2020 to 2021 Report of UK National Reference Laboratory for Food Microbiology Activities for Listeria monocytogenes, coagulase-positive ...
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2020 to 2021 Report of UK National Reference Laboratory for Food Microbiology Activities for Listeria monocytogenes, coagulase-positive staphylococci, Escherichia coli (including STEC), Campylobacter, Salmonella and antimicrobial resistance April 2020 to March 2021 1
2020 to 2021 Report of UK National Reference Laboratory for Food Microbiology
Contents
2020 to 2021 Report of UK National Reference Laboratory for Food Microbiology ..................... 1
Activities for Listeria monocytogenes, coagulase-positive staphylococci, Escherichia coli
(including STEC), Campylobacter, Salmonella and antimicrobial resistance ........................... 1
Contents....................................................................................................................................... 2
Executive summary ...................................................................................................................... 4
Abbreviation list ............................................................................................................................ 5
Introduction .................................................................................................................................. 6
COVID-19 and EU Exit ............................................................................................................. 8
Core Function One: Secretariat services ..................................................................................... 9
Dissemination of information from international organisations ................................................. 9
Production of NRL quarterly newsletters ................................................................................ 12
Co-ordination of the 2020 OL User Day ................................................................................. 13
Assist in disseminating and responding to EPIS and other alerts ........................................... 13
2019 Audit: Official Laboratories’ capabilities and requirements ............................................ 14
Review content of the UK Food Examiner register ................................................................. 14
Liaise with APHA regarding mutual NRL activities (Campylobacter, Salmonella and
antimicrobial resistance) ......................................................................................................... 14
Liaise with FSA regarding the new Official Control Regulation, (EU) 2017/625 ..................... 15
Liaise with Campden BRI to discuss and implement challenge testing activities ................... 15
Liaise with CEFAS for any overlapping NRL activities............................................................ 16
Provide regular updates to Food Standards Agency .............................................................. 16
NRL Web Content .................................................................................................................. 16
Core Function 2: Advice and representation within the UK and internationally .......................... 17
Provide impartial advice to FSA, OLs and other UK laboratories ........................................... 17
Representation at relevant international meetings and prepare meeting reports ................... 19
Attend training workshops at international organisations........................................................ 20
Keep abreast of methodology developments – membership of FW&E working groups and
other PHE steering committees .............................................................................................. 21
Participation in the BSI AW9 microbiology committee and other working groups ................... 22
Core Function 3: Production of standard operating procedures, codes of practice and
guidance documents .................................................................................................................. 23
22020 to 2021 Report of UK National Reference Laboratory for Food Microbiology
Update and expand food methods archive on NRL website ................................................... 23
Prepare specific guidance protocols for OLs and the FSA ..................................................... 24
Report of 4 years of OL performance of the EFL scheme ...................................................... 25
Core Function 4: Compliance assessment via audits and ring trials .......................................... 25
OL participation in the European Food Microbiology Legislation Proficiency Testing Scheme
............................................................................................................................................... 25
Participate as UK-NRL in EURL ring trials and other initiatives .............................................. 29
Organise Skype/classroom-based workshops for UK OLs ..................................................... 35
Core Function 5: Co-ordination within the UK of international initiatives .................................... 35
Support food aspect of the EU-wide AR monitoring (Decisions 2013/652/EU and 2020/1729)
............................................................................................................................................... 35
Participate in EURL activities relating to Whole Genome Sequencing ................................... 36
Annex – Documents produced from NRL Activities ................................................................... 37
Proposed PHE NRL Activities, April 2021 to March 2022 ......................................................... 40
32020 to 2021 Report of UK National Reference Laboratory for Food Microbiology
Executive summary
Public Health England provides the service as the UK’s National Reference Laboratory (NRL)
for food microbiology for the Food Standards Agency (FSA). This is to comply to the retained
Regulation (EU) 2017/625 for Official Control Regulations (OCRs) for food safety, which is now
UK Statutory Instrument 2019 No. 665. This annual report details the NRL’s activities between
April 2020 and March 2021 related to Listeria monocytogenes, coagulase-positive
staphylococci, Escherichia coli (including Shiga-toxin producing E. coli (STEC)),
Campylobacter, Salmonella and antimicrobial resistance (AR).
Despite the pressure of EU Exit and the COVID-19 (coronavirus disease-19) pandemic have
had on the service, the NRL has participated in all relevant EURL activities and have kept the
Official Laboratory (OL) network, the FSA and other stakeholders up to date with news and
information. NRL quarterly newsletters and EURL information were disseminated, and monthly
logs on NRL activities were made. A remote half day annual User Day was held to inform OLs
and other invitees of the NRL and EURL activities and foodborne incidents. The report of the
third OL audit is ongoing and planned for completion by the end of 2021. The NRL also advised
and contributed comments on the new OCRs to other departments in PHE, Department for
Environment, Food and Rural Affairs (DEFRA) and FSA.
The UK-NRL attended 5 of the 6 European Reference Laboratories (EURL) meetings remotely
and impartial advice was provided to FSA, OLs and other laboratories throughout the year. The
NRL also attended various EURL online training events and found them invaluable. The NRL
was active in the British Standards Institute (BSI) AW9 microbiology committee and has
continued to be a member of the European Committee for Standardization (CEN) TAG18 expert
working group for the revision of the ISO TS 13136 (Polymerase Chain Reaction (PCR)
detection of Shiga toxin-producing Escherichia coli).
There are 11 relevant methods provided by the NRL to OLs on GOV.UK, more publications are
planned and other methods not on the GOV UK website are available upon request.
All 14 OLs registered to the European Food Microbiology Legislation (EFL) External Quality
Assessment Scheme (EQA), under NRL support for 2020 to 2021. Overall, OL results were of a
high standard, however, detection of Listeria monocytogenes in powdered products are not
being identified by some as a relevant test; the legislation is unclear for these product types.
The NRL participated in 10 EURL proficiency tests (PTs) and there was satisfactory
performance for 8 of the 10 distributions. The NRL did not organise any face-to-face training
events but did support a virtual update for OL Laboratories on EU Exit and testing imported
foods.
Details of the proposed NRL activities for 2021 to 2022, and a timeline to achieve these
complete this report.
