July 2020 Newsletter

SARS- CoV-2 images

UK NEQAS for Microbiology

WHAT'S NEW?

Resuming of UK NEQAS Microbiology EQA services 2020-2020

In the UK, employees of UK NEQAS for Microbiology are embedded within Public Health England (PHE), its host organisation. PHE is a Category 1 responder to major public health incidents on behalf of the UK government. The suspension to our EQA service was a result of re-prioritisation of our activities to allow staff to assist with the COVID-19 pandemic. Many of the team were asked to assist with testing and providing support towards testing, working in the incident response centres, maintaining supply chain. This lead to a temporary suspension of EQA distributions between the months of April to July.

Whilst the COVID-19 response remains a priority, we are now in a position to be able to resume our services for this financial year (from August 2020 to March 2021), with a revised timetable (ukneqasmicro.org.uk/participant-info/distribution-timetable). The timetable details a reduced frequency of distributions for this year, which reflects reduced staffing available, our ability to keep staff safe and for us to comply with UK government guidance in place. However we have added a new Molecular detection of SARS-CoV-2 EQA, introduced to ensure laboratories are quality assessed for this test.
Please contact your distributor to register, or for participants not served by a distributor, email us at, organiser@ukneqasmicro.org.uk. This EQA complements the SARS-CoV-2 antibody EQA being run from UK NEQAS for Immunology, Immunochemistry & Allergy in Sheffield.

Teaching programmes: the Mycology teaching workshop will be cancelled for 2020/21. Parasitology teaching programmes will commence from August and details have been provided by the Parasitology teaching team on how these will go ahead.
A new workshop “back to basics” is in the process of being developed. Further details are included within this newsletter.

We would like to thank all our participants and distributors for being understanding and patient during this time.

Dear Participants,

Nita Patel Interim Head

I felt honoured and privileged to be asked to be the interim Head of United Kingdom National External Quality Assessment Service (UK NEQAS) for Microbiology on 3 March 2020. I have a wealth of experience in EQA and since June 2012 I have been the Scheme Organiser for the Food and Environmental Proficiency Testing Unit (FEPTU) which provides an EQA service to laboratories that tests food, water and environmental samples.

I am committed to ensure that the services provided by UK NEQAS Microbiology continue to meet the high standards that you already expect and I will be working with the rest of the team to further develop and improve the UK NEQAS EQA schemes for clinical laboratories.

It is interesting where your career path can take you, my previous experience includes 15 years working as part of UK NEQAS Microbiology, my responsibilities included a role in the development of EQA schemes, collaborative working with colleagues and stakeholders, and raising the profile, nationally and internationally, EQA services.

I am excited about this challenging role and I am looking forward to working with you to meet your EQA requirements in a rapidly changing environment for clinical testing. I am confident that the exceptional services provided by UK NEQAS will continue and I can assure you that your vested interest remains the number one priority for me.

Kind regards

Nita

Jaya Shrivastava selected to the ECCMID ESGCP executive committee:

Jaya has won the election for the ESGCP (ECCMID study group for Clinical Parasitology) executive committee. She will hold the term for two years and will take on the role of Education officer.

COVID-19 associated pulmonary aspergillosis

Professor Andrew Borman
PHE Mycology Reference Laboratory

COVID-19 associated pulmonary aspergillosis (CAPA) was recently reported as a potential infective complication affecting critically ill patients with acute respiratory distress syndrome following SARS-CoV-2 infection, with incidence rates varying from 8 to 33% depending on the study. However, definitive diagnosis of CAPA is challenging. Standardised diagnostic algorithms and definitions are lacking, clinicians are reticent to perform aerosol-generating bronchoalveolar lavages (BAL) for galactomannan testing and microscopic and cultural examination, and questions surround the diagnostic sensitivity of different serum biomarkers. Between 11th March and 14th July 2020, the UK National Mycology Reference Laboratory received 1267 serum and respiratory samples from 719 critically ill UK patients with COVID-19 and suspected pulmonary aspergillosis.

The laboratory also received 46 isolates of Aspergillus fumigatus from BAL, non-directed BAL (NBL) and tracheal aspirate (TA) secretions from COVID-19 patients. Three of these isolates exhibited resistance to the triazole antifungal drugs ruling out use of therapeutic voriconazole in these patients and raising the issue of increasing numbers of strains of Aspergillus fumigatus in the environment developing resistance to clinical azoles following exposure to environmental azoles used as crop protection. The commercial molecular Aspergenius™ assay was used to confirm presence of the mutations consistent with development of resistance due to environmental exposure.

We received respiratory specimens (bronchoalveloar lavages, tracheal aspirates, sputum samples) from a subset of 61 patients in additional to serum samples submitted and subjected to galactomannan testing, Aspergillus-specific PCR and microscopy and culture. The respiratory samples obviously represented a high potential infection risk so were only handled in the Containment Level 3 laboratory. Doubling gloving was employed within the Bio Safety cabinet and microscopic mounts prepared with calcofluor and KOH were sealed around with nail varnish and wiped down before removal from the cabinet for microscopic examination. The incidence of probable/proven and possible CAPA in this subset of patients was approximately 5% and 15%, respectively. Overall, our results highlight the challenges in biomarker-driven diagnosis of CAPA especially when only limited clinical samples are available for testing, and the importance of a multi-modal diagnostic approach involving regular and repeat testing of both serum and respiratory samples.

