Microbiology

The Microbiology department is based at University Hospital of North Durham and serves the CDDFT acute sites, community clinics and GPs throughout County Durham. A team of Medical Laboratory Assistants, Associate Practitioners, Biomedical Scientists and Consultant Microbiologists all work closely together to ensure that our patients and service users receive high quality results that support the patient's care journey.

The Microbiology department examines many different sample types to look for evidence of infection using a variety of different techniques, e.g:

Bacterial & fungal culture: specialised growth plates or broths are inoculated with patient specimens and incubated under different conditions and temperature to try and grow and identify bacteria or fungi that may cause infections (pathogens).
Antimicrobial sensitivity: bacterial pathogens are tested against a range of antimicrobial agents that could be used to treat the infection they have caused. These tests can help to identify the most appropriate treatment for the patient, as well as identifying antimicrobial resistance.
Molecular tests: these tests are useful when pathogens cannot be grown using traditional culture techniques, or would take a very long time. Molecular tests look for pieces of genetic material that are unique to a specific pathogen.
Serology / blood tests: these tests are also useful when pathogens cannot be grown using traditional culture techniques, or would take a very long time e.g. viral infections. A range of different tests are used to detect unique parts of a pathogen known as antigens circulating in patient blood. Other tests can detect specific antibodies (part of the natural immune response) to a known pathogen in patient blood. This can be used to detect current or previous infection.

The Microbiology department also works closely with CDDFTs Infection Control team and Public Health England providing testing, screening and epidemiological information relating to infection control. This includes monitoring of communicable diseases and multi-drug resistant pathogens.

Test Repertoire

The Microbiology test repertoire can be found via the test directory and individual handbook pages.

Referred Tests

See the microbiology referral test page for the tests sent via the microbiology department, including details of the referral laboratories and specimen requirements.

