December 2021 Newsletter

xmas22

December 2021 Newsletter

Re-Registration April 2022 - March 2023

 

Online re-registration process for 2022 – 2023 for UK participants and overseas laboratories not served by distributors 

 

The 2022/23 online re-registration form for UK NEQAS for Microbiology will be available through the secure login area of our website from 05 January 2022.

During this re-registration period, from 05/01/22 to 25/02/22, participants are encouraged to make any changes using the online form. Participants can amend the form multiple times up until the 25 February 2022. Please note, if there are no changes, submission of the form is still required to confirm participation subscriptions for the upcoming financial year.

Once re-registration details have been finalised, the form should be submitted via the online portal. It is advised that once details are submitted to print or save the updated information as a record.

Re-registration for participants served by a distributor shall be contacted by their distributor directly.

Yours sincerely

UK NEQAS Microbiology Operations team

UK NEQAS for Microbiology celebrated 50 years of delivering External Quality Assessment this year.

To commemorate this occasion, we delivered a series of webinars (earlier this year) on a variety of clinical hot topics of interest, presented by renowned experts in their field. If you missed the opportunity to listen to the webinar live, links to the recordings can be found on our website webinars.pdf (ukneqasmicro.org.uk).

A snap shot of how UK NEQAS was initiated to where the service is currently:

The first EQA was dispatched on 1st May 1971 from the Public Health laboratory, Sunderland by the then Scheme Organiser Dr. P.B Crone. Analysis of results was performed by Mr W.B Fletcher at the Epidemiological Research laboratory, Colindale, London. This first distribution was the equivalent to the UK NEQAS for General Bacteriology scheme which continues to operate to this day. Over the last 50 years, UK NEQAS Microbiology has expanded on  schemes provided and currently provide a total of 54 EQA schemes globally, including teaching programmes: blood and faecal parasitology teaching schemes and a mycology workshop and an Interpretive Comments (CPD) scheme

Scheme Organiser for the UK NEQAS for Microbiology Interpretive Comments Scheme

The UK NEQAS for Microbiology Steering Committee Chair, Dr Rohini Manuel, is inviting applications to fill the post of scheme organiser for the UK NEQAS for Microbiology Interpretive comments scheme on an honorary/ contractual basis.  The weekly commitment is 2 PA (8 hours) and can be shared between 2 colleagues.

About the Scheme organiser for Interpretive comments scheme

The scheme organiser for UK NEQAS for Microbiology Interpretive Comments scheme will be an expert of national or, ideally, international standing, preferably in the field of medical microbiology and/or virology and/ or infectious diseases. The successful candidate will lead the formulation and delivery of new interpretive comments EQA.

The scheme organiser for UK NEQAS for Microbiology Interpretive Comments scheme will also need to work effectively with the different scheme organisers and managers to provide strategic advice and respond to challenges, Microbiology steering committee, UK NEQAS board of trustees, the different special advisory groups (Virology Specialist Advisory Group, Antimicrobial Susceptibility Testing Advisory Group), other colleagues in UK NEQAS for Microbiology, and professional bodies such as RCPath, IBMS etc.

The scheme organiser for UK NEQAS for Microbiology Interpretive Comments scheme has a vital role to provide professional and clinical governance to the Microbiology Interpretive comments scheme by providing  challenging and stimulating clinical case studies on a monthly basis to a clinically qualified audience (consultants – both medical and non-medical, clinical scientists, trainees).

About the Interpretive comments scheme

Please visit the following link for more information:

https://ukneqasmicro.org.uk/interpretive-comments/

The scheme organiser for UK NEQAS for Microbiology Interpretive Comments should not be employed by or receive personal remuneration from industry, organisations or pressure groups that can have an impact on EQA delivery during his or her term of appointment.

A job description is available on the following link:

https://ukneqasmicro.org.uk/images/pdf/JD.pdf

How to apply

If you wish to know more about this role, please contact Dr  Sanjiv Rughooputh via email: sanjiv.rughooputh@phe.gov.uk

If you are interested in applying for this post, please send your current curriculum vitae and a covering letter to Dr Rohini Manuel (rohini.manuel@phe.gov.uk) copying Belinda Stobbs. (belinda.stobbs@phe.gov.uk) by  31st January 2022.