Membership for the Virology Specialists Advisory Group (VSAG) of United Kingdom National External Quality Assessment Service (UK NEQAS) – Microbiology Division

The Chair for UK NEQAS for Microbiology Virology Specialists Advisory Group (VSAG), Dr Matthew Donati, is inviting applications for a medically qualified clinical virologist.

The VSAG members are independent experts that advise UK NEQAS on Virology schemes.

About membership to VSAG

EQA is very important in improving patient outcome by monitoring the performance of participating laboratories and ensuring more accountability.

The members of VSAG will be practicing experts in the field of virology and will provide advice on formulation and delivery of new External Quality Assessment (EQA) for virology laboratories in the UK and worldwide. All VSAG members must work collaboratively with the chair, other members of the Microbiology Steering Committee, the different scheme organisers and managers to provide strategic and technical advice and help with responses to challenges on EQA.

Members of the VSAG are drawn from different professional backgrounds but have equally important roles in contributing to the group’s discussion and advice.

Members’ independence must be beyond question. The member should not be employed by, or receive personal remuneration from industrial organisations or pressure groups that can have an impact or influence on EQA delivery during his or her term of appointment.

Membership of VSAG is a honorary position without a salary, but reasonable travel expenses for attendance of meetings can be claimed.

There is one half day meeting per year which is likely to increase to two with one being virtual, with occasional advisory work necessary by correspondence throughout a year.

Current Vacancy

The VSAG functions best when there is representation from different professional backgrounds from the field of clinical and laboratory virology. The current vacancy is a replacement and is for a medical virologist with a clinical medicine training background. The candidate must understand EQA and have experience of an environment regularly using EQA.

About UK NEQAS Microbiology Division

The Microbiology division (http://www.ukneqasmicro.org.uk) of United Kingdom National External Quality Assessment Service (UK NEQAS) was established in 1971 providing external quality assessment service in the field of Microbiology.

It forms part of the UK NEQAS, (https://ukneqas.org.uk) a not for profit consortium of EQA providers in the UK. The income generated by participant subscriptions is used to for the delivery of schemes the participants subscribe to and for the development of new EQA schemes for the interest of patients. Equality, diversity and inclusion is very important to us and we employ staff from diverse backgrounds to deliver our work.

Currently there are more than 50 schemes that are offered which are UKAS accredited to the ISO/IEC 17043:2010 standards. There are several new schemes under development.

How to apply

If you are interested to join the VSAG of UK NEQAS, please send your current curriculum vitae and a covering letter indicating why you would be suitable for this position to Dr Sanjiv Rughooputh, who will also be very happy to answer any further questions that you may have.

Contact
Dr Sanjiv Rughooputh
UKNEQAS for Microbiology
National Infection Service
Public Health England
61 Colindale Avenue
London
NW9 5EQ
Email: sanjiv.rughooputh@phe.gov.uk
Tel :(+44) 0208 327 6913

COVID-19 UPDATES

Molecular detection of SARS-CoV-2 EQA

Sanjiv Rughooputh
Virology Scheme Organiser

Coronaviruses (CoVs), are single stranded RNA viruses that can infect animals and humans, causing respiratory, gastrointestinal, hepatic, and neurologic diseases.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing Coronavirus disease 2019 (COVID-19), was first reported in Wuhan, China, in December, 2019. Subsequently due to its rapid spread, on 30th January 2020, the World Health Organization (WHO) declared COVID-19 as a PHEIC “Public Health Emergency of International Concern”.

According to the latest updates from WHO (21st June 2020), the virus has been detected in 216 countries with almost 9 million confirmed cases of COVID-19 worldwide resulting in over 460,000 confirmed deaths.

This unprecedented pandemic caused by SARS-CoV-2 has posed challenges for public health laboratories in the UK and worldwide that have to cope with the increase in testing demands to identify and maintain the required containment of infected individuals as well as delay and mitigation of spread of the disease.

Molecular detection of the viral nucleic acid by Nucleic acid amplification test (NAAT) including reverse transcriptase(RT) quantitative PCR based on oral swabs are the methods of choice for the confirmation of COVID-19 disease.

This fast progression of the COVID-19 pandemic resulted in laboratories introducing NAAT based tests rapidly with varying level of sensitivities and specificity.

In order to assess laboratories performing molecular detection of SARS-CoV-2 by enabling them to monitor, evaluate and improve their own performance, UK NEQAS for Microbiology in collaboration with the UK NEQAS board of trustees and the UK NEQAS consortium distributed a first pilot study to over 100 testing laboratories in the UK and Northern Ireland.

This first pilot study was operated in collaboration with the National Institute of Biological Standards (NIBSC) supported by the Department of Health and Social Care (DHSC) and NHS England.

The first pilot study consisting of three frozen specimens were dispatched on the 21st May 2020, a prompt turnaround time of results (TAT) was expected and close of the distribution was set for Thursday 25th May.