Test	Referral Laboratory	Specimen / Container
16S Ribosomal RNA Pan-bacterial identification	Great Ormond Street Hospital	Sterile fluids / tissues in a universal container
Acanthamoeba	See individual test directory page
Adenovirus CFT	Infection Sciences, Bristol	Serum / SST (ochre top)
Adenovirus PCR	PCR Laboratory, Freeman Hospital, Newcastle	Blood / EDTA (purple top) or viral eye swab (green)
Amoebic Serology	University College London (School of Tropical Medicine)	Serum / SST (ochre top)
Antifungal Assay (Itraconazole, Fluconazole, Voriconazole)	Mycology Reference Centre, Manchester, Wythenshawe	Serum / SST (ochre top)
Anti-DNAse B	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
Aspergillus IgG Antibodies / Precipitans	Virology, Carlisle (see notes)	Serum / SST (ochre top)
Avian Antibodies (Farmers Lung)	Virology, Carlisle	Serum / SST (ochre top)
Bartonella Antibodies (Cat Scratch)	Discontinued - see comment	Serum / SST (ochre top)
Bilharzia (Schistosomiasis)	University College London (School of Tropical Medicine)	Serum / SST (ochre top)
BK Virus	Infection Sciences, Bristol	Blood / EDTA (renal transplant patients) Urine / sterile universal (white top) for bone marrow transplant patients
Bordatella pertussis antibodies Must be >14 days post onset of symptoms.	RVPBRU, PHE Colindale	Serum / SST (ochre top)
Bordatella pertussis PCR	PCR Laboratory, Freeman Hospital, Newcastle	Nasopharyngeal secretions / dry swab or sterile universal.
Borrelia Antibodies (Lymes Disease)	Virology, Carlisle	Serum / SST (ochre top)
Brucella Antibodies	University Hospital Aintree, Lower Lane, Liverpool, L9 7AL	Serum / SST (ochre top)
Cat Scratch (Bartonella Antibodies)	No longer tested, replaced by molecular testing of biopsy samples.
Chlamydia Antibodies	Discontinued - not a recommended test.
CMV (Cytomegalovirus) IgM	Serology, Freeman Hospital, Newcastle Hospital	Serum / SST (ochre top)
CMV (Cytomegalovirus) IgG	Serology, Freeman Hospital, Newcastle Hospital	Serum / SST (ochre top)
CMV avidity	Serology, Freeman Hospital, Newcastle Hospital	Serum / SST (ochre top)
CMV PCR	PCR Laboratory, Freeman Hospital, Newcastle	Blood / EDTA (purple top)
CMV PCR	PCR Laboratory, Freeman Hospital, Newcastle	Urine / sterile universal (white top)
Colistin antibiotic levels	Bristol Antimicrobial Reference Laboratory	Pre-dose Serum / SST (ochre top)
Coxiella Burnetii (Q fever)	Mycological Reference Laboratoryoratory, Bristol PHE,	Serum / SST (ochre top)
Coxsackie Virus	Epsom & St Helier, West Park Hospital, Epsom	Serum / SST (ochre top)
Cryptococcal Antigen	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
Delta Ab (Hep B)	PHE Colindale via serology at Freeman Hospital, Newcastle	Serum / SST (ochre top)
Dengue Fever	RIPL, PHE Porton	Serum / SST (ochre top)
Diphtheria antibody	RVPBRU, PHE Colindale	Serum / SST (ochre top)
E. coli O157 serodiagnosis	GBRU, PHE Colindale	Serum / SST (ochre top)
EBV (Epstein Barr)	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
EBV (Epstein Barr) VCA IgM	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
EBV (Epstein Barr) VCA IgG	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
EBV PCR	PCR Laboratory, Freeman Hospital, Newcastle	Blood / EDTA (purple top)
Enteric Virus Investigation inc. Enterovirus & Coxsackie A/B virus	Epsom & St Helier, West Park Hospital, Epsom	Serum / SST (ochre top)
Enterovirus IgM (not cardiac patient)	Epsom & St Helier	Blood / EDTA (purple top)
Enterovirus PCR (cardiac patient)	PCR Laboratory, Freeman Hospital, Newcastle	Viral swab of lesion (green) or faeces sample (sterile universal)
Enterovirus PCR	Epsom & St Helier	Blood / EDTA (purple top)
Eye swab for viral PCRs - Adenovirus, Herpes & VZV	PCR Laboratory, Freeman Hospital, Newcastle	Viral eye swab (green)
Filarial antibody	University College London (School of Tropical Medicine)	Serum / SST (ochre top)
Flu / Respiratory CFTs (blood)	Infection Sciences, Bristol	Serum / SST (ochre top)
Flu - full respiratory PCRs (viral swab - nose & throat)	PCR Laboratory, Freeman Hospital, Newcastle	Viral nose and throat swab (green) or NPA or BAL (sterile universal)