42020 to 2021 Report of UK National Reference Laboratory for Food Microbiology
Abbreviation list
AFBI Agri-Food and Biosciences Institute (Northern Ireland)
APHA Animal and Plant Health Agency
AR Antimicrobial resistance
BSI British Standards Institute
CEFAS Centre for Environment, Fisheries and Aquaculture Science
CEN European Committee for Standardization
COVID-19 Coronavirus Disease 2019
CPS Coagulase-positive Staphylococci
DEFRA Department for Environment, Food and Rural Affairs
ECDC European Centre for Disease Prevention and Control
EFL European Food Microbiology Legislation (scheme)
EFSA European Food Safety Authority
EPIS Epidemic Intelligence Information System
EQA External Quality Assurance
EURL European Reference Laboratory
FAO Food and Agriculture Organization of the United Nations
FEPTU Food and Environmental Proficiency Testing Unit
FSA Food Standards Agency
FSS Food Standards Scotland
FW&E Food, Water and Environment
FWEMN Food, Water and Environment Microbiology Network
GBRU Gastrointestinal Bacteria Reference Unit
ISO International Standards Organisation
JEMRA Joint FAO/WHO Expert Meetings on Microbiological Risk Assessment
MU Measurement Uncertainty
MIC Minimum inhibitory concentration
MLST Multi-locus sequence typing
NRL National Reference Laboratory
OL Official Laboratory (previously OCL, Official Control Laboratory)
OCR Official Control Regulations
PCR Polymerase Chain Reaction
PHE Public Health England
PT Proficiency Test
SOP Standard Operating Procedure
STEC Shiga-toxin producing E. coli
WGS Whole Genome Sequencing
WHO World Health Organisation
52020 to 2021 Report of UK National Reference Laboratory for Food Microbiology
Introduction
The EU Regulation 2017/625 for Official Controls requires each Member State to have a
National Reference Laboratory (NRL) to be responsible for different aspects for Listeria
monocytogenes, coagulase-positive staphylococci, Escherichia coli (including STEC),
Campylobacter, Salmonella and AMR. Public Health England (PHE) has provided this service
as the UK’s NRL for food microbiology since 2011 under a contract with the UK’s Central
Competent Authority, the Food Standards Agency (FSA). This and other EU regulations have
now been transferred into UK Statutory Instruments as the UK left the EU on 31 December
2020. The FSA has required these activities to continue to provide food safety and security for
the UK, with a public health protection consequence. Therefore, the NRL has retained these
activities for FSA until March 2023, when the agreement will be reviewed.
This report details the secretariat services, advice and representation within the UK/EU,
production of documents, coordinating and participating in audits, ring trials and European
Reference Laboratories (EURLs) initiatives and communication of results and data between
April 2020 and March 2021. Table 1 list the NRL core functions and the activities are described
in this annual report.
Table 1. PHE NRL Core Functions, April 2020 to March 2021
Core
Function Description
1 Secretariat services
1.a Disseminate information/advice from international organisations to FSA, OLs and
other UK laboratories in a timely and effective manner
1.a Produce and circulate quarterly newsletters to FSA, OLs and other UK
laboratories
1.a Co-ordinate the OL User Day to update UK OLs and other relevant UK
laboratories to the NRL core functions
1.a Assist in the dissemination and advice of EPIS and other alerts from the
appropriate authority
1.b Analyse and publish the audit results regarding the OL’s capabilities and
requirements
1.b Review content of the UK Food Examiner Register
1.b Continue liaison meetings with APHA for AR, Campylobacter and Salmonella
1.c Liaise with FSA in matters arising from implementing the new Official Control
Regulation, (EU) 2017/625
1.c Liaise with Campden BRI to discuss and implement challenge testing activities
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1.c Liaise with CEFAS for any overlapping NRL activities
1.d Provide regular updates to the FSA on NRL activities by producing monthly
reports and meet on a quarterly basis
1.d Produce and submit annual report to the FSA on NRL activities for 2020 to 2021
1.e Maintain and update the NRL web content on the PHE website
2 Advice and representation within the UK and internationally
2.a Provide impartial expert advice to FSA, OLs and other UK laboratories, upon
request
2.b Represent the UK at relevant international meetings and working groups; consult
FSA prior to meetings and submit an internal report after attendance of meetings
2.c Attend training workshop at international organisations, where relevant and after
successful applications
2.e Keep abreast of methodology developments and advise FSA and OLs (eg,
Service Level Agreement for CPS toxin testing)
2.g Participate in the BSI AW9 microbiology committee
2.g Participate in Working Group to revise the ISO/TS 13136:2012 (PCR detection of
STEC)
3 Production of standard operating procedures, codes of practice and guidance
documents
3.a Update and expand food methods archive on NRL website
3.a Prepare a guidance document for OLs and the FSA on the use and validation of
alternative methods for testing Official Controls
3.a Produce a poor performance protocol for OL participation in the EFL proficiency
test scheme
3.a Draft a manuscript for peer-review summarising 4 years of OL performance of
the EFL PT scheme
4 Compliance assessment via audits and ring trials
4.a Ensure consistency and quality of testing approached applied by UK OLs and
support where necessary
4.b Liaise with FEPTU and monitor OL’s comparative testing performance and assist
OLs in the implementation of corrective measures
4.b Evaluate OL’s performance using trend analysis
4.c Coordinate the participation of OLs in international method validation studies and
other initiatives and report to FSA
4.d Participate as UK-NRL in proficiency tests and method validation studies
organised by the EURL (where available) and report to FSA
72020 to 2021 Report of UK National Reference Laboratory for Food Microbiology
4.e Organise Skype/classroom-based workshops for UK OLs, dependent on the
outcome of the audit (1.b) and OL needs
5 Co-ordination within the UK of international initiatives
5.a Support the food aspect of the EU-wide AR monitoring (Decision 2013/652/EU),
liaising with FSA, OLs relevant Reference Laboratories and APHA.
5.a Liaise with APHA, audit and review strategy for harmonization of existing
antimicrobial resistance testing
5.a Provide information regarding Whole Genome Sequencing when requested from
the EURLs, and participate in any related workshops, proficiency testing, training
and guidance documentation, where necessary
6 Communication of results and data use
COVID-19 and EU Exit
During this annual report’s time period, COVID-19 emerged, spread and caused a pandemic
which has forced several lockdowns and different ways of working on a global scale. The NRL
activities were directly affected, as all 6 EURLs, situated in different EU countries, had to cancel
or postpone their planned activities. The NRL also offered mutual support to UK OLs in terms of
advice, procuring consumables or testing diverted samples for public health needs.