 

Job Description

Job title: UK NEQAS Microbiology Interpretive Comments Scheme Organiser
Division/Directorate: UKHSA Science Group
Pay grade/band:

Responsible to:

Through an honorary contract with local organisation

Nominated UK NEQAS for Microbiology Lead when dealing with UK NEQAS matters

Location: At normal place of work with visit to UK NEQAS for Microbiology Colindale at least once a month, but also to attend steering committee, NQAAP and other important meetings.
Hours per week:  8 hours per week (2.0 PA/ week). This can be shared between two colleagues
Job type:

(i.e. Fixed Term/Permanent)

On Contract ( renewable)

 

INTRODUCTION

UK Health Security Agency (UKHSA) exists to protect and improve the nation’s health and wellbeing, and to reduce health inequalities. We do this through world-leading science, knowledge and intelligence, advocacy, partnerships and the delivery of specialist public health services. We are an executive agency of the Department of Health and Social Care, and a distinct delivery organisation with operational autonomy. We provide government, local government, the NHS, Parliament, industry and the public with evidence-based professional, scientific and delivery expertise and support.

UK NEQAS for Microbiology is not for profit, self-financing. Monies are obtained by subscription to the services  provided.

UK NEQAS for Microbiology is accredited to ISO 17043: 2010 standards and is committed to providing   high standards of service to meet the present and future needs of clinical laboratories and laboratory professionals through EQA, CPD or training

UK NEQAS Microbiology provides:

A comprehensive EQA suite comprising sample based testing schemes, clinical scenarios, and associated training. The microbiology services encompass bacteriology (with antimicrobial susceptibility testing), mycology, virology, parasitology, with schemes based on a range of technologies including MALDI-ToF, molecular detection methods, and traditional methods. Schemes are under constant review and development. The schemes provide an international benchmark for quality. There are currently over 3000 participants in more than 80 countries.

Please see our website for further information: www.ukneqasmicro.org.uk

JOB SUMMARY

To provide professional and clinical governance to the Microbiology Interpretive Comments scheme.

To support other Division of Microbiology Scheme Organisers by providing professional direction to the design and delivery of the UK NEQAS Microbiology schemes, and professional input to allied EQA projects.

To promote and support the research, educational, training and development activities within UK NEQAS for Microbiology.

To effectively interact with other overarching professional bodies with which UK NEQAS for Microbiology is associated (UK NEQAS, Royal College of Pathologists) and maintain appropriate codes of conduct.

MAIN DUTIES AND RESPONSIBILITIES

  • To provide and maintain a rapid, reliable, efficient, comprehensive, effective and scientifically valid EQA service for clinical scenario or test based Interpretive Comments.
  • To be responsible for scheme design, development and scientific activity.
  • To provide a professional advisory role to participants and performance surveillance.
  • To comply with the UK NEQAS code of conduct in respect of all UK NEQAS activities
  • To provide expert scientific advice, liaison and interpretation on quality assurance to: scheme participants, steering committees, the UK NEQAS Board, Consortium, Executive and Office, other Scheme organisers and UK NEQAS staff, the Microbiology National Quality Assurance Advisory Panel (NQAAP), and all other relevant organisations and professional bodies.
  • To hold responsibility for the Interpretive Comments scheme budget. (In practice this is devolved to other Scheme Organisers in UK NEQAS for Microbiology).
  • To achieve and maintain accreditation to appropriate UKAS Proficiency Test standards (ISO 17043:2010) for the scheme.
  • To collaborate in the evaluation of new and improved procedures for EQA activities other than for interpretive comments scheme.
  • To promote awareness of UK NEQAS activities and maintain awareness of recent advances in the scheme activities through active participation in relevant departmental, regional, national and international scientific and medical meetings, societies and organisations.
  • To represent UK NEQAS interests appropriately at Trust, Regional, National and International level, including membership of appropriate boards and committees.
  • To Adhere to Department of Health guidance for management of EQA schemes.
  • To participate in appropriate continuing education programmes.