Fluconazole level	Mycology Reference Centre, Manchester, Wythenshawe	Serum / SST (ochre top)
Galactomannan (Aspergillus Ag test)	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
Galactomannan PCR	Manchester	Serum / SST (ochre top)
Glandular fever screen	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
Haemophilus Antibodies	Immunology, Carlisle	Serum / SST (ochre top)
Helicobacter Antibody	Discontinued -please send a faeces sample for Helicobacter antigen testing.
Helicobacter culture on Dents medium	GBRU, PHE Colindale	Biopsy in Dents media: must be ordered from the laboratory prior to testing (at least 10 days' notice)
Hepatitis A RNA (hepatitis A IgM confirmation)	Freeman Hospital, Newcastle	Serum / SST (ochre top)
Hepatitis B Markers	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
Hepatitis B Delta Antibody	PHE Colindale via serology at Freeman Hospital, Newcastle	Serum / SST (ochre top)
Hepatitis B Viral Load	PCR Laboratory, Freeman Hospital, Newcastle	Blood / EDTA (purple top) or Serum / SST (ochre top)
Hepatitis B Viral Load (Staff Screening)	West of Scotland Specialist Virology Centre	5 x EDTA (purple top)
Hepatitis C Antibody Confirmation	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
Hepatitis C Antigen	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
Hepatitis C Viral Load	PCR Laboratory, Freeman Hospital, Newcastle	Blood / EDTA (purple top) or Serum / SST (ochre top)
Hepatitis C Genotype	PCR Laboratory, Freeman Hospital, Newcastle	Blood / EDTA (purple top)
Hepatitis E IgM	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
Hepatitis E IgG	Serology, Freeman Hospital, Newcastle Hospital	Serum / SST (ochre top)
Hepatitis E RNA	Freeman Hospital, Newcastle will send sample to Virus Reference Department, PHE Colindale if get Hep E IgM positive	Blood / EDTA or Serum / SST (ochre top)
Herpes PCR	PCR Laboratory, Freeman Hospital, Newcastle	Viral swab (green)
Herpes Antibodies	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
HHV6 PCR	PCR Laboratory, Freeman Hospital, Newcastle	CSF / sterile universal or Blood / EDTA (purple top)
Legionella Urine Antigen	Serology, Freeman Hospital, Newcastle	Urine / sterile universal (white top)
Legionella Antibodies	No longer tested - see Legionella urine antigen test
Leishmaniasis	University College London (School of Tropical Medicine)	Serum / SST (ochre top)
Leptospirosis (Weils disease) Must be >7 days since onset of symptoms.	RIPL, PHE Porton	Serum / SST (ochre top)
Lymes Disease (Borrelia Antibodies)	Virology, Carlisle	Serum / SST (ochre top)
Malaria antibodies	Hospital of Tropical Diseases, University College London	Serum / SST (ochre top)
Malaria PCR	Malaria Reference Laboratory, London School of Hygiene & Tropical Medicine	Blood / EDTA (purple top)
Meningococcal PCR (see below)	Manchester Meningococcal Reference Laboratory	Blood / EDTA (purple top) or CSF / sterile universal
Meningococcal serology (surveillance)	Manchester Meningococcal Reference Laboratory	Blood / EDTA (purple top) <5 yr old also need serum / SST (ochre top)
Meningococcal serology (post vaccine)	Manchester Meningococcal Reference Laboratory	Blood / EDTA (purple top)
Mumps IgM	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
Mumps IgG	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
Mycobacteria / TB / AFB	TB Laboratory, Freeman Hospital, Newcastle	Sputum, BAL, tissues, fluids, CSF
Mycoplasma IgM (<16yrs old)	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
Mycoplasma IgG	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
Mycoplasma CFT (patients ≥16yrs old)	Infection Sciences, Bristol	Serum / SST (ochre top) Paired acute and convalescent samples sent.
Parvovirus IgM	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
Parvovirus IgG	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
Parvovirus PCR	Serology, Freeman Hospital, Newcastle ® Micropathology Ltd, Venture Centre, University of Warwick Science Park, Sir William Lyons Road, Coventry, CV4 7EZ	Blood / EDTA (purple top) or Serum / SST (ochre top)
PCP (Pneumocystis)	Microbiology, Freeman Hospital, Newcastle	Induced sputum or BAL
Pertussis Antibodies	RVPBRU, PHE Colindale	Serum / SST (ochre top)