In addition, the transition period to leave the EU was during this time period. The NRL has
liaised with FSA, DEFRA, and PHE EU Exit departments to ensure transparency and planning,
as communication and collaboration with the EURLs was at risk. Before the UK was due to
leave the EU, the NRL received a letter from the EU Commission, allowing the EURLs to accept
the UK (except Northern Ireland) as a third country to participate in their activities. Between
December 2020 and February 2021, the NRL have confirmed that all 6 EURLs accept the UK
NRL for Food Microbiology as a third country. Therefore, throughout this time the NRL has
continued to communicate with the EURLs.
Despite these challenges, the NRL has managed to successfully participate in all of the relevant
activities that the EURLs have offered, including attending meetings and training and
participating in proficiency testing, most of which were arranged between September and
December 2020.
82020 to 2021 Report of UK National Reference Laboratory for Food Microbiology
Core Function One: Secretariat services
Dissemination of information from international
organisations
The 6 EURLs send information concerning new reports, outbreaks and other related topics to
the NRL. Information is also sourced from other international organisations, such as the EU
Commission, World Health Organization (WHO), CODEX, European Food Safety Authority
(EFSA) and European Centre for Disease Prevention and Control (ECDC). These are then
cascaded to the appropriate personnel and stakeholder(s) (For example, OLs, FSA, Food
Standards Scotland (FSS), PHE FW&E, Epidemiology and Reference Units, Scottish Reference
Laboratories, Animal and Plant Health Agency (APHA), Agri-Food and Biosciences Institute
(AFBI) and Centre for Environment, Fisheries and Aquaculture Science (CEFAS)), with any
additional information or advice on further steps to be taken. The NRL also receives
questionnaires and surveys from the EURLs regarding NRL and/or country-wide practices.
These communications are described below by work activity with links to the EURLs’ websites
in the Annex; information concerning meetings, training, proficiency tests (PTs) and ISO
standards are incorporated into the relevant sections of this report. Where available, the EURLs’
work programmes can be found in the Annex.
General information disseminated
In April 2020, there was an EFSA call for an AMR tender for epidemiological expertise to
support topics related to Regulation 429/2016 or Animal Health Law, which the UK NRL did not
submit to. The FSA sent some ‘OCR laboratory guidance’ for Regulation (EU) 2017/625 in July
2020, which was circulated to OLs.
Information from DEFRA included a letter and guidance on testing and certification on high risk
foods of non-animal origin and a monthly Codex update newsletter, which the NRL have
registered for and have received 2 newsletters.
The NRL also received an invitation to a Spanish workshop; however, the meeting was local for
Spain and not directly applicable for the UK NRL to attend.
Listeria monocytogenes
From April 2020 to March 2021, the Listeria EURL sent 4 external reports, including the EFSA
opinion on ‘Public risk by Listeria monocytogenes in frozen fruit and vegetables including herbs,
blanched during processing’ and a Joint ECDC-EFSA; report on European monitoring of L.
monocytogenes isolates from food and clinical cases (ELiTE). In addition, 2 EURL-led reports
92020 to 2021 Report of UK National Reference Laboratory for Food Microbiology
were received regarding a frontline typing method to PCR-screen multi-locus sequence typing
(MLST) types (GenoListeria), and a review of consumer temperatures used in Europe to further
inform challenge testing guidance.
The Listeria EURL circulated clarification on the estimation of measurement uncertainty for L.
monocytogenes detection and enumeration, in April 2020, stating the unsuitability of ISO 19036
for intermediate values and qualitative methods.
In May 2020, the Listeria EURL informed the NRL network that their activities were affected by
the COVID-19 pandemic, and that some would be delayed until the Autumn. The EURL also
had a change in management announced in September 2020.
The Listeria EURL shared information regarding a rhamnose negative Listeria monocytogenes
strain, which was circulated to relevant colleagues.
Coagulase-positive staphylococci
The coagulase-positive staphylococci (CPS) EURL notified the NRLs in May and July 2020
regarding problems with a batch of Ridascreen SET Total kit for detecting staphylococcal
enterotoxins. The NRL does not use this kit, but information was sent to OLs.
Three EURL-led documents were circulated; 2 for whole genome sequencing (WGS) processes
and one to prepare material for proficiency testing for staphylococcal enterotoxins. There was
an invitation to submit articles to Toxins journal, which was sent to PHE bacterial toxin experts.
Organisational changes were also communicated from the CPS EURL; activities affected by the
COVID-19 pandemic, suspension of services for enumeration and typing for 2 weeks in January
2021 due to laboratory renovations and a new EURL CPS manager (Jacques-Antoine
Hennekinne) following the departure of Bertrand Lombard in 2020.
Escherichia coli (including STEC)
The NRL received 4 outbreak alerts from the EURL; 2 from USA, and 2 from Canada. This was
lower than previous years, possibly due to the pandemic.
The EURL requested all NRLs to check the contact details on the EURL website and also
cascaded their planned activities for 2021. In addition, in November 2020, the EURL informed
the network that their website was inaccessible due to platform migration work. At the time of
writing, the website has recently been launched (see Annex for weblink).
In March 2021, the EURL circulated a validation data report pertaining to the ISO TS 13136,
detection of STEC. This was forwarded to all OLs and other relevant laboratories.
102020 to 2021 Report of UK National Reference Laboratory for Food Microbiology
Campylobacter
In June 2020, the EURL sent an email regarding the process hygiene criterion 2.1.9 and
reporting the measurement uncertainty (MU); they recommended that the MU should be
calculated so if requested by the competent authority it is available. This information was sent to
OLs. The EURL concluded that further work is required to define MU in relevant matrices, which
will be shared with NRLs.
EURL Campylobacter informed the NRL network of an EFSA-ECDC tender to produce the EU
One Health Zoonoses Report; however, the UK was unable to apply for this tender due to
leaving the EU.
The EURL also circulated news of future events to all the NRLs, including the 2021 workshop in
September 2021, 2 PTs and 2 ILTs and a WGS training course.