The overall performance in this distribution was excellent with 98.3 % of participants returning the intended results.

There is an increased interest for the UK NEQAS Molecular detection of SARS-CoV-2 EQA with over 125 participants expressing interest to participate in the second pilot dispatched on the 25th June 2020, where additional data will be collected, analysed and presented in the distribution report. In these pilot studies, the simulated specimens were composed of a matrix that required maintenance in a frozen status and therefore shipment outside the UK was unfortunately not possible.

Due to the global importance of such an EQA and the overwhelming interest from participants, UK NEQAS for Microbiology is pleased to announce that a live scheme has been introduced and wil be dispatched on a monthly basis starting from August dispatch- please see section for New Schemes for more information.

Testing Support Cell

Belinda Stobbs (PA/Office Manager)

The Testing Support Cell was set up over the Easter weekend to support London Coronavirus Response Centre (LCRC). The Testing Support Cell has the responsibility of sending swabbing kits to care homes across London.

Registered adult care homes could apply for coronavirus tests via their local Health Protection Team, when they suspected that they had a coronavirus outbreak in their care home

There was a call out in April for assistance in getting swab kits out to care homes. My name was put forward as someone that may be able to assist.

I was delighted that someone thought that I could be useful in assisting with helping with this COVID-19 pandemic.  Especially as I am not a Biomedical Scientist and I was not sure how or where I could contribute best to the response. My current role is PA/Office Manager in UK NEQAS for Microbiology.

Luckily the volunteering role related to administration tasks and not any clever scientific stuff in the laboratory.  The role involved liaising with the London Response Team and care homes.

Thankfully I was supervised by Lynne Foster, Business Manager, Laboratories – Operations and Infrastructure National Infection Service at Public Health England. Lynne is a dedicated, hardworking, kind and organised colleague that has the patience of a saint, and provided  training and guidance.

I am part of a rota’d team committed to providing 7-day support to LCRC by arranging testing kits for distribution to care homes.  These vital test kits provide residents and frontline staff an opportunity to determine whether or not they are infected with the virus. If tested positive, they can promptly self-isolate to ultimately protect other vulnerable residents within the care home.

My role included, managing incoming Request forms from LCRC, updating records, corresponding with the LCRC team, and care home managers and staff,  processed the incoming orders and packaged the swab kits, which ranged in various sizes from two to 200 swabbing kits and arranged couriers for same day dispatch.  Additionally, arranging courier collections for the completed swab tests, to return to Colindale for laboratory testing.  To date over 15,500 swabbing kits have been sent to over 340 care homes across London.

I am really enjoying working in this team and will continue to, as long as I am needed.

Virology Cell

Li Sa Choo
Specialist Health care Scientist Research and Development

Since February 2020, I have been volunteering in the Virology Cell which is part of PHE’s COVID-19 incident response. The Virology Cell is responsible for supporting the incident by providing expert virology scientific, technical and clinical advice in the form of email responses, advice documents, guidance, and scientific publications.

As a Task Manager, my role is to be the primary contact for the Cell Lead and have oversight of the cell’s mailbox. I co-ordinate responses to any queries that come through to the cell which often have very tight deadlines. I communicate closely with people working across the incident to ensure that input is received in response to questions. Queries vary and can come from any of: the public, NHS, internally, academic organisations, Parliamentary, etc.

From the start, the cell has been a very fast-paced and high-pressure environment to work in, and I have enjoyed it greatly. Each day is different and I have had the chance to work with people that I wouldn’t ordinarily have in my day to day role. I have learned a lot and it has been very rewarding to take on more responsibility and be involved in a key part of the UK’s Coronavirus response.

PCR Testing COVID-19

By Vuyelwa Nkomo

I have found doing COVID-19 work very interesting and an educational time for me. I have been involved with the primer, probe and reagent validations that were needed for the testing. This involved reconstituting the primers and probes, and making them up to working stock, as well as testing them against in-use primers and probes to ensure that they were suitable to be used. The same method was used for the reagents as well.

I really enjoyed helping train other members of staff and guiding them with their knowledge and understanding of how the process works. This all helped create a robust system, with a team of people that were able to ensure business continuity. Overall, this has been a very rewarding experience for me.

PHE call for COVID-19 volunteer- feedback of experience

by Teodoro Fajardo – Healthcare Scientist Team Manager

I lead and coordinated a team to assist PHE with ensuring there was a steady supply of prepared reagents that were used in the testing of SARS-CoV-2. This required the efforts of many staff to ensure these reagents were always available and communications to allow the team was responsive to changes in requirements for testing over the course of the pandemic. This ensured that testing of specimens could be maintained.

This activity required commitment and focus from all involved and made me feel proud of my contribution towards the organisations efforts during COVID-19.

UK NEQAS Placement Student experience: Completing my portfolio during the COVID-19 pandemic

                            By Louise Twi-Yeboah

The period of time from when the COVID-19 pandemic took place in the UK till present has resulted in a lot of adjustments including for me as the placement student within UK NEQAS Microbiology for 2020-21. During the COVID-19 lockdown, I was unable to continue training within the laboratory and was limited to the resources available online. I used this time as an opportunity to dedicate to my IBMS Registration Training Portfolio.