Pertussis PCR	PCR Laboratory, Freeman Hospital, Newcastle	Nasopharyngeal secretions / dry swab or sterile universal.
Pneumococcal Antigen (blood)	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
Pneumococcal Antigen (urine)	Serology, Freeman Hospital, Newcastle	Urine / sterile universal (white top)
Pneumococcal Antibodies (blood)	Immunology, Carlisle	Serum / SST (ochre top)
Prevanar (pneumococcal) vaccine specific serotypes	Manchester Meningococcal Reference Laboratory	Serum / SST (ochre top)
Pneumococcal PCR (Blood, EDTA, CSF)	Manchester Meningococcal Reference Laboratory	Blood / EDTA or CSF / sterile universal
Psittacosis CFT	Infection Sciences, Bristol	Serum / SST (ochre top)
Q Fever (Coxiella burnetii)	Bristol Mycological Reference Laboratoryoratory	Serum / SST (ochre top)
Quantiferon Gold (see below)	TB Reference Laboratoryoratory, Freeman Hospital, Newcastle	QFG testing kit - contact laboratory for supply
Rabies Antibodies / Titres	Animal and Plant Health Agency, New Haw, Addlestone, Weybridge, Surrey, KT15 3NB	Serum / SST (ochre top)
West Nile Virus IgM	Rare and Imported Pathogens Laboratory, PHE Porton	Serum / SST (ochre top)
Tick Borne encephalitis Virus IgG (IF)
Japanese encephalitis virus IgG (IF)
Yellow Fever virus IgG (IF)
Chikungunya Virus IgG (EIA)
Chikungunya Virus IgM (EIA)
Chikungunya Virus RNA
V. equine encephalo. Virus IgG (IF)
Sandfly fever Sicilian virus IgG (IF)
Sandfly fever Naples virus IgG (IF)
Sandfly Toscana virus IgG (IF)
Sandfly Cyprus virus IgG (IF)
Spotted Fever Group IgM (IFA)
Spotted Fever Group IgG (IFA)
Epidemic Typhus Group IgM (IFA)
Epidemic Typhus Group IgG (IFA)
O. tsutsugamushi IgG (EIA)
O. tsutsugamushi IgM (EIA)
Rash (maculopapular) in pregnancy	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
Respiratory CFTs	Infection Sciences, Bristol	Serum / SST (ochre top)
Rickettsia	RIPL, PHE Porton	Serum / SST (ochre top)
Schistosoma (Bilharzia)	University College London (School of Tropical Medicine)	Serum / SST (ochre top)
Syphilis Confirmation	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
Syphilis screen (referred)	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
Syphilis PCR inc. HSV & H. ducreyi	STBRU, PHE Colindale	Swab of lesion / viral swab (green top) or dry swab (purple top)
Syphilis PCR on CSF (often organised through GUM)	PCR Laboratory, Freeman Hospital, Newcastle	Serum / SST (ochre top)
Swine Flu (as part of the respiratory viruses panel / flu screen)	PCR Laboratory, Freeman Hospital, Newcastle	Serum / SST (ochre top)
TATT screen	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
TB / AFB / Mycobacteria	TB Laboratory, Freeman Hospital, Newcastle	Sputum, BAL, tissues, fluids, CSF
Teicoplanin Levels	Bristol Antimicrobial Reference Laboratory	Serum / SST (ochre top)
Tetanus Antibodies	Immunology, Carlisle	Serum / SST (ochre top)
Thermoactinomyces PPT	Immunology, Carlisle	Serum / SST (ochre top)
Tobramycin Random Levels	Freeman Hospital, Newcastle	Serum / SST (ochre top)
Tobramycin Pre Dose Levels	Freeman Hospital, Newcastle	Serum / SST (ochre top)
Tobramycin Post Dose Levels	Freeman Hospital, Newcastle	Serum / SST (ochre top)
TORCH (mother)	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
TORCH (baby)	Serology / PCR Laboratory, Freeman Hospital, Newcastle	Serum / SST (ochre top)
Toxocara antibodies	University College London (School of Tropical Medicine)	Serum / SST (ochre top)
Toxoplasma IgM & IgG	Serology, Freeman Hospital, Newcastle	Serum / SST (ochre top)
Toxoplasma Dye Test	Toxoplasma Reference Laboratory, Swansea	Serum / SST (ochre top)
Varicella (Viral Swab)	PCR Laboratory, Freeman Hospital, Newcastle	Viral swab (green top)
Voriconazole level	Mycology Reference Centre, Manchester, Wythenshawe	Serum / SST (ochre top)
Weils Disease (Leptospirosis) Must be >7days since onset of symptoms	RIPL, PHE Porton	Serum / SST (ochre top)
West Nile Virus	RIPL, PHE Porton	Serum / SST (ochre top)
Zika Virus IgG (EIA) serum/ EDTA	RIPL, PHE Porton	Serum / SST (ochre top)
Zika Virus IgM (EIA) serum/EDTA	RIPL, PHE Porton	Serum / SST (ochre top)
Zika Virus PCR EDTA / urine	RIPL, PHE Porton	Serum / SST (ochre top)

