Category: News

Dear Client,

We are writing to update our users that we have made the transition from the Roche cobas 4800 platform to the Roche cobas 5800 instruments for HCV RNA and HIV-1 RNA quantitation assays.

As management and monitoring of HCV and HIV-1 infection continues to move forward, and in the light of increased test requests from our users, including the necessity to act at short notice as contingency for many laboratories around the UK, it is important to continue to strive to use the most appropriate instruments and assays that will continue to enable service provision for the future.

As part of our ongoing quality improvement of procedures at Micropathology Ltd, we replaced the Roche cobas 4800 HIV-1 and HCV quantification IVD/CE-marked assays with those for the new cobas 5800 system in January 2023. We have verified both assays and validated the HIV-1 RNA quantitation assay for CSF, as well as EDTA plasma. Results generated by the cobas 5800 HCV RNA and HIV-1 RNA assays are comparable to those produced by the outgoing cobas 4800 system and have been verified/validated against the relevant higher order reference standards. At the end of January 2023, Roche installed our second cobas 5800 instrument.

This change ensures we continue to meet the needs and requirements of users, while significantly increasing testing capacity and local contingency. We currently have the capacity to run more than 480 samples per day across our entire user base, meaning that we can rapidly respond to requests for processing of backlog samples from our users that do not ordinarily use this service in the event that contingency measures are required, by prior arrangement. Please contact us should you require this service.

These assays have the same reportable results ranges that we currently generate, and the chemistry remains unchanged (HCV and HIV-1 lower limits for quantitation are 15 IU/mL and 20 copies/mL, respectively). 

The Cobas 5800 quantitative assays requires a lower minimum volume of serum / plasma than the 4800 instrument, but we would like to continue to request that clients send at least 1.2 mL serum or plasma separated within the first 24 hours post blood draw to enable seamless continuation of service when we switch over in the coming months.

CSF is not validated by the manufacturer for the HIV-1 assay; however, we have validated this sample type in-house to enable testing to be performed and so respond to clinical needs, in the same way that we currently have for the current instrument. The new cobas 5800 instrument is comparable to the cobas 4800 in terms of result generation and report format.

Please note that serum will remain as an unvalidated sample type on the Cobas 5800 HIV-1 assay.  

We have also verified the cobas 5800 instrument for HBV DNA quantitation. This is to enable us to perform EPP worker monitoring in the future. It will also allow us to rapidly expand testing capacity, should users require it.

If you wish to discuss this in more detail, please contact us by telephone (02476 323222) or email (info@micropathology.com).

Yours Sincerely,

Dr Paul Scott (Clinical Scientist – Virology).

We are pleased to announce the launch of a probe based carbapenem resistance gene detection assay at Micropathology Ltd.

Carbapenems constitute some of the most effective and broadest-spectrum antibiotics available and are typically reserved for severe and multi-drug-resistant infections. Acquired carbapenemases are enzymes which inactivate carbapenems and most other β-lactam antibiotics, including penicillins and cephalosporins, and can result in infections with severely limited treatment options. At Micropathology, we have developed a probe based multiplex qPCR assay that is rapidly capable of detecting the ‘big five’ prominent carbapenemase resistance gene families including bla_KPC, bla_IMP-1, bla_VIM, bla_NDM-1 and bla_OXA-48-like.
See below for genes that are detectable using our assay:

Carbapenemase Family	Variants
blaKPC	KPC-2-8, KPC-10-19, KPC-21-123, KPC-125-128, KPC-130-135, KPC138-148, KPC-151, KPC-153, KPC-155-157
blaNDM	NDM-1-31, NDM-33-50 (including NDM-16a and NDM-16b)
blaVIM	VIM-1-20, VIM-23-80, VIM 82-83, VIM-86
blaIMP	MP-1, IMP-3, IMP-6, IMP-10, IMP-25, IMP-30, IMP-34, IMP-40, IMP-42, IMP-52, IMP-55, IMP-60, IMP-61, IMP-66, IMP-70 IMP-76, IMP-77, IMP-78, IMP-79, IMP-80, IMP-88, IMP-97, IMP-98,
blaOXA-48-like	OXA-48, OXA-162, OXA-163, OXA-181, OXA-199, OXA-204, OXA-232, OXA-244, OXA-245, OXA-247, OXA-252, OXA-370, OXA-405, OXA-416, OXA-438, OXA-439, OXA-484, OXA-505, OXA-514, OXA-515, OXA-517, OXA-519, OXA-538, OXA-546, OXA-547, OXA-566, OXA-567, OXA–788, OXA-793, OXA-833, OXA-894, OXA-918, OXA-920, OXA-922, OXA-923, OXA-924, OXA-929, OXA-933, OXA-934, OXA-1038, OXA-1039, OXA-1055, OXA-1119, OXA-1146, OXA-1181

Assay sensitivity for all five targets is approximately 200copies/mL and the current test turnaround time is 3 days from sample receipt. The assay is validated for various sample types including faecal swabs, faeces, tissue, cultures, EDTA WB, eye fluid, joint fluids and urine.

If you have any questions or require further information about the carbapenem resistance gene detection assay, please email info@micropathology.com or phone 02476 323222.

We are pleased to announce our transition to a new next-generation sequencing (NGS) drug resistance screening service, which provides improved detection capabilities over traditional Sanger based drug resistance screening  for low-level drug resistance mutations. Our NGS screening assays can reliably detect drug resistance mutations as low as 5% frequency within the viral population (compared to traditional Sanger methods which typically detect mutations at 15-20% frequency).

With enhanced NGS capabilities, we aim to incorporate sub-population percentages for drug resistance mutations into your result reports in order to support clinical decision-making for treatment strategies.  For instance, upon detecting mutations such as M184MV, we will provide more detailed information on the proportion present in the specimen (e.g., M184MV (M184V present at 25%).

We understand that rapid turnaround from sample receipt to result is very important to our clients and therefore we are conducting our improved NGS drug resistance screening service with equivalent turnaround times to our current Sanger based screening methods.

The following drug resistance screening assays will now be conducted using our NGS assay:

Virus	Assay Targets	Turnaround Time
HIV-1	Protease, Reverse Transcriptase, Integrase	9 working days
HSV-1	UL23, UL30	9 working days
CMV	UL54, UL97. UL56, UL89	9 working days
HBV	RT domain	9 working days

If you have any questions or require further information about our NGS drug resistance screening service, please email info@micropathology.com or phone 02476 323222.