Salmonella
Four quarterly EURL newsletters were received by email, informing NRLs of EURL activities,
such as proficiency tests, workshop preparation and literature searches of relevant Salmonella
scientific papers. These were forwarded to the FSA, the OCLs and other relevant laboratories in
the UK. The EURL newsletters can be found in the Annex.
There was EURL correspondences concerning 2 Epidemic Intelligence Information System
(EPIS) Salmonella clusters in May 2020 and September 2020. The NRL log these and contacts
the relevant staff in PHE to respond back to the EURL with the requested information.
Antimicrobial resistance
In April 2020, the EURL-AR forwarded a message from the EU Commission to laboratories
regarding maintaining accreditation for diagnostic testing during the COVID-19 crisis; this was
sent to FSA for information. The EURL also informed NRLs in September that new rules for
monitoring AMR in food will be adopted into EU legislation (published in November as Decision
(EU) 2020/1729). Linked to this Decision, a working group meeting report and presentation was
sent from the EURL in March 2021 to present the monitoring framework of the new Decision as
well as the EURL WGS protocol.
The EURL announced in May 2020 of WGS information on their website and in June a list of
upcoming activities. The EURL sent their annual newsletter to all NRLs in December 2020 (see
Annex), featuring the new AMR Decision (2020/1729/EU) and the new minimum inhibitory
concentration (MIC) panels to support this, using ResFinder 4.0 for genotyping and in silico
antibiograms and other research and development and projects in the EU.
The EURL forwarded external communications regarding antimicrobial resistance over the
reporting period to the NRLs, including country AR reports and action plans from Sweden,
112020 to 2021 Report of UK National Reference Laboratory for Food Microbiology
Denmark, Canada and the US, meeting invitations and reports for the World Antibiotic
Awareness Week, the WHO GLASS Technical document launch, implications of the Nagoya
Protocol and an extended-spectrum Beta-Lactamases E.coli Tricycle protocol webinar. An EMA
concept paper to reduce resistance for Article 40(5) of Regulation (EU) 2019/6 and an FDA
public consultation to discuss ‘Potential Approach for Ranking of Antimicrobial Drugs according
to their importance in human medicine; a risk management tool for AR drugs’ was received. The
EURL also circulated an external newsletter from Food and Agriculture Organisation of the
United Nations, which is funded by the EU Health Programme. These were all assessed and
circulated to appropriate colleagues in the UK.
Parallel correspondence from various EURLs
EURLs are involved in joint horizontal activities and regulations; consequently, the UK NRL
receives the same information from different EURLs. Between April 2020 and March 2021, the
following were received and cascaded to relevant stakeholders.
An in-house ‘Standard Operating Procedure (SOP) on library preparation for
sequencing’ from the CPS and Listeria EURLs
CEN/ISO 2020 plenary reports from EURL Listeria and CPS, including a tailored
report affecting CPS
From the CPS and Listeria EURL, a letter of Bertrand Lombard’s retirement as
EURL coordinator.
Related to Core Function(s): 1.a, 1.c, 2.d, 2.e, 2.f, 4.c, 5.a
Production of NRL quarterly newsletters
Since 2016, the NRL have produced quarterly newsletters to disseminate information to OLs
and other stakeholders of NRL activities and aspects of food microbiology that could affect
them. A brief description of the newsletters’ content is listed below and are available in the
Annex.
June 2020 included EURL and FEPTU activities under lockdown, the 2019 OL
Audit, and a brief document update.
September 2020 described 3 of the EURL’s workshops, which were held virtually,
the OL performance in the 2019 to 2020 EFL PT scheme and upcoming relevant
events.
December 2020 detailed how EU Exit has affected how the NRL will interact with
the EURLs, of the OCRs being transferred into UK Statutory Instruments, the OL
User Day in October and a method update.
March 2021 reported supporting an EU Exit and testing imported foods session
together with the PHE Food, Water and Environment Microbiology Network
122020 to 2021 Report of UK National Reference Laboratory for Food Microbiology
(FWEMN), the EU One Health 2019 Zoonoses report, and the updated Food Law
Code of Practice being published.
Related to Core Function(s): 1.a, 2.d, 2.e, 2.f
Co-ordination of the 2020 OL User Day
The NRL held the eighth annual User Day on 20 October 2020. This was arranged via Microsoft
Teams, due to COVID-19 restrictions and organised as a shorter half day meeting. The agenda
focused on activities from the EURLs, the 2018 EU One Health Zoonotic report and a review of
foodborne incidents in 2019 to 2020 (see Annex for agenda). It was well received, with over 30
delegates attending from 13 OLs, PHE’s Gastrointestinal Bacteria Reference Unit (GBRU) and
the Food and Environmental Proficiency Testing Unit (FEPTU), FSA, APHA and Campden BRI.
Feedback was good from those attended and we had some useful suggestions, including
having a second virtual meeting in the Spring and to cut the number of presentations to allow for
further discussion. Some delegates replied that it was useful to attend virtual meetings which
allowed other colleagues to attend from their laboratory whilst not needing to travel. In contrast,
others missed the face-to-face interaction including the opportunity to network. Slide
presentations are available on request.
Related to Core Function(s): 1.a, 1.b, 1.c, 2.a, 2.d, 2.e, 2.f
Assist in disseminating and responding to EPIS and
other alerts
The NRL have been receiving EPIS and other alerts from the EURLs since April 2018.
However, only 2 from the Salmonella EURL were received for this reporting period, and this
may be due to both the UK leaving the EU and the COVID-19 pandemic.
The EPIS and other alerts are logged by the NRL and relevant staff in PHE are contacted, as
the EURL are requesting information on any related isolates from non-human origin. The
specialist PHE staff then looks in the UK database to identify any closely related strains relating
to the cluster concerned. The NRL then responds to the EURL of any information from PHE
colleagues concerning the enquiry.
Related to Core Function(s): 1.a, 2.a
132020 to 2021 Report of UK National Reference Laboratory for Food Microbiology
2019 Audit: Official Laboratories’ capabilities and
requirements
The UK NRL has undertaken 3 audits since 2013 to ascertain the Official Laboratories’
capabilities and range of microbiological testing for food. These audits have helped identify
training and educational gaps, which the NRL organised and delivered to the OLs. The most
recent audit in October 2019 was performed to update existing information and to ascertain if
OLs need support concerning recent updates in ISO Standards and the new EU Official Control
Regulations (EU 2017/625).
