update on the annual reporting of vtec in the eu and on ... · pdf filefor e. coli in the eu...

9th Annual Workshop of the NRLs for E. coli in the EU Rome, 20-21 October 2014

Update on the annual reporting of VTEC in the EU and on EFSA activities for molecular typing data collection for food ad animal isolates

NEW EFSA STRUCTURE

AGENDA

Update on the annual reporting of VTEC in the EU

EFSA activities for molecular typing data collection for food ad animal isolates

VEROTOXIGENIC ESCHERICHIA COLI

• 21 MSs and one non-MSs reported data on VTEC in

food

• 11 MSs reported data on VTEC in animals

• Different investigations are not necessarily directly comparable owing to differences in sampling strategies and the analytical methods applied

o The most widely used analytical method, ISO 16654/2001, aims to detect only VTEC O157,

o Fewer investigations have been conducted with analytical methods aiming at detecting all VTEC or selected non-O157 serotypes of VTEC (e.g. ISO/PRF TS 13136:2012)

In 2012, nine MSs reported data on VTEC in fresh bovine meat out of 4,603 units tested: 1.3% VTEC-positive and 0.1% VTEC O157-positive


N pos % pos N pos % pos

Austria fresh at retail single 25 g 56 1 1.8 0 0

O51:H49 eae positive

vtx1 negative vtx2

positive

carcase at

slaughterhouse,

carcase swab

single 1,600 cm2 453 4 0.9 1 0.2

fresh at processing batch 25 g 374 2 0.5 2 0.5

Czech Republic

carcase at

slaughterhouse,

carcase swab

batch 400 cm2 622 8 1.3 0 0

O103 eae positive vtx2

positive (1), O103 eae

positive vtx1 positive

(1), O104 (3), O145

eae positive vtx1

positive (1), O145 (2)

France fresh at processing single 25 g 1,923 7 0.4 3 0.2


and stx1 positive (2),


and stx2 positive (2),

O157:H7 eae positive,

stx1 and stx2 positive

(2), O157:H7 eae

positive and stx2

positive (1)

Germany

carcase at

slaughterhouse,

carcase swab

single 25 g 315 18 5.7 0 0

Hungary fresh at processing single 25 g 77 0 0 0 0

Netherlands fresh at retail single 25 g 555 18 3.2 0 0

Polandfresh at unspecified

sampling levelbatch 25 g 25 0 0 0 0

Romania

carcase - chilled at

slaughterhouse,

carcase swab

batch 100 cm2 203 0 0 0 0

Total (9 MSs) 4,603 58 1.3 6 0.1

Country DescriptionSample

unitN

VTEC VTEC O157VTEC serogroups

Sample

weight

Belgium

In 2012, seven MSs reported data on VTEC in cattle out of 7,843 units tested: 7.4% VTEC-positive and 1.8% VTEC O157-positive


N pos % pos N pos % pos

adult cattle over 2 years at

slaughterhouse,

recto-anal swab

animal 56 18 32.1 0 0

eae negative vtx1 negative vtx2 positive: O113:H21 (2), O178:HNM (1),

O39:H48 (1), O113:H4 (1), O46:H2 (1), O43:Hrough (1), O178:H19 (1),

ONT:H21 (1)

eae negative vtx1 positive vtx2 positive: O183:H18 (2), O91:H21 (1),

Orough:H28 (1), O178:H19 (1), O179:HNM (1), O15:H2 (1), Orough:H2 (1)

eae positive vtx1 positive vtx2 negative: O129:HNM (1)

young cattle (1-2 years) at

slaughterhouse,

recto-anal swab

animal 56 20 35.7 1 1.8

eae negative vtx1 negative vtx2 positive: Orough:H21 (1), O91:H10 (1),

O91:H21 (1), O179:H8 (2), O39:H48 (2), ONT:Hrough (1), O36:Hrough (1),

O179:Hrough (1), O109:H16 (1), O113:H4 (1)

eae negative vtx1 positive vtx2 negative: O168:H8 (2)

eae negative vtx1 positive vtx2 positive: O15:HNM (1), O91:H21 (1),

O178:H12 (1), O22:H8 (2), Orough:HNM (1), O185:H5 (1), O36:H2 (1)

eae positive vtx1 positive vtx2 negative: O103:H2 (1), O26:HNM (3)

eae positive vtx1 positive vtx2 positive: O157:HNM (1)