KEY WORKING RELATIONSHIPS

  • Bacteriology and Mycology Scheme Organiser
  • Virology and Molecular Scheme Organiser
  • Parasitology Scheme Organiser
  • Other key UK NEQAS Microbiology team members(e.g. management board, IM&T)
  • UK NEQAS (Board, Executive, Microbiology Steering Committee)
  • Interpretive Comments scheme participants
  • Royal College of Pathologists
  • UKAS

 

Person specification

(Please ensure the total number of rows below the knowledge and experience and skills and capabilities headings does not exceed 15)

 

Description Essential Desirable Assessment
Qualifications
FRCPath (UK) or equivalent A/I
Higher qualification in medical microbiology and/or virology A/I
Registration with GMC/HCPC A/I
Knowledge and experience
Extensive experience in clinical medical microbiology and/or   virology A/I
Commitment to Clinical Governance and Good Laboratory Practice, A/I
Commitment to Continuing Professional Development A/I
Prior involvement with accreditation schemes or quality management schemes   A/I
Knowledge of modern (including molecular) investigation techniques   A/I
Prior involvement with performance management   A/I
Skills and capabilities
Able to write a concise report A/I
Good team player with skills to work across disciplines A/I
Able to develop and implement a strategy for the Interpretive Comments scheme  √ A/I
Foster good relationships with colleagues across Microbiology and Virology and Lead a panel of Peer Reviewers  √ A/I
Able to rapidly write/edit scenarios to support the scheme strategy  √ A/I
An understanding of and commitment to equality of opportunity and good working relationships. A/I
Able to provide timely scientific advice to support other scheme organisers at UK NEQAS for Microbiology  √ A/I
Equality and diversity
An understanding of and commitment to equality of opportunity and good working relationships. I
*Assessment will take place with reference to the following information

A = Application form            I = Interview              C = Certificate                   T = Test

 

ADDITIONAL INFORMATION

In addition to the job specific requirements above, this role will require adherence to the following:

Appraisal

All staff are required to participate in a joint annual review of their work with their main employing organisation.

Code of conduct and revalidation process for professionally qualified staff groups

All staff are required to work in accordance with their professional group’s code of conduct and revalidation process as appropriate and relevant to their role (e.g. GMC, HCPC, RCPath, IBMS)

Information governance

All data and information must be managed in accordance with the requirements of data protection and related law, and best practice standards and guidance.

You are responsible for:

  • protecting the confidentiality of UKHSA data and information by:
  • complying with the Data Protection Act 2018 (incorporating the General Data Protection Regulation)
  • complying with the common law duty of confidentiality, the Caldicott Principles and the NHS Code of Practice on Confidentiality when processing personal data
  • complying with the policies, procedures and guidance in place to protect the confidentiality of UKHSA data and information, for example by:
    • only accessing the UKHSA data and information you have approval to use for your role, and not sharing this access to UKHSA  data and information with anyone else
    • not attempting to circumvent the managerial, procedural and technical security controls in place to protect UKHSA data and information
    • not processing UKHSA personal data outside UKHSA office sites without approval
  • complying with the policies, procedures and guidance in place to protect the integrity (in other words, the accuracy and completeness) of UKHSA data and information, for example by:
  • only altering UKHSA data and information if you have approval to do so as part of your role
  • complying with the policies, procedures and guidance in place to protect the availability of UKHSA  data and information, for example by:
  • complying with the policies, procedures and guidance on the secure and acceptable use of ICT systems and equipment
  • complying with the law and policies, procedures and guidance on the management of records, including the proper use of the Government Security Classifications
  • reporting incidents affecting the confidentiality, integrity and availability UKHSA data and information, for example, unauthorised access to UKHSA  data and information, or the loss or compromise of ICT systems or equipment
  • completing the annual information governance training appropriate to your role

You are personally accountable for deliberate or avoidable data protection breaches. Failure to comply with the Data Protection Act 2018 may result in you being reported by UKHSA to the Information Commissioner’s Office, which may lead to criminal prosecution.

