The food categories considered in the survey included the food groups most commonly consumed by the population. The food categories and food areas analysed by the FBO laboratories and considered in the survey were the following: dairy products, fish and seafood, meat and products thereof, vegetables and fruits and products thereof, bakery products, egg products, beverages, ready-to-eat mixed meals, and food processing areas and environmental surfaces. Food processing areas referred to any place where foodstuffs are prepared or processed for human consumption, such as rooms for cutting, grinding, cooking or packing food products; and environmental surfaces included surfaces of equipment, floors, walls, ceilings, drains, among others within a food processing plant.

Each food category or food area was analysed by a minimum of 14 and a maximum of 29 FBO laboratories. Beverages was the food category analysed by the lowest proportion (40%) of FBO laboratories participating in the survey, whereas dairy products was analysed by the highest proportion (82.9%) of laboratories. The global trend of dairy consumption has been stable over the time compared to meat and eggs consumption. Currently, Europe has the highest level of dairy consumption with 443.5 kg/capita per year, with the projection to increase (Henchion et al., 2021). Hence, food safety concerns on dairy products, consisting of milk, butter and ghee, and cream could explain the highest proportion of FBO laboratories analysing them. A large proportion (65.7%) of FBO answering the questionnaire analysed five or more food products in their laboratories. Additionally, the majority (62.9%) of FBO laboratories analysed both ready-to-eat and non-ready-to-eat products, probably because nearly all food categories, except beverages, include products in both presentations for human consumption.

FBO laboratories were requested to provide the average number of analysed samples for each of the priority pathogens investigated in the period of 2018—2020. Regarding the six bacterial species, FBO laboratories analysing Campylobacter spp. processed 6,007 samples out of which 636 were positive, FBO laboratories analysing Listeria monocytogenes processed 168,522 samples out of which 62,698 were positive, FBO laboratories analysing Salmonella spp. processed 203,078 samples out of which 61,107 were positive, FBO laboratories analysing Shiga toxin-producing E. coli processed 18,307 samples out of which 128 were positive, FBO laboratories analysing Shigella spp. processed 286 samples out of which 1 was positive, and FBO laboratories analysing Yersinia spp. processed 704 samples out of which 14 were positive. Regarding the five parasites, FBO laboratories analysing Trichinella spp. processed 9,000 samples out of which 1 was positive, FBO laboratories analysing Cryptosporidium spp. processed 800 samples out of which 300 were positive, FBO laboratories analysing Echinococcus granulosus (Sensu lato) and Echinococcus multilocularis processed 500 and 300 samples, respectively, which were all negative, and FBO laboratories analysing Toxoplasma gondii did not process any sample in this period.

Samples of Campylobacter spp., Listeria monocytogenes, Salmonella spp. and Shiga toxin-producing E. coli accounted for 97.2% of the samples analysed by the FBO laboratories during the period of 2018–2020. The four pathogens are regulated by Directive 2003/99/EC, EU member states are obliged to include them in their zoonoses and zoonotic agents monitoring programmes, and moreover, are associated with the highest risk of bacteria-related foodborne diseases in the EU (European Commission, 2003; Lee & Yoon, 2021). FBO laboratories analysing Salmonella spp. processed 49.9% of the samples, followed by FBO laboratories analysing Listeria monocytogenes which processed 41.4% of the samples; probably as a result of the fact that 31 and 28 FBO laboratories considered for this study analysed Salmonella spp. and Listeria monocytogenes, respectively. Regarding parasite-related foodborne diseases, FBO laboratories analysing Trichinella spp. received the majority of samples (9,000), most likely due to Trichinella spp. being the only of the investigated parasites for which there is compulsory-targeted surveillance in slaughterhouses and meat-producing animals placed on the EU market (European Commission, 2015; van der Giessen et al., 2021).

Respectively, 77.1% and 74.3% of FBO laboratories had ISO-standards or an alternative method implemented. Alternative methods included national standards, such as the DIN standards for Germany, and validated alternative methods certified by organizations such as AFNOR, MicroVal, NordVal or others. Accreditation for ISO-standards or an alternative method was reported in 68.6% and 62.9% of FBO laboratories, respectively.

Implementation and accreditation for the ISO-standards or an alternative method was in place in a considerable proportion of FBO laboratories, but did not cover all the pathogens investigated. Official food controls and veterinary laboratories in the European Union, are required by Regulation (EC) No. 882/2004 to implementing a quality management system based on international laboratory management standards, such as EN ISO/IEC 17025 on ‘General requirements for the competence of testing and calibration laboratories’ (European Commission, 2004b; Wilson et al., 2015). The aforementioned aims the improvement of products and customer satisfaction, and to add quality and reliability to the services provided by these laboratories (Neves et al., 2017). Therefore, the respective 77.1% and 74.3% of FBO laboratories with ISO-standards or an alternative method implemented found in the study could be explained.

