Volume 33 Issue 6
Jun.  2020
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Adebowale Oluwawemimo, Dipeolu Saheed, Oduguwa Adebankemo, Fasanmi Gabriel Olubunmi, Folorunso Oludayo Fasina. Capacities and Functionalities Assessment of Veterinary Laboratories in South-west Nigeria Using the FAO Laboratory Mapping Tool[J]. Biomedical and Environmental Sciences, 2020, 33(6): 458-463. doi: 10.3967/bes2020.062
Citation: Adebowale Oluwawemimo, Dipeolu Saheed, Oduguwa Adebankemo, Fasanmi Gabriel Olubunmi, Folorunso Oludayo Fasina. Capacities and Functionalities Assessment of Veterinary Laboratories in South-west Nigeria Using the FAO Laboratory Mapping Tool[J]. Biomedical and Environmental Sciences, 2020, 33(6): 458-463. doi: 10.3967/bes2020.062

Capacities and Functionalities Assessment of Veterinary Laboratories in South-west Nigeria Using the FAO Laboratory Mapping Tool

doi: 10.3967/bes2020.062
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  • Corresponding author: Adebowale Oluwawemimo, Tel: 2349085608043, E-mail: oluwawemimo1@yahoo.com, adebowaleoluwawemimo1@gmail.com
  • Received Date: 2019-11-18
  • Accepted Date: 2020-03-31
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  • [1] Masanza MM, Nqobile N, Mukanga D, et al. Laboratory capacity building for the International Health Regulations [IHR(2005)] in resource-poor countries: the experience of the African Field Epidemiology Network (AFENET). BMC Public Health, 2010; 10, 1−7. doi:  10.1186/1471-2458-10-1
    [2] Food and Agriculture Organization of the United Nations. Strengthening veterinary diagnostic capacities: the FAO laboratory mapping tool, 2016. http://www.fao.org/emergencies/resources/documents/resources%20detail/en/c/1039809/. [2019-2-13].
    [3] Schulz LL, Hayes DJ, Holtkamp DJ, et al. Economic impact of university veterinary diagnostic laboratories: A case study. