefrom the Clinical Microbiologists, relevant telephone numbers are listed below.3 Key contact numbersCONTACT NUMBERSDr. SG JonesMicrobiology Handbook - Version: 4.9. Index: Microbiology 34. Printed: 01-Jul-2020 09:57Dr. Aiden J PlantSue PageMr Stephen FarleyConsultant MicrobiologistsExt.6489 / mobile via SwitchboardExt.7915 / bleep 2306 / mobile via SwitchboardMedical SecretaryExt.6793Laboratory ManagerExt.7125Clinical Nurse Specialist Infection ControlExt.5805, 5830, 5817, 5816 / Bleep 8208, 8079Routine hoursOut-of-hoursService providedfrom homeMicrobiology EnquiriesExt.7127Available by mobile via switchboard (a rota operates for thisservice)On-call Consultant Biomedical ScientistContact via switchboard4 Location of DepartmentThe Microbiology Department is located within the main Pathology Services Building at theManor Hospital on Route 020. On exiting the hospital through the main rotary doors, turn leftthen continue to walk around the perimeter of the main building. The entrance is 70 metreson the left, signposted ‘020 Pathology’.The address of the department is;Department of MicrobiologyWalsall Manor HospitalMoat RoadWalsallWest MidlandsWS2 9PSMicrobiology Handbook - Version: 4.9. Index: Microbiology 34. Printed: 01-Jul-2020 09:57ISO Standard: 5.4.2Authorised on: 01-Jul-2020. Authorised by: Sital Patel. SOP Unique Reference: 403-93931632. Due for review on: 04-Feb-2021Author(s): Rebecca Prince, Sital Patel, Stephen Farley, Stephen JonesPage 6 of 45

Walsall Healthcare NHS TrustUser HandbookDepartment of MicrobiologyPolicy (Microbiology)5 Laboratory Opening HoursThe Laboratory is open between 8.45 a.m. and 5.30 p.m. during the week, between 8.00 amand 4.00 pm on Saturdays, Sundays and Bank Holidays (except Christmas Day which is oncall only). Routine samples are accepted in the department between 9.00 a.m. and 5.00p.m. on weekdays. Samples arriving after 5.00 p.m. will be refrigerated overnight unless prearranged by phone.6 Emergency (on-call) requestsMicrobiology Handbook - Version: 4.9. Index: Microbiology 34. Printed: 01-Jul-2020 09:57The on-call service is provided by on-call Biomedical Scientists (BMS) from home.The On-call BMS must be contacted by the requesting doctor (after the specimen hasbeen obtained) via the switchboard, and the specimen delivered to the laboratory. Therequesting doctor must make all arrangements for specimen delivery to the pathologydepartment. Investigations should only be requested on-call when the results are requiredfor immediate patient management. Advice on specimen management may be obtainedfrom the medical microbiologist on-call via the switchboard.Guidelines for on-call requests are given below. If asked by the on-call Biomedical Scientistfor your reason for requesting a test, you should give the clinical indications, no reasonablerequest will be refused but the Biomedical Scientist will be at liberty to ask you to consult theon-call Consultant Microbiologist to discuss the necessity for the investigation.You must complete the request form and include your contact point (telephone or bleepnumber).6.1Guidelines for On-call requestsSampleTypeOn-call systemCSF SamplesAscitic fluidSynovial fluidSputum, SwabsUrine SamplesWill always be examined in cases of suspected infectious meningitis.Urgent requests will always be examinedPus / AbscessStoolSamplesRespiratoryPCREmergency investigation is rarely useful.All urine samples should be dipstick tested prior to consideration for urgentmicroscopy. A visually clear sample with a negative result on dipsticktesting is very unlikely to grow significant organisms. For the majority ofpatients, empirical antibiotic therapy may be started, after the appropriatesamples are taken for processing the following day.Emergency microscopy may direct empirical antibiotic therapy; however aGram stain could be misleading, particularly if the patient is alreadyreceiving antibiotics.Norovirus may be performed only in agreement with the ConsultantMicrobiologist.Seasonal out of hours testing may be performed only in agreement with theConsultant Microbiologist.7 Laboratory SuppliesRoutine items can be found in West Wing Blood Bank. These include:Microbiology Handbook - Version: 4.9. Index: Microbiology 34. Printed: 01-Jul-2020 09:57ISO Standard: 5.4.2Authorised on: 01-Jul-2020. Authorised by: Sital Patel. SOP Unique Reference: 403-93931632. Due for review on: 04-Feb-2021Author(s): Rebecca Prince, Sital Patel, Stephen Farley, Stephen JonesPage 7 of 45

Walsall Healthcare NHS TrustUser HandbookDepartment of Microbiology Policy (Microbiology)Blood culture bottlesUniversal containersCharcoal Trans-swabsThe following items can be obtained from the Microbiology Department: Viral transport medium Chlamydia transport media (for swabs and urine) ENT fine Trans-swabs Blue topped flexible pernasal swabs EMU bottles for TB culture Red transport box Bags labelled UN3373, ‘COVID-19’Microbiology Handbook - Version: 4.9. Index: Microbiology 34. Printed: 01-Jul-2020 09:57GP practices can order supplies using a consumables order form. Spare forms are availablefrom the Department of Pathology.Advice and information regarding specimen containers is available from the Microbiologydepartment8 Ordering TestsWherever possible requests for Microbiology/Virology should be made using the Ordercomm. system. Instructions for using the Order comm. are available here.Please ensure that the sample collection date is completed on the hard copy of theform.Please supply all appropriate clinical details.Requests made other than by Order comm. should be sent using Microbiology forms.ALL MICROBIOLOGY/SEROLOGY REQUESTS FOR VIROLOGY NEED TO BECOMPLETED ON MICROBIOLOGY FORMS. DO NOT USE, OR ADD TO, BLOODSCIENCES REQUEST FORMS AS THIS WILL CAUSE UNNECESSARY DELAYS.A separate Microbiology request form is required for each specimen.Illegible or incorrect information can lead to problems of interpretation of analysis andreporting. Urgent specimens should include contact details (bleep/phone number).All specimens must be accompanied by a request form fully completed and include: The Full name of the patientDate of birthSex of patientHospital unit number/NHS NumberWardName of requestor (clinician, healthcare provider or other person legally authorisedto request examinationsInvestigation requiredSample type – including site where appropriateSignificant clinical information – Quality of results depends on the detailsprovidedAntibiotic therapyMicrobiology Handbook - Version: 4.9. Index: Microbiology 34. Printed: 01-Jul-2020 09:57ISO Standard: 5.4.2Authorised on: 01-Jul-2020. Authorised by: Sital Patel. SOP Unique Reference: 403-93931632. Due for review on: 04-Feb-2021Author(s): Rebecca Prince, Sital Patel, Stephen Farley, Stephen JonesPage 8 of 45

Walsall Healthcare NHS TrustUser HandbookDepartment of Microbiology Policy (Microbiology)Request dateThe patients GP (if known)Date and time of specimen collectionThe sample must have a minimum of 2 patient identifiers. NB first and last name equates toone identifier therefore a DOB or NHS/hospital number must also be included.9Addit

15 01/07/2020 Var Amendments to COVID-19 testing S Patel Page 5 of 45 Microbiology Handbook - Version: 4.9. Index: Microbiology 34. Printed: 01-Jul-2020 09:57 Authorised on: 01-Jul-2020. Authorised by: Sital Patel. SOP Unique Reference: 403-93931632. Due for review on: 04-Feb-2021 Author(s):

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