At the time of writing, the data is being analysed and compared to the previous audits: a report
will be published by the end of the year.
Related to Core Function(s): 1.b, 2.d, 2.e, 4.a
Review content of the UK Food Examiner register
Since 2014, the NRL has established and maintained a Food Examiner register to assist FSA to
rapidly contact appropriate local support from the OLs. The register was updated using data
from the audit and sent in July 2020 to FSA.
Related to Core Function(s): 1.b, 4.a
Liaise with APHA regarding mutual NRL activities
(Campylobacter, Salmonella and antimicrobial
resistance)
There are shared UK responsibilities for Salmonella, Campylobacter and antimicrobial
resistance (AR), and which participation in EURL activities are mutual between PHE and APHA.
EU Exit has impacted on these mutual activities and therefore liaison meetings between the
NRLs from PHE, APHA and AFBI for Northern Ireland increased from 6-monthly to 3 in the
reporting year; July 2020, November 2020 and February 2021. Due to the COVID pandemic,
EURL workshops were remote and the UK were allowed to join these at no cost from both PHE
and APHA. Contingency planning and participation of all EURL activities such as the annual
workshops, training events and participation in ring trials, were discussed and agreed at these
liaison meetings. These meetings have strengthened relations and allows transparency
between the 2 NRLs, to ensure there is co-ordination of activities.
Related to Core Function(s): 1.b, 4.c, 5.a
142020 to 2021 Report of UK National Reference Laboratory for Food Microbiology
Liaise with FSA regarding the new Official Control
Regulation, (EU) 2017/625
The relevant OCR Articles pertaining to OLs came into force on 14 December 2019, and after
some consultation with stakeholders (including the UK NRL), Defra and FSA issued a guidance
to OLs to clarify obligations to comply to the new OCRs. Related to this, a workshop was
arranged by FSA in September 2020, to provide an update on the government’s plans for EU-
GB imports post transition period and how this could affect sampling levels for imports in the
future. All the UK NRLs and OLs were invited and the UK NRL contributed to discussions. As a
follow-up to this meeting, FWEMN arranged a meeting in March 2021 and invited FSA to
present an update regarding EU-GB imports to the UK NRL OLs.
FSA has also sent relevant documents for the UK NRL to comment on before issuing and
finalising. The ‘Questionnaire for designation of Official food/feed laboratories’ was received in
October 2020 and relates to Article 37 in the OCRs which require laboratories to be designated
as OLs in writing from the Competent Authority (FSA). The UK NRL sent comments and
clarifications back to FSA. The ‘Draft memorandum of understanding between UKAS and FSA
and FSS’ was also sent to the UK NRL in October 2020, to clarify the responsibilities for each
body in relation to the OCRs, and the UK NRL submitted comments to FSA.
The UK NRL will continue to support and advise FSA regarding the new OCRs, as these have
been transferred into UK Statutory Instrument 2019 No. 665.
Related to Core Function(s): 1.c, 2.a
Liaise with Campden BRI to discuss and implement
challenge testing activities
The UK NRL arranges yearly meetings with Campden BRI, as they are experts in a wide variety
of challenge testing approaches. They attend working group meetings and participate in
challenge testing proficiency tests organised by the Listeria EURL and are on working groups
for relevant ISO Standards. A meeting was held remotely in May 2020 and the ISO Standard
20976 series on challenge tests in food were discussed, along with EURL shelf life documents,
participation in PTs and other relevant guidance.
Related to Core Function(s): 1.c, 2.a
152020 to 2021 Report of UK National Reference Laboratory for Food Microbiology
Liaise with CEFAS for any overlapping NRL
activities
Since January 2019, as a result of restructuring the EURL for monitoring bacteriological and
viral contamination of bivalve molluscs (previously held by CEFAS), CEFAS became the UK
NRL for foodborne viruses and bacteriological contaminants of shellfish. Therefore, CEFAS
joined the mutual NRL networks for E.coli and Salmonella and the UK NRL forwarded any
correspondence from the 2 EURLs relating to PT participation and meeting attendance.
Related to Core Function(s): 1.c, 2.a
Provide regular updates to Food Standards Agency
Due to the pandemic and social restrictions, NRL representatives met with FSA quarterly via
MicrosoftTeams (17 June 2020, 16 September 2020, 14 December 2020, 23 March 2021) to
discuss progress made, difficulties met, and future or new activities (see Annex for minutes). In
addition, monthly reports listing NRL activities have been submitted electronically to the FSA
(see Annex).
Related to Core Function: 1.d
NRL Web Content
Information about the NRL has been held on the Public Health England section of the GOV.UK
website since 2013. There is access to NRL annual reports, 10 standard methods, a public
health management guidance, and reports of the 2016 and 2013 OL audits. There is also
general information about the NRL, expert witness information, and contact details on the web
page. The standard methods are periodically reviewed and updated, and the NRL will continue
to increase the collection, where relevant.
For ease of access, OLs and other stakeholders are advised to use a search engine and type
‘fwe nrl’, as the NRL web page is normally the top hit.
Related to Core Function(s): 1.a, 1.b, 1.e, 3.a
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Core Function 2: Advice and representation
within the UK and internationally
Provide impartial advice to FSA, OLs and other UK
laboratories
Requests are received for expert advice to the NRL from small business organisations to
European institutes, and these have increased as the UK NRL has become established. Those
between April 2020 and March 2021 are briefly reported and categorised below.
General
1. Eight separate requests to microbiologically test food or water, which was forwarded
to the relevant laboratories.
2. A private biotech company requesting a collection of microorganisms, where they
were advised to contact the National Collection of Type Cultures (NCTC).
3. One request for Summer placement at NRL from a biological sciences student; they
were referred to the PHE FW&E Microbiology Services.
4. Eight laboratory enquiries concerning methodology; 4 concerning media availability
or methods for Salmonella detection, specific testing of STEC detection for irrigation
waters, an overseas request for PHE PCR methods and outbreak investigations,
enquiry of which DNA extraction method is used for L. monocytogenes and another
NRL asking other EU laboratories how they share their WGS data openly; all of
these were dealt by NRL experts.
5. Following NRL disseminating material on Measurement Uncertainty (MU), 2 queries
were received; one regarding the calculations for MU and the other on the use of
MU.