This was a particularly challenging task, as so far, I had been working in the laboratory whilst completing the portfolio. This balance had aided the process as my laboratory training allowed me to understand the concepts addressed within the portfolio.

To overcome these challenges, I have remained in contact with a variety of staff members across UK NEQAS Microbiology, finding alternative ways to communicate. The use of digital and electronic methods such as Skype and Zoom meetings have been a great benefit at this time.  Additionally, I have had to become more resourceful by finding various ways to obtain information and develop my understanding of these topics. This has included utilising documents, such as Standard Operating Procedures electronically (Q-pulse) and UK SMI manuals. Following on, I have conducted further research to ensure that I have fully understood concepts, as well as comparing sources to ensure information is up to date.

Although, this has been a challenging process, it has also been rewarding as I have developed many skills, such as adaptability, resilience, and proactivity. Numerous activities that had been scheduled as part of my training and student experience had been cancelled or altered to fit a digital version. This required me to show a degree of flexibility, to utilise my own initiative and to ask for help when needed.

Self-motivation and discipline have been a key part of this process as I have been working outside of my usual professional environment and at times outside of the plans, I had set for myself. To ensure productivity, I have had to remain focused and determined throughout this time.

The aspect I have struggled the most with has been working outside of the laboratory as I have missed the practical elements of my training. Additionally, I have missed working alongside my team members. The greatest benefit has been learning how to adapt and utilise time to gain the most out of a situation.

This process was made achievable through the help and support of my UK NEQAS Microbiology colleagues.

candidaAuris

SCHEME UPDATES

General bacteriology

We are always looking at improvements to our schemes, especially those which would make the scheme more aligned with routine practices in clinical diagnostic laboratories. It is therefore our aim to introduce urine quantification within the General bacteriology scheme. There are currently several culture methods used in the quantification of urine, including the calibrated loop technique, multipoint technology and the sterile filter paper strip method. Research has illustrated that bacterial counts of ≥108 cfu/L (≥105 cfu/mL) are indicative of infection in the large majority of patients. However, there are certain circumstances where clinical information provided should be taken into account, as lower bacterial numbers can be significant in certain patient groups. As urine quantification is being introduced, it will not be scored initially whilst we evaluate the results. This will be reviewed going forward.

Antimicrobial susceptibility

Expert commentary is a valuable source of feedback given as part of the Antimicrobial susceptibility scheme. Over the last year our participants have experienced severe delays with receiving this information as part of their report and performance analysis, we sincerely apologise for the delay in expert comments published for this scheme. As a resolution for this discrepancy, we are working towards publication of a document which will include all expert comments for the duration of 2019-2020. This will also contain detailed information on the scheme including a ‘frequently asked questions’ section. The document will be emailed to all participants and made available to view on our website. Going forward, we are actively working towards ensuring there are mechanisms in place, with the aim to prevent the delay of the expert comments in prospective distributions.

Scheme specific updates…

1. Following the inclusion of various clinical sites (e.g. sterile fluids, CSF, wound, respiratory), is the standardisation of the antibiotic panels (soon to be available on our website). These panels were devised in consultation with an external specialist advisory group.

2. A mini questionnaire will be accompanying the first distribution dispatched on the 3rd August, to collate method data. This will allow to identify the methods used for Antimicrobial susceptibility by all participants, with the aim to change the presentation of reports. Methods used will replace the histograms, currently displaying the zone diameter using disk diffusion. Illustrating the methods used by participants will hopefully prove a more useful tool when reviewing reports.

3. From previous distributions over 2019-2020, there are has been a significant decline in the number of participants reporting following CLSI guidelines. It has been decided by the advisory group that from August 2020, participants reporting results following CLSI guidelines will not be analysed in the contents of expert comments, This is because, there is insufficient data (<12% of participants using this method) to conduct accurate analysis.

We also recently advertised an ‘expression of interest’ for a new member to our specialist advisory group has been recently advertised. This group is made up of independent experts, who provide information and contribute to discussions on which isolates with varying antibiograms are to be included in the scheme.

Scheme Updates: Parasitology

Publication from our work on WHO Malaria Molecular scheme:

On 30th March, 2020 the Parasitology team published results of the global malaria EQA scheme that is run collaboratively with the WHO.

Results from the first three rounds were published in the Malaria journal. (https://malariajournal.biomedcentral.com/articles/10.1186/s12936-020-03200-0).
Salient feature of this publication was that the work proved the need for a robust EQA scheme for nucleic acid detection of Malaria and the utility of such schemes in safeguarding the reliability of clinical diagnoses.

Mycology Teaching Workshop, January 2020

 

UK NEQAS for Microbiology delivered another successful round of the three one-day mycology workshops with attendance by 120 delegates attended over the three days. The course is aimed at beginners: for those interested in looking at furry fungi and becoming confident in handling and identifying them.

To kick off the course, the one day sessions included a presentation on the introduction to the diagnosis of fungal infections—including identification of fungi the traditional conventional way.

Delegates had the opportunity to handle of over 40 different species of filamentous fungi for physical macroscopic and microscopic examination.