Denmark at slaughterhouse, faeces animal 25 g 251 21 8.4 21 8.4

Estonia at slaughterhouse, hide animal cm2 246 13 5.3 13 5.3

Finland at slaughterhouse, faeces animal 10 g 1,553 27 1.7 27 1.7

at farm, domestic animal 925 127 13.7 2 0.2 VTEC O103 (2), VTEC O26 (1), VTEC O91 (1)

at farm, domestic herd 709 101 14.2 2 0.3 VTEC O103 (2), VTEC O26 (1), VTEC O91 (1)

calves (under 1 year) at farm,

domesticanimal 542 12 2.2 2 0.4 VTEC O103 (2), VTEC O26 (1)

calves (under 1 year) at

slaughterhouse, caecum,

domestic

animal 25 g 325 78 24.0 0 0

calves (under 1 year) at farm,

domesticherd 692 89 12.9 2 0.3 VTEC O103 (2), VTEC O26 (1)

Italy at slaughterhouse, domestic animal g 112 2 1.8 2 1.8

Swedenat slaughterhouse, faeces,

domesticanimal 2,376 73 3.1 73 3.1 VTEC O157:H (73)

Total (7 MSs) 7,843 581 7.4 145 1.8

Country DescriptionSample

unitN

VTEC VTEC O157VTEC serogroups

Sample

weight

Austria

Germany

With regards to the data reported on VTEC isolates from food and animal samples, it is evident that the analytical method used to detect the bacteria has a major influence on the number of positive samples observed.

Human pathogenic VTEC strains were detected by the reporting MSs from fresh bovine meat occasionally and at low levels. The human pathogenic VTEC serogroups isolated from bovine meat and cattle samples included VTEC O157, O26, O91, O103 and O145.


The importance of bovine meat as a source of human VTEC infections in humans is confirmed by the reported food-borne outbreak data from 2012. Overall, 41 outbreaks caused by human pathogenic E. coli were reported. Out of the total, 12 were supported by strong-evidence. 9 outbreaks were due to VTEC O157, 1 to VTEC O113:H4, 1

to ‘other’ VTEC serogroups, and 1 to non-grouped E. coli positive for LT genes.

Six of them were linked to bovine meat and products thereof. Moreover, 10 strong-evidence VTEC waterborne outbreaks were reported, all by Ireland, and seven were reported to be linked to private water supplies or wells.


AGENDA

Update on the annual reporting of VTEC in the EU

EFSA activities for molecular typing data collection for food ad animal isolates

MOLECULAR TYPING DATA COLLECTION IN THE EU

• The Standing Committee on Food Chain and Animal Health

(representing all EU Member States) approved in December 2012

Vision paper on the development of databases for molecular testing of food-borne pathogens in view of outbreak

preparedness

• The paper was prepared by the EU Commission in consultation with ECDC, EFSA and the EU Reference Laboratories (EURLs).

• The purpose is to encourage collection of molecular typing data to allow integration of data on isolates from human cases, food and animals.

• Regular joint analyses of the data by ECDC, EFSA and EURLs – integration at the EU level

o ECDC to collect molecular typing data from food-borne pathogens isolated from human cases

o EFSA to collect similar data from food, feed and animal isolates, in close collaboration with relevant EURLs

• Ownership of the data

o The reporting Member States

o EU Commission if it has financed EURL’s typing or other research projects

• The data collection to cover initially Salmonella, VTEC and Listeria with PFGE and MLVA (S. Typhimurium) methods

• Other methods and pathogens can be taken aboard later on



In particular, EFSA is requested:

1. to develop and manage a database on the above specified isolates from food and animals; access to the database will at all times require the agreement of EFSA, except for national data which should remain accessible for the respective national institutes;

2. to develop, jointly with the ECDC and in consultation of the relevant EURL, a data dictionary with harmonised parameters for the data fields and terminology to be used, when appropriate, in both the database on food and animals isolates and in the database developed by ECDC on human isolates;

3. to develop tools for the uploading of data by the EURL, the respective food/feed NRLs and other official control laboratories;

Terms of Reference


In particular, EFSA is requested:

4. to develop a tool allowing relevant EURL to be involved in the curation of the incoming molecular testing data and the regular verification of database consistency; the involvement of the EURL will be part of their work programme financed by the EU;

5. when considered necessary, to update, jointly with ECDC and in consultation with the relevant EURL, scientific parameters (experiment settings, terminology) included in the database;

6. to regularly provide scientific analyses of the data in collaboration with ECDC and the relevant EURL.