6. Two queries concerning disinfectants against COVID-19.
7. An overseas query as to whether the UK NRL are serving them as their NRL for
CPS, which the UK NRL does not.
8. Five FSA requests or consultations for Official Control or Food Law related
documentation, including the OL designation questions, a draft memorandum of
understanding between FSA, FSS and UKAS, and a review of the Food Law Code
of Practice, Food Law Practice Guidance and implementation of the Competency
Framework.
9. Five other miscellaneous queries from FSA; 2 concerning testing methods, 2
regarding EURL or NRL activities and a WHO call for Technical Expert Group on
Food Safety.
10. Four OL queries including 2 relating to Official Control work and a request for FW&E
National and local survey reports.
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11. General public enquiry regarding yeast allergy and vitamin B; NRL advised enquirer
to their local authority trading standards office.
12. One pricing enquiry from an NHS Trust for Listeria testing.
13. Codex call for experts on water safety used in production of fishery and dairy
products, which was passed to PHE and NRL experts.
Listeria
1. In June 2020, the Listeria EURL informed the NRL network that a working group
would be set up for a RT-PCR scheme to screen MLST Clonal Complexes; the UK
declined the invitation as WGS is used as the primary typing tool at PHE.
2. All NRLs were requested to update their contact details for the EURL website, which
the UK NRL completed.
3. Two guidance documents were circulated from the Listeria EURL and received for
comments; the ‘Technical Guidance on challenge test and durability studies’ and
‘technical guidance on sampling food premises for Listeria detection’; the NRL
commented on both.
Coagulase-positive staphylococci
1. All NRLs were requested to update their contact details for the EURL website, which
the UK NRL completed.
2. In November 2020, a draft SOP was circulated to the NRL network on artificial
contamination of CPS enterotoxin in food matrices for PT from the EURL; as the UK
NRL does not routinely test for staphylococcal enterotoxins in food, this was
archived.
3. The EURL requested NRLs to submit strains for their CPS reference strain
collection, via a mutual agreement, to develop typing procedures; the UK did not
send any relevant isolates.
Campylobacter
In August 2020, the EURL Campylobacter requested information on foods that have
been analysed for Campylobacter in Member States, which the NRL completed.
Ahead of the EURL meeting, 2 surveys were received from the EURL regarding
transportation and WGS practices and the NRL collated information from experts
and submitted responses.
In September 2020, the EURL Campylobacter requested information regarding
Preston broth use; as the NRL at PHE does not use Preston broth, the NRL did not
comment.
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Salmonella
In March 2020, the EURL launched an EU monitoring of S. Mikawasima isolates in
food, animals, animal feed and the environment for 2020, to investigate the source
of human cases; the NRL periodically checked the UK database and found no
isolates from food or the environment.
The Salmonella EURL briefed the NRL network that there would be an ISO vote of
whether ISO 6579-4 (identification of monophasic S. Typhimurium using PCR)
should become a New Work Item Proposal; the NRL did not comment as the draft
was at a very early stage.
The EURL notified the network there was a Salmonella Typhimurium/S. Anatum
investigation into contaminated nuts; however, the UK was already involved and had
sent further WGS data.
STEC/E.coli
In March 2021, the EURL E.coli requested update contact information to publish on
their new website, which the UK NRL completed.
Antimicrobial resistance
1. Two emails originating from the One Health Harmony CAP project was forwarded
via the AR EURL; in May 2020 requesting AR methods and in September a survey
collecting sampling and testing information for Salmonella and Campylobacter; the
NRL collated and submitted information.
2. The NRL received a public consultation of an EFSA (BIOHAZ) scientific opinion on
the ‘maximum levels of cross-contamination for 24 microbial active substances in
non-target feed’.
3. In February 2021, the AR EURL request all NRLs to check and update their contact
information, which the UK NRL completed.
Related to Core Function(s): 2.a, 2.d
Representation at relevant international meetings
and prepare meeting reports
To be inclusive of all network meetings for 2020 to 2021, the reporting period has been
extended back to January 2020 to incorporate all 6 EURL meetings. Due to the COVID-19
pandemic and that the UK had entered that transitionary period of EU Exit, there have been
restrictions concerning attendance to EU meetings. Consequently, the UK NRL was unable to
192020 to 2021 Report of UK National Reference Laboratory for Food Microbiology
attend the Listeria EURL meeting but were able to attend the remaining 5 EURL meetings;
coagulase-positive staphylococci (CPS), Escherichia coli (incl. STEC), Campylobacter,
Salmonella and antimicrobial resistance (see Table 2). Where available, agendas for the
meetings were forwarded to the FSA as they were received (see Annex); a presentation from
the UK was made at the Campylobacter meeting. Notes were consolidated from attendance and
individual meeting reports were submitted to FSA (see Annex).
Table 2. List of international meetings, January 2020 to March 2021
EURL Meeting Date: From Date: To Location Attendees
Listeria 30 January
monocytogenes 29 January 2020 2020 Paris, France Unable to attend
Coagulase- Shona Neal
positive 24 April Amisha Vibhakar
staphylococci 22 April 2020 2020 Virtual Kevin Longmaid
Shona Neal
Antimicrobial 29 April Amisha Vibhakar
resistance 29 April 2020 2020 Virtual Frieda Jorgensen
18 Amisha Vibhakar
September Shona Neal
Salmonella 17 September 2020 2020 Virtual Marie Chattaway
22 Shona Neal
September Amisha Vibhakar
E. coli 21 September 2020 2020 Virtual Heather Aird
30 Amisha Vibhakar
September Shona Neal
Campylobacter 29 September 2020 2020 Virtual Frieda Jorgensen
Related to Core Function(s): 1.a, 2.b
Attend training workshops at international
organisations
Due to the COVID-19 pandemic, most of the EURL training was cancelled or postponed, as
these are held best in a face-to-face environment and require practical hands-on experience in
a laboratory setting. Despite this, the UK NRL were able to register and attend for the
‘implementation of colony-count technique according to Standard ISO 7218’, organised by the
Listeria and CPS EURLs, held in September 2020. The training was given online over a day
duration and the attending individual found it useful and would recommend it to other
202020 to 2021 Report of UK National Reference Laboratory for Food Microbiology
colleagues. Learning material and links to web sources for further information on this training
was circulated to FW&E colleagues.