Additionally, accreditation for ISO-standards or an alternative method was reported in 68.6% and 62.9% of FBO laboratories, respectively. This majority of accredited FBO laboratories could be due to the fact that laboratory accreditation provides a level of standardisation and ensures integrity and accuracy of current food testing results required by national regulatory institutions and other end users to accept laboratory data in support of an integrated food safety system (Wangsness et al., 2017).

10.4% of FBO laboratories sent their isolates for further confirmation to external laboratories (Figure 1).

Sending isolates for further confirmation to external laboratories was not performed by FBO laboratories analysing parasites neither was common for FBO laboratories analysing bacteria. The issue behind this could be that the majority (89.6%) of FBO laboratories have the capacity to process the samples and subtype the isolates received from self-control programmes and consequently do not send their isolates to external laboratories. Moreover, national and international regulatory frameworks support early identification of foodborne outbreaks, and thus the sharing of information and prompt communication, comparability of data, efficient laboratory subtyping and intersectoral collaboration. Nevertheless, this remains occasional and mainly occurring when laboratories are required to a further confirmation of their results by sending their isolates to National Reference Laboratories (Mylius et al., 2018; O’Brien et al., 2020).

Storing isolates was more frequently established but not for all the pathogens investigated. Therefore, 51.1% and 45.8% of FBO laboratories analysing bacteria and parasites, respectively, stored their isolates. FBO laboratories storing their isolates, stored them typically for longer than 1 year (Figure 2).

In order to send isolates for further analyses to National Reference Laboratories or for characterisation and typing of isolates for research, source attribution, collection or conservation purposes at a later stage, laboratories need to improve their preservation procedures and storage capacity. An average of 48.5% of FBO laboratories storing their isolates may reflect lack of awareness of the relevance of storing isolates, insufficient storage capacity and limited budget allocation for the costly use of a cold chain for preservation of isolates. Additionally, the viability of isolates could be reduced after a long-term storage (more than 1 year), hence the laboratories might not invest for this purpose. For instance, isolates of Salmonella spp., E. coli and Shigella spp., preserved by using Tryptic Soy Broth with 15% glycerol, may remain 100% viable even after 5 years of storage under deep freezing (−70 to −80 °C); however, Campylobacter spp. isolates may be more sensitive to temperature changes and preservation techniques, maintaining a lower viability (66.7%) under the same conditions (Sunarno et al., 2021).

Regarding characterisation and typing methods, around 60% of FBO laboratories participating in the study used more than one typing or characterisation method, predominantly MALDI-TOF, antimicrobial resistance typing and PCR, while 40% of FBO laboratories did not type nor characterise the investigated pathogens. Although characterisation methods provide various advantages, like being more sensitive, reliable, time-efficient and less laborious than conventional culture-based methods to detect viable pathogens in foods (Zhao et al., 2014; Foddai & Grant, 2020), they generally demand higher costs, require trained personnel and specialised instruments (Law et al., 2015), which FBO laboratories might not be willing to pay as it is no legal requirement for self-control programmes.

FBO laboratories analysing bacteria used a wider variety of typing and characterisation methods than FBO laboratories analysing parasites. Variability between FBO laboratories was also observed as regards use of Whole Genome Sequencing (WGS) (Figure 3). Despite providing substantial support for surveillance programmes and foodborne outbreak investigations, source attribution studies, and genomic information for antimicrobial resistance, pathogenicity and virulence, only 17.1% of FBO laboratories reported using it (Uelze et al., 2020). Culture-based methods are still considered the gold standard for microbiological analysis of food. These methods represent the first alternative for FBO to comply with Regulation (EC) No. 2073/2005 on microbiological criteria for foodstuffs, because they need easy to use, sensitive and inexpensive tests to monitor foods for the presence of particular pathogens in certain categories of food products (European Commission, 2005; Foddai & Grant, 2020), for either a prompt communication with the competent authorities or to take the correspondent actions in case of unsatisfactory results based on the aforementioned legislation.

In addition to conventional methods, WGS is employed to subtype bacteria by having the ability to look at the entire genome and therefore identifying genes that would determine its survival (Franklin et al., 2021). This, although advantageous for food monitoring and assessments, is not a compulsory requirement for FBO self-control programmes to implementing corrective actions when the microbiological criterion is not met. Moreover, introduction and application of WGS in routine monitoring programmes remain challenging as long as national authorities allocate insufficient resources, like budget and expertise, for WGS capacity building at public health and food safety/veterinary laboratories (García Fierro et al., 2018). Furthermore, the lack of harmonised data, concerns on the legal aspects associated with the collection of genomic data, and in some countries the limited number of collected isolates, generate a false perception that investment in WGS implementation is unnecessary (Nouws et al., 2020).