What are turnaround times?

The local microbiology turnaround time (TAT) for each test is defined as the time of the receipt of the specimen into the pathology laboratories (UHND, BAGH or DMH) to the time when the report is available to the requester (electronically in most cases). TATs are specific to individual tests or specimen types.

How are average turnaround times measured in microbiology?

The average TAT for a test is determined using information from all of the tests performed in the previous year i.e. how long 'on average' they took from receipt to report. This data takes into account all tests, taken at all times, with all combinations of negative and positive results and follow-up work.

TATs can vary greatly depending on a number of factors including the time of receipt, culture or test result and priority of testing so the individual test results within this measured average TAT are usually spread over a wide timeframe.

Defined turnaround times in microbiology

Some microbiology tests have nationally agreed TATs, or are agreed with service users, for example antenatal screening tests and sexual health molecular tests. In these cases our local TAT are measured against these targets.

Why are microbiology turnaround times much longer than for other pathology services?

The majority of microbiology tests are still based on the culture of bacteria which require incubation for days rather than hours. Further confirmatory testing, e.g. antimicrobial sensitivity testing, also relies on the growth of the bacteria for a further period of time.

What about urgent results?

The TAT listed below are from the time of receipt to the finished report being available to the user. Interim reports may also be issued for urgent or partial results e.g. a microscopy result will be available within the same day but the culture result may take a further few days to complete the report.

The consultant microbiologists are informed of results that require notification prior to the completed report and contact the requesting clinician to advise as appropriate.

All urgent requests should be communicated to the laboratory e.g. CSFs, urgent gram stains, etc. See individual handbook pages for further details.

Turnaround Times in Microbiology

Test (C&S = culture and sensitivity)	Average Measured TAT to completed report (based on previous year)	Defined TAT to completed report (agreed or nationally defined target)
Bacteriology & Mycology
Blood culture C&S	<6 days	-
CSF C&S*	< 4 days	-
Ear swab C&S	< 5 days	-
Eye swab C&S	< 5 days	-
Faeces C&S, virology and parasitology	< 5 days	-
Sterile fluid C&S*	< 11 days	-
Genital swab C&S	< 5 days	-
N.gonorrhoeae (GC) C&S	< 5 days	-
MRSA screen	< 2 days	-
Nasal swab C&S	< 5 days	-
Mouth swab C&S	< 4 days	-
Mycology microscopy & culture	< 20 days	-
Pleural fluid C&S*	< 6 days	-
Pre-operative screening swab (S.aureus)	< 3 days	-
Sputum C&S	< 7 days	-
Tissue & biopsy C&S	< 13 days	-
Throat swab C&S	< 5 days	-
Urine microscopy, C&S	< 4 days	-
Wound swab	< 5 days	-
Molecular
Chlamydia trachomatis	<7 days	7 days
N.gonorrhoeae (GC)	< 7 days	7 days
Herpes Simplex Virus (HSV)	< 8 days	-
Serology
Antenatal screening	<7 days	8 days
Anti-Streptolysin O	<12 days	-
Hepatitis A Total Ab	<12 days	-
Hepatitis B Core Ab	<9 Days
Hepatitis B Surface Ab	<9 days	-
Hepatitis C Screen	<9 days	-
HIV Screen (non-neonatal)	<7 days	-
Syphilis Screen	<7 days	-