Conflict of interests

The honorary contract holder must not engage in outside employment that conflicts with their UKHSA work, or is detrimental to it. In accordance with UKHSA’s Conflict of Interest policy, you must inform your UKHSA line manager if there is the possibility of a conflict of interest and register the interest where appropriate.

In addition, the Policy requires you to declare all situations where you or a close relative or associate has a controlling interest in a business (such as a private company, public or voluntary organisation) or in any activity which may compete for any contract to supply goods or services to UKHSA. You must register such interests with UKHSA, either on appointment or whenever such interests are acquired. You should not engage in these activities without the written consent of UKHSA, which will not be withheld unreasonably. It is your responsibility to ensure that you are not placed in a position that may give rise to a conflict between your private interest and your UKHSA duties

Diversity

You are at all times required to carry out your responsibilities with due regard to the organisation’s diversity policy and to ensure that staff receive equal treatment throughout their employment.

Health and safety

You must co-operate with management in discharging its responsibilities under the Health and Safety at Work Act 1974 and take reasonable health and safety of yourself and others and ensure the agreed safety procedures are carried out to maintain a safe environment for service users, employees and visitors.

Centre/divisional directors – are responsible for coordinating health and safety activities in their centres/divisions and will determine the necessary management structure and arrangements. Directors will ensure that their actions and decisions at work reinforce the requirements of health and safety policy and arrangements.

Managers – are responsible for implementing the organisation’s health and safety policies and arrangements and for ensuring that risk assessments, safe systems of work, control measures and staff training are up to date and effective. Managers will inspect premises, ensure accidents and incidents are reported/investigated and assist in auditing health and safety management arrangements.

All staff must comply with any health and safety training: report all accidents, incidents, illnesses and untoward occurrences to line management without undue delay and must not interfere with or misuse anything provided in the interest of the health, safety and welfare of other employees.

Risk management

All staff have a responsibility to report all clinical and non-clinical accidents or incidents promptly and, when requested, to co-operate with any investigation undertaken.

UKHSA People Charter

All staff should be aware of and adhere to the UKHSA People Charter which outlines the values and behaviors expected of all UKHSA staff and underpins how all UKHSA policies should be applied. Applicants and employees will be expected to demonstrate an understanding of and commitment to these values and behaviors, which will be assessed through the recruitment, selection and appraisal processes. This job description should be read with reference to the UKHSA People Charter which outlines the values and behaviors expected of all UKHSA staff.

SCHEME UPDATES

Very shallow focus, on flagella of the foreground objects.

UK NEQAS for Mycobacterium (Molecular) scheme

The report will no longer provide the VNTR and spoligotyping results, as the reference laboratory no longer perform these tests. A comment was included on the September 2021 distribution informing participants.

UK NEQAS for Antimicrobial susceptibility scheme

Previous communication informed all of the possibility to incorporate histograms displaying MICs and methods used by participants within the report. Due to restriction within the remit of software feasibility, this could not be accommodated.

UK NEQAS Microbiology and the Antimicrobial Susceptibility Testing Specialist Advisory Group (ASTSAG) are currently in discussion on how the report and scoring could be developed. Further information will be provided in due course.

There have been significant changes to EUCAST susceptibility testing and interpretation over the past few years. Of significant concern in diagnostic laboratories has been the implementation of the “redefinition of the I category” and area of technical uncertainty (ATU). Both are fundamental changes to the way we interpret susceptibility testing results and have clear implications for reporting. Diagnostic laboratories may struggle to understand and implement these changes. An educational session hosted on the British Society of Antimicrobial (BSAC) website may be helpful to those scientists and clinicians involved with susceptibility testing:

(https://bsac.org.uk/susceptibility/susceptibility-testing-education/ast-webinar/)

UK NEQAS for Microbiology initially opted to not score agents that fell into the ATU. However, going forwards if >80% concordance is achieved by our participants the agent will be scored.