The sessions were this time held on the 14th, 15th and 16th January 2020 at a new venue, the ‘Superlab’ based in the London Metropolitan University located in North London, which has the capacity to hold 240 students/delegates. The venue allowed each delegates workstation to have their own monitor and headphones so the presentation could be clearly heard and slides easily viewed. The attendees had plenty of room to manoeuvre and converse with each other exchanging experience and ideas.

We had a team of assistants to help with scientific and technical queries thereby providing hands on teaching to all delegates.

During the course, delegates were also given the opportunity to examine unknowns to test their learning from the workshop, this was well received 😊
The feedback from our delegates from the UK and overseas (combination of clinical scientists, biomedical scientists and medics) was an overwhelming positive one! 100% of all delegates would recommend this course to their colleagues.

 

Mycology Teaching Workshop 2020/21

Due to the current COVID-19 pandemic and implementation of UK governmental social distancing guidelines, we have taken the difficult decision to postpone the workshops for this year.

We hope to re-introduce the workshop in the new financial year (as from April 2021) and information will be available during our re-registration processes undertaken in the new year.

Parasitology Teaching Workshop

 

Parasitology teaching going electronic:In their responses to COVID-19, universities closed for face-to-face teaching and moved to on-line systems. That meant the Parasitology Teaching Scheme, which relied on use of a laboratory to enable hands-on practical learning, could not run in those institutions. Therefore, we had no alternative but to cancel some of our regional teaching. The need for continuing education and training in Parasitology remains and we are keen to ensure that participants do not miss out on this.

If it proves impossible to run face-to-face teaching due to non-availability of a suitable laboratory, we shall provide on-line teaching. This will consist of lectures, morphology demonstrations and the ability to ask questions via the chat room facility in the on-line system. On-line teaching will NOT be limited to two students from each laboratory, so as many staff who wish to take part will be able to do so, subject to their manager’s approval, at no extra charge. We shall also continue to provide each laboratory with a bench-side manual and a set of take-home slides, as we currently do for laboratories which send students to the face-to-face teaching.

 

Rapid identification of Candida auris isolates

Professor Elizabeth M. Johnson
PHE Mycology Reference Laboratory

The pathogenic yeast Candida auris is quite unlike other yeast species in that it can spread readily from patient to patient, persist in the environment and often shows reduced susceptibility to azole, and sometimes other antifungal drugs. It has been responsible for multiple nosocomial outbreaks worldwide, including three in the UK, many of which have proved hard to control and are still on-going. Patients with Candida auris infection and/or colonisation should be isolated or cohorted and barrier nursed. However, it can be laborious to identify colonised patients, requiring multiple surveillance cultures. These are often performed by swabbing key body areas such as nose, axilla and groin onto Sabouraud’s agar, incubating the plates and identifying any resultant yeast colonies by MALDI-ToF MS. Many of these will prove to be other harmless commensal yeast species.
The Mycology Reference Laboratory has recently been involved in validation of a novel chromogenic agar CHROMagar™ Candida Plus that permits the rapid identification of Candida auris (1). On this agar isolates of Candida auris appear as white colonies with a blue halo after 36 h incubation at 35oC.

Figure 1 illustrates the differential appearance of yeast colonies on this agar. The first 10 spots are isolates of Candida auris representative of clades I – IV and all show the distinctive cream colony with a clear blue halo. The remainder include different, common commensal yeast isolates such as Candida tropicalis in spot 14, Pichi kudriazeveii (Candida krusei) in spot 15, Nakaseomyces (Candida ) glabrata in spot 16,Candida albicans in spot 17 and Candida parapsilosis in spot 18. In all we tested 74 different yeast isolates from 50 different species, including those species closely related to Candida auris and only the vanishingly rare Candida diddensiae gave a similar appearance.

Figure 2 shows a mixture of Candida auris (cream colonies with distinctive blue halos) and Saccharomyces cerevisiae (magenta colonies) grown on CHROMagarTM Candida Plus (upper hemisphere) and conventional Sabouraud dextrose agar containing chloramphenicol (lower hemisphere). This clearly demonstrates the ease with which Candida auris colonies can be distinguished from other yeast when grown in mixed culture and suggests this novel agar may be very helpful in distinguishing colonised patients in a timely fashion.

1. Borman AM, Fraser M and Johnson EM. CHROMagar™ Candida Plus: A novel chromogenic agar that permits the rapid identification of Candida auris. Medical Mycology, 2020, 0, 1–6 doi:10.1093/mmy/myaa049

candidaAuris2

NEW PILOTS AND SCHEMES

Molecular detection of SARS-CoV-2

As many countries all over the world are navigating their way out of the Covid-19- pandemic accurate diagnostic testing for SARS-CoV-2 by molecular methods to kerb the viral transmission, is becoming crucial.

UK NEQAS for Microbiology is pleased to announce the launch of a new External Quality Assessment (EQA) scheme ‘Molecular detection of SARS-CoV-2’, with the first live distribution going out on the 3rd of August 2020.
‘Molecular detection of SARS-CoV-2’ EQA scheme will be distributed monthly until March 2021, with two lyophilised specimens included in each distribution. The freeze-dried format of the samples is suitable for global shipment. Specimens aim to simulate clinical material in all aspects and will contain cellular material to mimic respiratory sites, thus making them suitable for tests that include cellular targets as controls.