Other training was delivered by the AR EURL, including a 5-day virtual course in October 2020,
covering phenotype interpretation and genotype and WGS analysis. As the training was online,
several colleagues from the UK NRL/PHE were able to register and attend. The EURL AR used
Microsoft Teams as the platform and were able to share documents and recordings of the
sessions so that training could be done by participants at their next available free time. The
feedback was very good as they learnt about epidemiological cut-off values and MIC reading;
microbroth testing will be implemented in PHE. Participants are encouraging others to use the
material available for training and knowledge purposes (see Annex).
The AR EURL also arranged 3 webinars to present topics related to the new Commission
Implementing Decision (EU) 2020/1729 for the monitoring and reporting of antimicrobial
resistance in zoonotic and commensal bacteria, which applied from 12 January 2021. The
webinars, held in November and December 2020, were; ‘New Sensititre plate production for the
EU monitoring of AMR in food’, ‘Compliance to the new AMR Decision’ and ‘Protocol for WGS
and bioinformatic analysis of bacterial isolates related to the EU monitoring of AMR’. The UK
NRL circulated connection details for all 3 webinars and were attended by at least one person
representing the UK NRL. However, it is unclear at the time this report was written, if UK will
report AR data to the EU now the UK has left the EU.
Related to Core Function(s): 2.c, 2.e
Keep abreast of methodology developments –
membership of FW&E working groups and other
PHE steering committees
Due to the low referrals of food to request detection of Staphylococcal enterotoxin, the UK NRL
outsources this method to an NRL in the Netherlands. Requests for this test on official control
samples has not been received from an OL for over 3 years. This arrangement is known to the
FSA.
Since 2016, the NRL has increased its involvement within the FW&E methods and training
working groups to advise, support and facilitate relevant implementation from international
method changes and training events. The NRL participation to meetings, proficiency trials and
external working groups equips the NRL team with information to keep abreast with
methodology, access to training and key changes in the areas of responsibility. These aspects
are used to maintain the UK capability in these areas.
212020 to 2021 Report of UK National Reference Laboratory for Food Microbiology
The NRL has been tasked by the FW&E Methods working group to review EU legislation that
has been adopted into UK law and the impact these have on FW&E methodology and guidance
documents. The NRL has also advised on improvements to the design of the European Food
Legislation proficiency scheme based on a continual assessment of OL performance data and
has acted as scheme consultant and attended a FEPTU steering group meeting this year.
Related to Core Function(s): 2.e, 2.f
Participation in the BSI AW9 microbiology
committee and other working groups
Due to COVID-19 restrictions, the BSI AW9 committee met virtually twice, in May and August
2020. At least one representative from PHE/UK NRL for food microbiology attended the
meetings where the status of the related ISO Standards were reviewed. The UK NRL
representative was asked to select and invite representatives from: APHA and a statistician
from PHE to join the committee, which they did and had a positive outcome for the APHA
representative.
The NRL representative receives draft and final draft ISOs (DIS and FDIS) from the BSI AW9
portal throughout the year. Consequently, the NRL submitted comments for the following DIS or
FDIS Standards:
• parts 3, 4 and 5 of the ISO 16140 series (Method validation)
• ISO 20836 (Performance of thermal cyclers)
• ISO 6888 parts 1 and 2 (Enumeration of coagulase-positive staphylococci
(Staphylococcus aureus and other species))
• ISO 23418 (Whole Genome Sequencing for typing and genomic characterization of
foodborne bacteria)
There was also a call for comparison data for ACC pour vs spread/spiral counts in June 2020.
The NRL received data from one OCL and this was forwarded to the working group.
A representative of the UK NRL is a member of the CEN TAG18 expert working group for the
revision of the ISO TS 13136 standard (PCR detection of shiga toxin-producing Escherichia
coli) which met remotely in November 2020. Revision of the 2 parts of the ISO standard were
discussed, which included:
• changes in the enrichment conditions, including the medium and the temperature,
from modified tryptone soya broth or BPW incubated at 37°C to BPW at 41.5°C.
• detection of eae to be included in Part 1; it is important to pursue isolation of STEC for
all stx positive samples, even when eae is absent
222020 to 2021 Report of UK National Reference Laboratory for Food Microbiology
• informative texts describing dilution and/or acid treatment of enrichment before
streaking/plating to enhance the growth of single colonies
• to add the identification of all stx subtypes and the presence of the eae gene in Part 2
A UK NRL representative from Campden BRI, who has expertise in challenge and shelf life
studies, has attended various working group meetings and commented on the EURL Listeria’s
‘Technical guidance on challenge tests and durability studies for assessing shelf-life of ready-to-
eat foods related to Listeria monocytogenes’. In November 2020 a final draft of Version 4 was
sent to the NRL network awaiting final approval.
There was also an invitation to join 2 working groups from the Listeria EURL; one to update
their guidance on ‘Sampling food procession areas and equipment for the detection of Listeria
monocytogenes’ and the other to explore a ‘ Multi-Locus Sequence Typing Clonal Complex
determination, Real-Time PCR scheme (Geno-Listeria)’. The UK NRL submitted a null response
for both working groups; however, comments were sent from the UK NRL for the sampling
guidance.
Related to Core Function(s): 2.e, 2.f, 2.g
Core Function 3: Production of standard
operating procedures, codes of practice and
guidance documents
Update and expand food methods archive on NRL
website
There are currently 11 Standard Methods and/or guidance available on the NRL website (Table
3). These methods are based on PHE in-house methods and ISO standards, and assist OLs to
comply with the requirements of the EU Microbiological Criteria Regulations. Most of the
relevant ISOs been revised under Mandate M/381, and the corresponding NRL methods are
undergoing review and updates. Other relevant PHE Standard Methods have been identified
that complement the NRL activities; these are also under the re-formatting process and will be
archived on the NRL website. In addition, PHE SOPs are available to OLs upon request.
232020 to 2021 Report of UK National Reference Laboratory for Food Microbiology
Table 3. List of Standard Methods archived on the NRL website, March 2021
Version
Document No. Title No.