A series of webinars were also delivered by UK NEQAS for microbiology, the first on ‘How to Handle the EUCAST New Definitions of S, I & R and the ATU’, delivered by Professor Gunnar Kahlmeter. The recording can be viewed on the UK NEQAS microbiology website:

webinars.pdf (ukneqasmicro.org.uk)

UK NEQAS for Carbapenemase Producing Organisms (CPO) scheme

Following the success of the pilots, the scheme is planned to go live in April 2022. This scheme will include four distributions per year, each containing two simulated rectal specimens in swab format. Please visit our website on how to register for this scheme.

UK NEQAS for Mycology scheme

There are a plethora of methods clinical diagnostic laboratories have employed in the identification of filamentous fungi. A mini questionnaire will be sent accompanying the distribution in January 2022, to all participants of the mycology scheme (located on the final page of the web reply form). This will allow UK NEQAS to collate information on the methods currently used to identify fungi by participating laboratories.

We endeavour to illustrate the methods in our future reports.

Special Surveys

UK NEQAS for Microbiology are proud of the ongoing collaborations with leading international organisations WHO (World Health Organization) and ECDC (European Centre for Disease Prevention and Control) for a consecutive number of years, providing bespoke EQA programmes for the examination of significant causative agents of infectious diseases.

A brief summary of current delivery of EQA programmes:

WHO Invasive Bacterial Vaccine-Preventable Diseases (IB-VPD), 2014-present:

The WHO coordinates the Global Invasive Bacterial Vaccine-Preventable Diseases Surveillance Network, to support vaccine introduction decisions and use. The network was established to strengthen surveillance and laboratory confirmation of meningitis caused by Streptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis.

UK NEQAS in collaboration with WHO, provided an EQA annually (2014-2020) to over 120 clinical diagnostic and regional reference medical microbiology laboratories globally. An EQA for 2022 is currently in discussion.

WHO European Antimicrobial Resistance Surveillance network (EARS-Net), 2000-2020:

The high levels of antimicrobial resistance (AMR) remains a serious challenge worldwide and is considered to be one of the biggest threats to public health today.

A panel of six microorganisms exhibiting a variety of resistance mechanisms were distributed to over 900 laboratories from 30 countries, to identify and perform antimicrobial susceptibility testing on agents for treatment of sepsis.

Laboratories that participated in this EQA had the opportunity to review their individual performance and evaluate all areas where they did not achieve concordance with intended results.

WHO Central Asia and Eastern European Surveillance Antimicrobial Resistance (CAESAR), 2013-present:

A panel of six microorganisms exhibiting a variety of resistance mechanisms were distributed to over 300 laboratories from 30 countries, to identify and perform antimicrobial susceptibility testing on agents for treatment of sepsis.

Laboratories that participated in this EQA had the opportunity to review their individual performance and evaluate all areas where they did not achieve concordance with intended results.

The next distribution is planned for February 2022.

WHO Diphtheria, 2021:

UK NEQAS with the support of WHO Global Collaborating Centre for Reference and Research on Diphtheria and Streptococcal Infection, provided an EQA in 2021. Diphtheria is a severe illness of public health importance caused by toxin producing C. diphtheriae and C. ulcerans. The first distribution was dispatched in July 2021, and included four simulated throat specimens for the detection of Corynebacterium species (toxigenic/non toxigenic) to 40 clinical diagnostic laboratories from 36 countries. Final report preparations currently in progress.

WHO Respiratory Syncytial Virus (RSV), 2019, 2021:

Respiratory Syncytial Virus (RSV) is a leading cause of hospitalisations due to acute lower respiratory infections in infants and young children.  The World Health Organization (WHO) embarked on an ambitious project to establish an RSV surveillance between 2016-18 in order to provide the evidence base to guide the development of RSV vaccines and monoclonal antibodies and inform immunization policy and practice. The RSV surveillance is in alignment with and contributes to WHO’s General Program of Work towards preparedness and prevention strategies for priority pandemic / epidemic prone disease.  In order to ensure that laboratories worldwide were well equipped to fulfil this objectives, UK NEQAS for Microbiology was requested to run an external quality assessment (EQA) program to identify gaps in participating laboratories capacity to detect and type RSV A and B.

The first round of the EQA was carried out in 2019, to around 25 countries. The results obtained from the participating laboratories were excellent.  The second round of the EQA exercise is presently underway, with an extended participation base of over 65 countries.