Participants will initially be asked to assess the specimens for the presence or absence of SARS-CoV-2 nucleic material. However, going forward we aim to provide samples suitable for SARS-CoV-2 antigen testing as part of the ‘Molecular testing of SARS-CoV-2’ EQA scheme.

Two pilot distributions of ‘Molecular detection of SARS-CoV-2’ were dispatched on the 21st of May 2020 and the 25th of June 2020 to laboratories in the United Kingdom and Ireland. Information gathered during the pilot distributions has helped to inform specimen design for the upcoming scheme.

Given the potential impact of false-positive and false-negative results on patients and the wider public this EQA scheme will aim to frequently challenge testing platforms and routinely provide participating laboratories with educational specimens.
UK NEQAS is a non-profit organisation and the ‘Molecular detection of SARS-CoV-2‘ will be run on a minimal cost-recovery basis. As Covid-19 is already presenting a huge burden on healthcare systems globally we aim to keep the cost of the EQA scheme as low as possible for our participants.

For more information please e-mail organiser@ukneqasmicro.org.uk. Alternatively, laboratories from outside of the United Kingdom who have a UK NEQAS for Microbiology distributor in their area should contact the distributor directly.

Launch of new scheme for molecular detection of Faecal parasites:

On 3rd March 2020 UK NEQAS Parasitology distributed the first pilot for its brand new molecular scheme- Faecal molecular. 95 labs participated in this first pilot. Results of this pilot was presented at the ECCMID 2020 via inclusion in its abstract book.

The EQA scheme has been set up for molecular detection of faecal pathogens- Giardia, Cryptosporidium and E.histolytica in the first instance. The EQA scheme has been designed to match the advent of molecular methodologies, especially RT-multiplex PCR towards detection of faecal pathogens.

Based on the success of the pilot scheme- the scheme is now set to go LIVE from August 2020. Samples will be supplied as freeze dried faecal specimens and there will be two distributions in one calendar year. 3 specimens will be distributed for each round.

 

EQA in development: for the molecular detection of bacterial pathogens associated with gastrointestinal disease: The future of syndromic external quality assessment

By Natasha Bundock, Healthcare Scientist Specialist,

UK NEQAS for Microbiology

Gastrointestinal disease most commonly presents as gastroenteritis where symptoms are usually mild diarrhoea, abdominal discomfort and fever and is usually self-limiting but can lead to more serious conditions. Campylobacter species are most commonly associated with gastroenteritis (Standards for microbiology investigation, 2014). Other causes include some of the hazard group 2 (HG2) Salmonella species, Plesiomonas shigelloides and Shigella spp
More severe diseases are enteric fever, which is an invasive disease commonly caused by Salmonella Typhi and Paratyphi A, B or C. Dysentery which can be caused by any of the Shigella species but particularly S. dysenteriae serotype 1. Disease caused by various Escherichia coli such as VTEC (verocytotoxic E. coli), Enteroaggregative E. coli (EAEC), Enteroinvasive E. coli (EIEC) and Enterotoxigenic E. coli (ETEC).
The previously mentioned pathogens are considered core isolates to test for when investigating faecal specimens, but some clinical situations will require investigation of less common pathogens such as Clostridioides difficile, Yersinia enterocolitica, Yersinia pseudotuberculosis, Helicobacter species and Aeromonas species.
Providing excellent patient care is paramount in cases of gastrointestinal disease as mild infection have the capacity to become invasive and cause more serious pathologies. Especially with the ability to travel such an easy route of spreading unusual diseases. Part of the delivery of excellent patient care is participating in external quality assessment.

Molecular testing is increasingly used routinely to diagnose and monitor pathologies in clinical microbiology, so it has been identified that the introduction of molecular detection schemes are beneficial to many laboratories. UK NEQAS have recently introduced and now offer schemes for molecular detection of both parasites and viruses but there is the opportunity to develop a scheme for molecular detection of bacterial pathogens causing gastrointestinal disease.
The purpose of this study is to establish if a new external quality assessment (EQA) scheme is in demand by participants of existing EQA schemes. The scheme would offer participants the opportunity to detect bacterial causative agents of gastrointestinal disease using various PCR platforms.

The design of the lyophilized specimens will be used to challenge laboratory procedures, PCR platforms, reporting, and interpretation and assess the technical ability of the laboratory scientist in diagnostic laboratories.
The goal is assisting laboratories in identifying strengths and weaknesses in procedures to improve turnaround times (TAT), quality control staff competence and lead to overall better patient care.
The final aim of this study is in line with the syndromic approach and to combine molecular detection of gastro intestinal bacterial pathogens with the existing schemes for molecular detection of gastro intestinal viruses and parasites.