The majority (76.5%) of FBO laboratories participated in External Quality Assessment (EQA) programmes or proficiency testing programmes, probably because it is considered key component to monitor laboratory performance through reverification of samples, inter-laboratory comparisons and on-site evaluations; and pivotal in laboratory quality management systems to detect and control infections in humans, animals and food (James et al., 2014; Carter, 2017). Additionally, participation in EQA programmes is a requirement for international laboratory accreditation (Manjengwa et al., 2021). Nevertheless, participation in EQA programmes demands costs and resources for capacity-building programmes to support continuous training, which might explain the 23.5% of FBO laboratories that did not participate (Pedersen et al., 2018; Mogeni et al., 2021).

Five countries accounted for the 23.5% of FBO laboratories that did not participate in EQAs: France, Portugal, Netherlands, Finland and Sweden. The two respondent FBO laboratories in France, the eight respondent FBO laboratories in Portugal and the eight respondent FBO laboratories in Netherlands did not participate in EQAs for the analysis of seven (Listeria monocytogenes, Shiga toxin-producing E. coli, Shigella spp., Yersinia spp., Cryptosporidium spp., Echinococcus granulosus (Sensu lato), and Echinococcus multilocularis), six (Campylobacter spp., Salmonella spp., Listeria monocytogenes, Shigella spp., Yersinia spp., and Trichinella spp.) and four (Campylobacter spp., Shiga toxin-producing E. coli, Shigella spp., and Yersinia spp.) of the pathogens investigated, respectively. Shigella spp., and Yersinia spp. were not analysed by any of these countries.

Seven out of nine FBO laboratories analysing Shigella spp., the only non-regulated pathogen among the investigated foodborne hazards, did not participate in EQAs. All participating EU/EEA countries use a passive surveillance system for Shigella spp. France, for instance, has a voluntary notification system for this pathogen and therefore laboratories are not required to participate in EQAs for further accreditation (ECDC, 2022a). Since according to Directive 2003/99/EC it is not compulsory to include Shigella spp. in the monitoring of zoonoses and zoonotic agents in EU member states (European Commission, 2003), laboratories do not have to undergo proficiency testing or EQAs to evaluate and compare their detection protocols for this pathogen with other internal and external laboratories.

Four out of seven FBO laboratories analysing Yersinia spp. did not participate in EQAs. Although Yersinia spp. is a regulated pathogen, its monitoring is subject to the epidemiological situation in each EU/EEA country (European Commission, 2003). For instance, there is neither active monitoring of Yersinia spp. in foods nor national coverage for yersiniosis infections in France. Detection of Yersinia spp. in France follows ISO 10273 standard, based solely on conventional microbiology, followed by isolation of the strain and PCR only in case of positive findings. In Netherlands, Yersinia spp. surveillance system does not exist (ANSES, 2017; ECDC, 2022b). This absence of mandatory surveillance and national coverage in some EU/EEA member states may contribute to lower participation of FBO laboratories in EQAs as accreditation of detection methods for this pathogen may not be relevant.

Four out of nine FBO laboratories analysing Shiga toxin-producing E. coli (STEC) in food did not participate in EQAs. The four FBO laboratories were from France and Netherlands. STEC is notifiable at a national level in all participating EU/EEA countries (European Commission, 2003), except for France where reporting is instead voluntary and based on paediatric haemolytic-uremic syndrome (HUS) surveillance (Jones et al., 2019; ECDC, 2022c); therefore, EQAs for detection methods might be unnecessary for FBO laboratories (EFSA & ECDC, 2021). Furthermore, as stated in the tenth EQA scheme for typing of Shiga toxin-producing E. coli in Europe, further reasons for non-participation in EQAs could be: lack of laboratory capacity, lack of financial means, characterisation or typing method was not relevant to the laboratory, among others (ECDC, 2021).

Harmonisation of sampling and analytical protocols between official laboratories and FBO laboratories could strengthen relationships and build trust between the public and private sectors. Multiple investigations for reconfirmation of results would not be necessary and therefore interventions would become more cost-effective for both sectors. FBO could obtain better trading opportunities by following official control analytical protocols. For instance, the compliance of official control analytical protocols could be used as recognition by the FBO to allocate their products in the market with, perhaps, an increased consumer acceptance. In a hypothetical scenario, national stakeholders and the EU commission could promote the use of official analytical protocols such as the total aerobic viable count (TVC), ELISA, chromatographic tests (e.g., HPLC), the use of ISO-standards as analytical reference methods (European Commission, 2005), and in the same way consider the potential of rapid on-site testing of microbial contamination in food products (Visciano & Schirone, 2020; Santovito et al., 2022), through regulations that reward the FBO that apply these control protocols and consequently, encourage the rest of FBO to perform accordingly.