WHO Malaria Molecular scheme (MM) 2017-present:

Malaria remains a global disease of concern. The WHO recommends diagnosis of malaria to be based on parasite identification, both in endemic and non-endemic settings. Furthermore, there has been an increase in usage of molecular techniques for identification of malaria infections. Molecular assays have lots of benefits, however, are not without their challenges- such as lack (or limited use of) standards and lack of reproducibility primarily due to variation in protocols amongst labs. Hence the need for a robust EQA scheme targeted towards molecular diagnostics was recognised by the WHO in order to offer an independent and periodic means for clinical, reference and research laboratories to verify the quality of their molecular diagnostic methods and to monitor performance over time.

An expert group meeting on establishing a WHO EQA scheme for malaria molecular diagnostics was held in June 2015 in London, UK, following which the WHO Global Malaria Programme worked with UK NEQAS Parasitology to launch a global EQA scheme in January 2017. The scheme has been operational now for 4 years running with over 50 participating labs globally.

ECDC European Gonococcal Antimicrobial Surveillance programme (EUROGASP), 2015-2020:

Antimicrobial Resistance in Sexually Transmitted Infections (ARMSTI) (UKHSA) recruited UK NEQAS in provision of an EQA delivering specimens containing strains of Neisseria gonorrhoeae for identification and performance of antimicrobial susceptibility testing to 37 clinical diagnostic laboratories from 36 countries.

ECDC Legionella, 2019-present:

Legionnaires’ disease is a serious form of pneumonia with a case fatality rate of between10 -15%. The aim of the European Legionnaires’ Disease Surveillance Network (ELDSNet) is to detect, control and prevent cases, clusters and outbreaks of Legionnaires disease in EU/EEA countries and assist with detection and response outside of these countries. The network supports Member states and other involved countries to share information and collaborate on response actions to provide better protection from travel associated Legionnaires disease.

ECDC to support the ELDS-Net endorsed UK NEQAS and FEPTU (Food Environment Proficiency Testing Unit) in the provision of an EQA, which provided an outbreak scenario with a panel of both clinical and environmental specimens.

The participating laboratories were given the opportunity to examine the simulated specimens for Legionella spp. depending on their capacity and technical protocols.

In the pipeline:

WHO Typhoid

Heart Valve project

Bacteria Streptococcus thermophilus, 3D illustration. Probiotic Gram-positive spherical bacteria used in cheese and yogurt production

FURTHER UPDATES

EUCAST update for 2022

Every year on the 1st of January EUCAST updates the breakpoint table – the 2022 table is version 12.0. As always it is freely available to all. Many of you will have discovered that you can be automatically updated monthly by providing your email address in the upper right hand corner of the website (www.eucast.org).

This year EUCAST offers a number of new and useful additions. For each of them you can read more on the website. Here is a summary of what is new:

  1. Revised breakpoints and disk diffusion methodology for anaerobic, fast-growing, clinically relevant anaerobic species (Bacteroides spp, Prevotella spp, Fusobacterium necrophorum, Clostridium perfringens, Cutibacterium acnes). The medium is FAA without additives, the incubation time 16-20 hours (extended incubation not allowed). Breakpoints for more antibiotics will be developed during 2022. For anaerobic species not yet developed there is a section on anaerobic bacteria in the guidance document “What to do when there are no breakpoints”.
  2. Prolonged incubation of Rapid AST directly from positive blood culture bottles (RAST). So far RAST plates could be incubated and read after 4, 6 or 8 hours and extended incubation was not allowed. During the first quarter of 2022 we will publish breakpoints for extended incubation (16 – 20h).
  3. Vibrio spp – breakpoints, methodology and disk diffusion correlates are made available for the 5 most pathogenic Vibrio species, including Vibrio cholerae. The method is a straightforward disk diffusion 16-20 hours on MH plates with no additives.
  4. Meropenem-vaborbactam disk diffusion criteria – after having solved some difficulties with meropenem-vaborbactam disks, zone diameter breakpoints are now available. A wide area of technical uncertainty (ATU) provides methodological robustness for when an S, I or R report can be offered to the clinical colleague.
  5. A guidance document on EUCAST recommended screening methods is made available with links from where “screen only” criteria are listed in the breakpoint table.
  6. For laboratories that have realised that disk diffusion is a flexible and cheap method and which have also understood the importance of acquiring high quality material (media and disks) and of performing and reacting to stringent internal (and external) EQA, EUCAST publishes all MIC / inhibition zone diameter correlations on the website. By comparing zone diameter distributions in the clinical laboratory to these you can quickly determine how relevant the breakpoints are in relation to your proficiency with plates and disks. This is where you find them: https://www.eucast.org/ast_of_bacteria/calibration_and_validation/