The initial stage of the project will be to send a questionnaire to all laboratories registered to participate in the General bacteriology and Clostridioides difficile detection schemes. The questionnaire will ascertain interest in a molecular scheme to detect bacterial pathogens including which targets and platforms are used routinely by clinical diagnostic labs. This will also capture method data so that the commonly reported platforms identified can be compared and assessed on performance, TAT and costing.
On return of the questionnaire the responses will be analysed and specimens will be designed to include various bacterial pathogens.
The design of the freeze dry specimens will take into consideration the quantity of target pathogen within the specimen, including common commensal bacteria to simulate an authentic faecal specimen therefore the matrix in which the potential pathogen will be freeze dried in, will be actual faecal material whereby the normal flora will be fully characterized.
Quality assessment of these specimens is paramount as an EQA provider so extensive confirmatory testing will be performed both in house and via specialist reference laboratories. Sensitivity, specificity of platforms will be assessed as well as homogeneity across specimens of the same intended result.
Specimens will be distributed within a pilot group of participants to investigate and report their results using the current online reporting system. Results will be collated and analysed with reports being produced. Results analysis will allow for any adjustments and improvements which need to be made ready for second pilot distribution.

Carbapenemase Producing Organisms (CPO) Scheme

 

The carbapenem class of antibiotic are considered a last treatment resort for the critically ill or for infections caused by multi-drug resistant bacteria. Carbapenemases are enzymes which can hydrolyse this class of antibiotic, rendering the drug not effective. Worryingly, over the last several years, the number of isolates testing positive for possession of a carbapenemase has been increasing.

Using traditional phenotypic tests, there can be difficulty in differentiating between carbapenemase production versus carbapenemase resistant organisms. Enterobacterales with AmpC and ESBL enzymes, in addition to porin loss, can result in carbapenem resistance. The importance in the differentiation and identification of carbapenemase production, is the ability of these organisms to transfer resistance between strains (via plasmids or transposons).

UK NEQAS are designing a scheme which will assess the successful detection of CPOs. This will include the ‘big five’, NDM, KPC, OXA-48, IMP and VIM. And encompass Enterobacterales, in addition to Pseudomonas spp. and Acinetobacter spp.

There has already been a pre-pilot and a questionnaire to determine current screening protocols in place for the detection of CPOs. We are hopeful that we can progress with this project work for the remainder of this year and send out the pilot in 2021-22.

Educational Objectives 
Back to Basics’ Microbiology Workshop
By Li Sa Choo, Healthcare Scientist

A ‘back to basics’ microbiology teaching workshop is in the planning stages ready to be introduced in the new financial year (April 2021 onwards ) and will be open to all interested participants. The workshop will embrace conventional microbiology identification practices, including traditional staining techniques and a wide range of biochemical tests.

This practical workshop will look to inform attendees on the principles of a variety of practical techniques that have been replaced by automated methodology in recent years, and in particular, may benefit: trainee Healthcare and Clinical scientists, Medical Laboratory Assistants, Medics training for the FRCPath, as well as laboratory staff who have not performed traditional tests before.

If there are any specific techniques that you are interested in being covered, please get in contact at organiser@ukneqasmicro.org.uk whilst we are at the planning stage.

 

STARTERS AND LEAVERS

Pratima Mahajan
Quality Manager UK NEQAS for Microbiology

My experience spans over 26 years from starting as a MLA in a Microbiology Laboratory and working my way up to Acting BMS3, working at various London hospitals and private companies full time or as a locum. With my MSc, I gained IBMS Fellowship. My Quality career started in 2005 with NHSBT, Colindale. I then went on to do some consulting work in South Africa and Dubai and am now working as Quality Manager for UK NEQAS for Microbiology since Nov 2019.

I have gained experience in MHRA regulations, ISO 9001, ISO 15189 and now ISO 17043 with qualifications in the IBMS Quality Management certificate, the ILM Leadership and Management Certificate and more recently am IRCA registered as an Internal auditor.

I enjoy my role as Quality Manager. There is a lot to learn but very happy to be part of a great team that deal with important EQA samples, sent nationally and internationally. My role involves all aspects of the process and auditing to ISO 17043. Everything from design to dispatch and results for schemes.

Time away from quality: I love making pottery in my studio and gardening in my spare time. I love Netflix serials and BBC Dramas.

Marit Orav
Virology Scheme Manager UK NEQAS for Microbiology

I joined UK NEQAS for Microbiology in November 2019 as a HCS Team Manager. In the beginning of 2020 I successfully applied for the position of the Virology Scheme Manager and took up the post in April.

I am happy and excited to have joined the wonderful Virology team and the wider UK NEQAS family.

My background lies in academic research. I have a BSc and MSc degrees in Genetics and a PhD in Biomedicine. I have spent almost a decade researching human papillomaviruses and their mechanism of multiplying in infected cells. I started researching the topic during my MSc and PhD studies at the University of Tartu and continued throughout my position as a post-doctoral researcher at McGill University. After moving to the UK I decided to forge a path outside of academia and am now looking forward to continuing my career in External Quality Assessment.

Teodoro Fajardo
Senior Executive Officer/Healthcare Scientist Team manager 

Dr. Ted Fajardo finished his medical technology (biomedical science) degree from the Philippines worked as bacteriologist and unit head of the National TB reference Laboratory of the Bureau of Research and Laboratories, Department of Health.