FNES63 Determination of pH in food and water samples 2
FNES67 Determination of water activity in food 2
FNES8 [F12] Enumeration of coagulase positive staphylococci 4
(Staphylococcus aureus and other species)
FNES26 [F2] Preparation of samples and dilutions, plating and sub-culture 4
FNES3 [F8] Enumeration of β-glucuronidase positive Escherichia coli: Pour 3
plate method
FNES22 [F19] Detection and enumeration of Listeria monocytogenes and 4
other Listeria species
FNES28 [F22] Enumeration of β-glucuronidase positive Escherichia coli – 3
most probable number technique
FNES16 [F13] Detection of Salmonella species 4
FNES15 [F21] Detection and enumeration of Campylobacter species 4
FNES4 [E1] Detection and enumeration of bacteria in swabs and other 4
environmental samples
FNES18 [Q4] Guidance on Public Health response: involvement of PHE 3
Food Water and Environmental Microbiology laboratory staff in
the investigation of outbreaks of food or waterborne disease
Related to Core Function(s): 1.a, 1.e, 3.a, 4.a
Prepare specific guidance protocols for OLs and the
FSA
The NRL are producing guidance for validating alternative methods in place of the reference
method for the testing of food-borne organisms in food, feed and environmental samples, as
requested by the FSA. The ISO/CEN revision of the relevant Standard (ISO 16140 series) has
been substantially delayed and has impacted on this guidance. In addition, it is the third and
fourth part of this standard which is most relevant to the FSA (Part 3: Protocol for the verification
of reference and validated alternative methods implemented in a single laboratory and Part 4:
Protocol for single-laboratory (in-house) method validation), and these were published in
January 2021 and July 2020 respectively. Therefore, the NRL is leading on a new method for
the FWEMN on the Verification and Validation of Methods based on this ISO Standard series.
The subsequent guidance for FSA will be finalised in 2021 to 2022.
242020 to 2021 Report of UK National Reference Laboratory for Food Microbiology
A poor performance protocol is required if any OLs generate repeated poor results from the EFL
EQA Scheme. However, there has been no consistent poor performance from participant
results (see next section).
A method for Measurement Uncertainty in Testing was drafted by the NRL and approved for
use by the PHE FWEMN in May 2019 (FNES66), and revised in March 2021. To complement
this method, an Excel tool for calculations, based on the international standard ISO 19036/2019,
was developed and revised in March 2021. In this reporting period, an impact assessment was
performed on FNES66 to align this with the new Measurement Uncertainty Standard, ISO
19036:2019, which was published in October 2019.
Related to Core Function: 2.a, 2.d, 3.a, 4.a
Report of 4 years of OL performance of the EFL
scheme
There has been some progress made but it is not yet completed, due to other work priorities
including COVID-19. Therefore, this activity is transferred to the 2021 to 2022 work programme.
Related to Core Function: 3.a, 4.b
Core Function 4: Compliance assessment
via audits and ring trials
OL participation in the European Food Microbiology
Legislation Proficiency Testing Scheme
The National Reference Laboratory is required by the UK Statutory Instrument 665 that adopts
European Regulation (EC) 625/2017 to organise and assess performance of official laboratories
through relevant comparative testing such as interlaboratory studies.
In January 2020, the UK OLs for Food Microbiology were invited to register to the 2020 to 2021
EFL EQA Scheme, as provided by the PHE FEPTU. Based on the requirements of EU
Regulation 2073/2005 (as amended) for the microbiological criteria for foodstuffs, the scheme
enables the performance assessment on the identification, examination and interpretation of
microbiological results of samples tested against these legislative criteria. A full scheme
comprises of 12 samples from 4 distributions based on food categories within the regulation and
results are submitted on a webbased form. However, due to the COVID-19 incident and the
252020 to 2021 Report of UK National Reference Laboratory for Food Microbiology
statutory PHE response, FEPTU suspended their services from April 2020. Business was
resumed in July 2020, but with a limited service and a reduced scheduling of PT schemes (see
Annex). The EFL scheme was redesigned to comprise of 2 distributions, the first in August 2020
(ready-to-eat (RTE) foods) followed by another in March 2021 for miscellaneous foods.
Further details on the food legislation scheme including the revised schedule from July 2020
can be found on the ‘Proficiency testing for food, water and environmental microbiology’ page.
The NRL supports OL participation of this scheme which allows direct performance comparison
across the network of official laboratories but also act independently from the scheme
organisers and the resumption of FEPTU services allowed this to continue for 2020 to 2021.
Results are anonymised, and reports do not disclose the identity of any laboratory. However,
the NRL does monitor the performance of each laboratory, and invite laboratories to seek
assistance from the NRL when experiencing difficulties.
Despite an unprecedented year due to COVID-19, all OLs (14) were registered to receive
samples for the first distribution (EFL53, RTE foods), and 13 the second distribution (EFL54,
miscellaneous foods). Table 4 summarises the samples for 2020 to 2021 and the performance
of laboratories that carried out the examinations.
All laboratories have continued to demonstrate high proficiency for achieving the correct results
to comply with EC 2073/2005 (as amended); all submitting laboratories correctly identified all
testing parameters for the 3 samples in the RTE distribution and for 2 samples in the
miscellaneous distribution. This was followed by a good return from laboratories for the correct
batch requirements for each testing parameter, the correct microbiological results and then
providing the correct conclusion based on the result and no issues were observed for the
detection of Salmonella species, or the enumeration of Enterobacteriaceae and coagulase-
positive staphylococci. Listeria monocytogenes was also identified correctly for most samples,
and laboratories went on to score full marks for this examination. However, the need to detect L.
monocytogenes in powdered products at manufacture saw few laboratories identifying this test.
For sample EFL161 (powdered milk taken at manufacture), only 4 laboratories correctly
identified and examined this sample for L. monocytogenes. A fifth laboratory did identify L.
monocytogenes to be tested, but this was according to the incorrect food safety criteria 1.3 for
the enumeration of L. monocytogenes instead of the correct criteria of 1.2 for the detection of L.
monocytogenes. A similar performance was observed in a previous, almost identical sample
(EFL143, dried milk powder, February 2019), where only 3 laboratories identified the correct
examination for Listeria and the legislation remains unclear on the interpretation of these
products types.
Overall, result entry for the scheme was very good, with most returns gaining full marks for
examination. The reporting of microbiological result remained good with over 97% of detection
and enumeration values being reported correctly. Salmonella species and L. monocytogenes
were the only pathogens included in the scheme this year for qualitative testing, and the
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