Do not hesitate to contact your National AST committees (https://www.eucast.org/organization/general_committee/) or EUCAST directly (www.eucast.org) in case you need assistance.

Gunnar Kahlmeter, M.D., Professor of Clinical bacteriology

Clinical microbiology for Blekinge and Kronoberg counties

Head of the EUCAST Development Laboratory and EUCAST Technical Data Coordinator and Webmaster

Head of the Swedish reference laboratory for phenotypic susceptibility testing of bacteria

www.eucast.org

gunnar.kahlmeter@eucast.org

SARS-CoV-2 point of care EQA

Dr Sanjiv Rughooputh ~ Scheme organiser for Virology and Molecular schemes.

Morbidity and mortality caused by SARS-CoV-2 responsible for COVID-19 is still on the rise with over 261 million confirmed COVID-19 cases globally and mortality associated with COVID-19 now reaching over 5.2 million.

SARS-CoV-2 is evolving and adapting through new mutations, leading to the emergence of new variants. Until recently, Delta variant (B.1.617.2) has been more prominent, but the spotlights are now on a new variant  called Omicron (B.1.1.529) that was first reported in November 2021. This variant has multiple spike mutations, including in the receptor binding domain and furin cleavage site and additional mutations outside spike of uncertain significance. Some of these mutations are thought to enable immune escape, risks of reinfections and growth advantage. The emergence of this variant poses some questions on the efficacy of vaccines being rolled out to halt the spread of COVID-19

With around 54.5% of the world population being vaccinated with one dose and only 6% of people in low- income countries receiving at least one dose of a vaccine against SARS-CoV-2, more than 50% of the world population is at risk of being infected.

Number of new cases of SARS-CoV-2 infections is on the increase worldwide and is mainly due to person-to-person transmission.

Early laboratory diagnosis of both asymptomatic and symptomatic patients using reverse transcription polymerase chain reaction (RT-PCR) to detect SARS-CoV-2 viral RNA in patient samples plays a pivotal role and is considered the gold standard, but the amount of test requests for detection of SARS-CoV-2 is posing a challenge to diagnostic laboratories using RT-PCR.

To alleviate this pressure on diagnostic laboratories, methodological simplification of diagnostic algorithms is being adopted, thus benefitting patient care and infection control. New assays for SARS-CoV-2 are being developed and rolled out to cope with this demand.

The U.S. Food and Drug Administration (FDA) has granted emergency use authorisation (EUA) for antigen tests that can detect SARS-CoV-2, which are now being deployed for mass testing.

Antigen tests for SARS-CoV-2 albeit being generally less sensitive than RT-PCR, can have a big impact on management of patients or people with suspected COVID-19, or for identification of infected people during screening, especially that most antigen tests are performed outside laboratory settings.  Other Point of care assays such as Loops Mediated Isothermal Amplification (LAMP) and Q PCR are becoming more popular

However, proper interpretation of the antigen test results is therefore important for accurate clinical management of infected individuals.

To provide confidence in the results produced by these tests and also to monitor the performance of institutions offering antigen or molecular based Point of care testing for SARS-CoV-2, UK NEQAS for Microbiology has launched a SARS-CoV-2 Point of care EQA external quality assessment (EQA) scheme since June 2021 after successfully completion of 2 pilot studies in February and March 2021.

The scheme consists of 6 distributions of 4 specimens  in viral transport medium simulating  nasopharyngeal swabs; making it suitable for point of care settings and also for any organisation testing for SARS-CoV-2 that do not have  conventional laboratory settings.