He also worked as Microbiologist at the National reference Laboratory for HIV, Hepatitis and other STIs and as food and drug analyst at the Food and Drug Administration, both an attached agency of the Department of Health.

During his stint as microbiologist, he was awarded a scholarship grant from the Civil Service Commission and studied Master of Public Management from the Development Academy of the Philippines. He was then awarded another scholarship grant to study Master of Science in Molecular Biology and Virology at the Universidad Autonoma de Madrid, Spain and later continued the grant award to a PhD in Molecular Biology and Virology at the same university.

After earning his PhD, he was recruited from Spain to London to work as Post-Doctoral Scientist Fellow at the London School of Hygiene and Tropical Medicine, Department of Pathogen Molecular Biology where he worked in molecular virology and biotechnology of double stranded viruses (Bluetongue virus, Rotavirus, Epizootic Haemorrhagic Disease Virus and other double stranded RNA viruses) working to understand the molecular mechanisms of RNA virus genome packaging towards developing antivirals through the use of nucleic acid based approach.

He was then recruited by Cambridge University to work as a Post-Doc Scientist to work on single stranded RNA viruses (Zika and Dengue Viruses) to understand its complex RNA structure and how this regulates the translation process of the host cell using modern molecular virology and virus culture, cloning and other advanced biotechnology procedures.

He received several awards and grants and invited for local conferences as speaker around United Kingdom and international conferences in different countries. He has published paper in peer reviewed journals on double stranded and single stranded positive sense RNA viruses.

He is currently an HCPC registered biomedical scientist and working as a Senior Executive Officer/Healthcare Scientist Team manager at the National Infection Service, UK NEQAS for Microbiology, Public Health England, UK.

Empowering others, health and safety

By Jane Appiah
Health and Safety Coordinator

Microbiology services across the world have had to face the challenges associated with continuing to deliver services in the wake of the ongoing COVID-19 pandemic amidst limited resources.
Changes to health and safety requirements, have had a huge impact on operational delivery. Staff here at UK NEQAS have risen to the challenge and have adapted to these ongoing changes in order to remain compliant with safety regulations and maintain the high-quality standard of service that participants have come to expect.
I joined UK NEQAS in July 2018 as a Health & Safety and Training Manager, and now after 2 years I am moving on into another Health and Safety role outside the organisation. As I reflect on my time here, I recall the first tutorial I led, with the team which had two main aims. Firstly, to introduce myself and the objectives of my role and then to provide an understanding of what the bigger picture of health and safety is and how this will influence the action plan objectives for health, safety and training.
The tutorial aimed at getting staff to select from a list of words they had strong association with. These words described values. Values are the key to understanding what is most important to individuals, and if you can identify this, then you can capture how best to tailor and motivate people to drive a health and safety initiative forward. I strongly associate with the value of empowering others and as I reflect on this, there has never been a more important time to re-examine our own values and how this influences people around us. An organisation’s ability to grow, adapt and thrive is dependent on this.

I would like to take this opportunity to thank the entire team UK NEQAS Microbiology team for their support, I look forward to embarking on new health and safety ventures.

Jane Appiah

Vipul Sharma, (leaver) HEO Operations Manager at UK NEQAS for Microbiology

I have had the honour to have worked with colleagues in UK NEQAS Microbiology for the last 16 years. I have been inspired throughout my career there at how well UK NEQAS is able to deliver excellent educational service through its EQA schemes and teaching programmes.

My time in UK NEQAS Microbiology allowed me to grow and develop. This came on the basis of a strong foundation in quality practices, technical guidance and advice and a strong team of colleagues. This enabled me to carry out my job to the best of my ability.

I would like to take this opportunity to share with you all the incredible pride I feel when I think of UK NEQAS as an organisation and how the service provided assists in increasing quality assurance in laboratories in the UK and overseas.

Parasitology

Leaver

Nikita Chauhan: Nikita left the team in March 2020 to move to a different city with fiancé. We wish her the very best in this new phase of her life.

Starters

Vaibhavi Mistry: We are very happy to say that Vaibhavi Mistry has recently been appointed as the Laboratory Support Staff replacing Nikita. Vay joins us from the Microbiology team and brings with her years of Operational experience. Welcome to the team Vay.

Starter –internal promotion

Agatha Saez: We are very happy to state that Agatha Saez had successfully been recruited to a more senior position within Parasitology. We are delighted by this very well-deserved promotion for Agatha!

We would like to welcome the following new starters

Teodoro Fajardo – FTC Healthcare Scientist Team Manager

Aidan Wiggins – HCS Support Worker Apprentice

Chloe Campbell – HCS Support Worker

 

We wished farewell to the following staff:

Nikita Chauhan – HCS Support Worker

Vipul Sharma – Operations Manager

Binta Hanakuka – HCS Practitioner

Jane Appiah – Health & Safety Coordinator EQA Services & Standards Unit

 

Please contact our Operations team if you have any customer queries on: organiser@ukneqasmicro.org.uk

Internal changes of job roles:

Vaibhavi Mistry from AO in Operations to AO in Parasitology

Agatha Saez recruited to role of HCS Team Manager, with Quality management responsibility

Marit Orav recruited to Virology Scheme Manager