Metagenomics Pathogen Detection – Service Summary
Metagenomics is a broad-range test that utilises deep sequencing
to sequence total RNA and total DNA in a clinical specimen; this
has the potential for un-targeted pan-pathogen detection.
Metagenomics is particularly useful in difficult-to-diagnose
syndromes, such as encephalitis, in which an infectious aetiology
is suspected but cannot be identified by routine methods.
In CSF, the sensitivity is similar to targeted real-time PCR for
both RNA and DNA pathogens.
In tissue, the sensitivity for RNA viruses is similar to
targeted real-time PCR. For DNA viruses, bacteria and fungi the
sensitivity in tissue is reduced (approximately 100-fold) compared
to targeted real-time PCR but comparable to pan-bacterial and
pan-fungal PCR (16S and 18S). Low level DNA pathogens in tissue may
not be detected.
Please note this test is under on-going validation and as such
is not yet accredited by UKAS against ISO 15189:2012.
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Test Description
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Specimen required
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NHS Price
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Turnaround Time
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Request Form
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Metagenomics
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Tissue biopsy (fresh/frozen or FFPE)
CSF
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£1350
£700
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2-4 weeks
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Click here
for request form
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Specimen Requirements
Metagenomics is currently offered for tissue biopsies and CSF.
The recommended specimen type is fresh tissue collected directly
into RNALater.
See below for collection and storage requirements.
CSF
500 µl whole CSF (not filtered or centrifuged). We recommend
CSFs are stored at −80 °C within 24 hours of collection (maximum 72
hours) to minimise RNA degradation. CSF is not stable at room
temperature.
CSF collected with RNALater (1:4 ratio of RNALater:CSF) is
stable for up to 1 week at ambient temperature and at least 1 week
at +4 °C. CSF in RNALater can be shipped at ambient temperature or
with ice packs.
Smaller volumes, sub-optimal storage or any pre-processing (e.g.
filtering or centrifugation) will reduce ability to detect
pathogens.
Fresh tissue -
RNALater
Specimens must be collected directly into RNALater at the point
of collection (e.g. in theatre); this is to rapidly stabilise RNA
and prevent degradation. Specimens stabilised in RNALater can be
stored at room temperature for up to 1 week or at +4 °C for up to
one month prior to shipping.
Aliquots of RNALater are available on request from GOSH
Microbiology/Virology labs or from laboratory reagent
suppliers.
Fresh tissue -
Frozen
Specimens that are not stabilised in RNALater should be
immediately collected onto dry ice (e.g. in theatre) and stored at
−80 °C prior to shipping. It is important to avoid any freeze-thaw
cycles.
Fresh tissue -
unstabilised
Tissue that has not been immediately stabilised in RNALater nor
frozen is not recommended for metagenomics due to rapid degradation
of RNA. Tissue in saline is not suitable.
Please be aware sub-optimal specimen collection, storage or
transport will result in RNA degradation which will significantly
reduce ability to detect RNA pathogens.
FFPE (formalin
fixed paraffin embedded) tissue
4x 10 µm or 2 x 20 µm rolled sections
Please be aware the ability to detect low-level pathogens will
be reduced in FFPE tissue compared to fresh tissue due to
degradation of nucleic acid during formalin fixation. FFPE is a
sub-optimal specimen type but can be processed in the absence of
fresh tissue.
Specimen Transport
| Tissue in RNALater: |
Ambient temperature |
| FFPE: |
Ambient temperature |
| Frozen tissue: |
Dry ice |
| CSF: |
Dry ice |
Coming Soon
Metagenomics for other body fluids; including blood,
urine and respiratory specimens
Please send samples accompanied by request form
to:
Virology Laboratory
Level 4, Camelia Botnar Laboratories
Great Ormond Street Hospital for Children
Great Ormond Street
London WC1N 3JH
Hays Dx: GOSH DX 6640203, Bloomsbury 91 WC
General and Technical Enquiries:
Dr Julianne Brown
Tel: 020 7405 9200 Ext 5929
Email: Julianne.Brown@gosh.nhs.uk
Clinical Enquiries:
Professor Judy Breuer
Tel: 020 7405 9200 Ext 42129 / 020 3108 2130
Email: j.breuer@ucl.ac.uk
Relevant publications arising from metagenomics service
in our laboratory
1. Brown JR, Bharucha T and Breuer J (2018). Encephalitis
diagnosis using metagenomics: application of next generation
sequencing for undiagnosed cases. Journal of Infection, 76 (3):
225-240.
2. Bucciol G, Moens L, Payne K, Wollants E, Mekahli D,
Levtchenko E, Vermeulen F, Tousseyn T, Gray P, Ma CS, Tangye SG,
Van Ranst M, Brown JR, Breuer J and Meyts I (2018). Chronic Aichi
virus infection in a patient with X-linked Agammaglobulinemia,
Journal of Clinical Immunology, 38 (7): 748-752.
3. Morfopoulou S, Mee ET, Connaughton SM, Brown JR, Gilmour K,
Chong WK, Duprex WP, Ferguson D, Hubank M, Hutchinson C,
Kaliakatsos M, McQuaid S, Paine S, Plagnol V, Ruis C, Virasami A,
Zhan H, Jacques TS, Schepelmann S, Qasim W, Breuer J (2016). Deep
sequencing reveals persistence of cell-associated mumps vaccine
virus in chronic encephalitis, Acta Neuropathologica, 133 (1):
139-147.
4. Lum SH, Turner A, Guiver M, Bonney D, Martland T, Davies E,
Newbould M, Brown J, Morfopoulou S, Breuer J, Wynn R (2016). An
emerging opportunistic infection: fatal astrovirus (VA1/HMO-C)
encephalitis in a pediatric stem cell transplant recipient,
Transplant Infectious Disease, 18(6): 960-964
5. Morfopoulou S, Brown JR, Davies EG,
Anderson G, Virasami A, Qasim W, Chong WK, Hubank
M, Plagnol V, Desforges M, Jacques TS, Talbot
PJ, Breuer J (2016). Coronavirus HCoV-OC43 Associated with
Fatal Encephalitis, New England Journal of Medicine, 375(5):
497-8.
6. Duncan JAD, Mohamad SMB, Young DF, Skelton AJ, Leahy TR,
Munday DC, Butler KM, Morfopoulou S, Brown JR, Hubank M, Connell J,
Gavin PJ, McMahon C, Dempsey E, Lynch NE, Jacques TS, Valappil M,
Cant AJ, Beuer J, Engelhardt KR, Randall RE and Hambleton S (2015).
Human IFNAR2 deficiency: Lessons for antiviral immunity, Science
Translational Methods, 7 (307).
7. Brown JR, Morfopoulou S, Hubb J, Emmett WA, Ip W, Shah D,
Brooks T, Paine SML, Anderson G, Virasami A, Tong CY W, Clark
DA, Plagnol V, Jacques TS, Qasim W, Hubank M, Breuer J (2015).
Astrovirus VA1/HMO-C: an increasingly recognised neurotropic
pathogen in immunocompromised patients. Clinical Infectious
Diseases, 60 (6): 881-888.