The specimens are prepared from X- ray irradiated SARS-CoV-2 virus and hence non-infectious and therefore can be handled outside the conventional laboratory settings. Participants are allowed to return results for up to 2 methods they use.

The overall performance for participants returning results for the  two pilot studies were very good with 95.8% of participants reporting  the intended results for their first method and approximately 88% of participants reporting the intended results for their second method.

Since then there has been several distributions. The  first live distribution of the  21st June 21,  saw an excellent overall performance  of 97.5%  for the first method and 93%  for the second method reported by the participants, indicating an improvement in performance of the participating laboratories.  Subsequent distributions have seen participant’s performance improve and in some case highlighted issues that may be inherent to kits or methodologies being employed.

Distribution (5153) that was dispatched on the 4th October highlighted issues on reproducibility of testing affecting the results submitted, which  could be due to random errors in pipetting the correct volume of reagents/ specimens suggesting training issues or a systematic error due to faulty equipment/ method employed. Hence the scheme is of educational value.

The interest in this scheme is growing with more enquiries and registrations. The scheme has until now been run only in the UK, but will be available internationally in the new financial year

Variants such as the Alpha, Beta, Delta etc are now included in distributions.

The table below illustrates the distribution schedule and closing dates.

Table 1: Distribution schedule for the UK NEQAS SARS-CoV-2 Point of Care EQA

Interested? Please email us email: organiser@ukneqasmicro.org.uk  stating “SARS-CoV-2 Point of care EQA”

References:

Centre for Disease Control and Prevention: SARS-CoV-2 Variant Classifications and

Definitions. https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variantsurveillance/

variant-info.html

Our World in Data- COVID-19 vaccinations: https://ourworldindata.org/covid-vaccinations

UKHSA- SARS-CoV-2 variants of concern and variants under investigation in England-

Technical briefing 29 (26th November 2021)

SARS-CoV-2 variants of concern and variants under investigation

(publishing.service.gov.uk)

Rastogi, M., Pandey, N., Shukla, A. et al. SARS coronavirus 2: from genome to

infectome. Respir Res 21, 318 (2020). https://doi.org/10.1186/s12931-020-01581-z

https://outbreak.info/situation-reports?pango=B.1.1.7&muts=S%3AL452R.

https://www.ecdc.europa.eu/en/covid-19/variants-concern

https://viralzone.expasy.org/resources/nCoV_genome_bis.png

WHO Coronavirus Disease (COVID-19) Dashboard: https://covid19.who.int

https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-

variant-of-concern (Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern)

 

We would like to welcome the following new starters

Paul Ejiofor – Laboratory Support Worker (18/10/2021)

Ariana Derguti – Laboratory Support Worker (12/07/2021)

Jake de los Reyes – Laboratory Support Worker (26/07/2021)

Aishwarya Arunagirinathan – Healthcare Scientist Practitioner (18/10/2021)

Rhian Fraser – Healthcare Scientist Specialist (10/08/2021)

Ethige Shane Dhanuke Silva – Operations Administrator (13/12/2021)

Liya Jain – Placement Student (09/2021)

Lewis Hull – Healthcare Scientist Practitioner (13/12/2021)

Rachel Prince – Production Supervisor (18/10/2021)

Margaret Babatunde – Healthcare Scientist Associate (01/09/2021)

Anisa Hussain – Healthcare Scientist Associate (01/09/2021)

 

We wished farewell to the following staff:

Jake de los Reyes – Laboratory Support Worker (03/12/2021)

Muna Jama – Healthcare Scientist Practitioner (03/09/2021)

Viraj Acharya – Operations Administrator (01/12/2021)

 

 

UK NEQAS Christmas closure 2021

UK NEQAS for Microbiology will be closed 23 December 2021 to 3 January 2022.

We will respond to any queries upon our return on 4 January 2022

Thank you to all our participants, distributors, steering committee and advisory members, expert advisors, freight-forwarders, panel members and UKHSA for their continued support during this challenging year. We look forward to working with you in 2022

 

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