Terms of Reference


EFSA has set up a Working Group:

Objectives:

To define the structure of the data collection system and integration with the human data

To guarantee compatible data collection systems for human, food, feed and animal isolates, based on:

Common nomenclature

Common data dictionaries

Experts from:

ECDC

EURL Salmonella

EURL Listeria

EURL E. coli

National reference laboratories

WG Meetings: 10 meetings held


EFSA has launched three procurements for assistance related to establishing molecular typing data collection for isolates from food, feed and animals.

• Objectives:

– To produce Standard Operating Procedures for molecular testing of Salmonella, Listeria and VTEC isolates and interpretation of molecular typing data

• Procurements signed with the relevant EURLs:

– Salmonella,

– Listeria,

– E. coli

• Meetings: 4 meetings held

• Deliverables: Final SOPs (under final approval)

STRUCTURE OF THE MOLECULAR TYPING SYSTEM

Laboratories from

food/veterinary side

TESSy server

Human reference

laboratories

curators

· Data curation

· Reference data typing

· Joint cluster analysis

· Web interface

Joint

EFSA-

ECDC

database

EFSA environment ECDC environment

EFSA Server

EFSA

molecular

typing

database

Selective

data transfer

Typing Data and

Limited set of Epidemiological Data

Data retrieval

Curated data

Reference type

Curator’s comments

Cluster code

Users and their roles in the Joint ECDC-EFSA database

User Role for food/feed/ animal data Role for human data

Users at MS level

Nominated users for food/veterinary side Data Provider -

Nominated users for Public Health side - Data Provider

Curators

EURL Data Curator / Data analyst -

ECDC curator - Data Curator / Data analyst

European bodies

EFSA Data manager/ Data analyst Data analyst

ECDC Data analyst Data manager/ Data analyst

1

MOLECULAR TYPING DATA COLLECTION


NOTE: Data should be provided at result-based level according to the Standard Sample Description version 2 (SSD2).


Data providers shall guarantee the uniqueness of the identifiers for each submitted PFGE image, result, isolate, sample taken at the national level. If one country has several data providers collecting data, it shall coordinate internally to guarantee the uniqueness of the codes at national level. The responsibility to guarantee uniqueness is completely on MS side and each country can freely adopt any approach to coordinate laboratories in order to satisfy the requirement of having unique ids.

• Epidemiological Data: data about an isolate in terms of sampling time and place, origin (food/ animal type, country of origin, producer) etc. - partly sensitive data

• Typing Data: the results of typing experiments performed on an isolate. e.g. serotype, PFGE pattern, antimicrobial susceptibility results, MLVA results – non sensitive data


EPIDEMIOLOGICAL DATA (PARTLY SENSITIVE) TYPING DATA (NOT SENSITIVE BY ITSELF)

ID Country Animal/Food

Type

Area in the

country

Date of

Sample Serotype PFGE_XbaI AST_NAL

EFSA-001 BE Smoked salmon X 2012-06-01 STANLEY S

EFSA-002 HU Turkey Y 2012-07-01 STANLEY R


Accessibility to the joint database

The access to joint EFSA-ECDC database depends on the type of data (sensitive and non-sensitive) and the users.

Use of data

In line with the orientations provided in the Vision paper, a Collaboration Agreement will be signed by all parties to define data ownership, access, use, publication, procedures and confidentiality.

‘Data owners are always consulted for their permission before

any written or oral publication and/or communication of the data which have not yet been published’

STATUS OF PROGRESS

WG activities

No other meeting of the WG are scheduled.

The technical requirements for the pilot phase have been agreed.

The technical report will be published by end of the year.

Procurements (SOPs for molecular testing and interpretation)

Final reports are under final approval and will be published on the EFSA website.

Trilateral meeting with EC and ECDC

Discussion on policy for data access, cluster analysis, collaboration agreement, Steering Committee.

NEXT STEPS

A Collaboration Agreement is under preparation to ensure a common understanding and approach between all the parties involved with regard to:

data ownership, availability, access, use, publication, procedures, confidentiality.

A Steering Committee will be set up to:

Monitor and evaluate the pilot phase

Identify needs for revision of the data collection system

Develop standard operating procedures for scientific data analyses

It will be a joint Committee composed by staff members from ECDC and EFSA, the relevant EURLs and ECDC’s curators.

Contacts in EFSA [email protected]

http://www.efsa.europa.eu/en/contact/askefsa.htm

All our reports are on www.efsa.europa.eu

mailto:[email protected]

http://www.efsa.europa.eu/en/contact/askefsa.htm



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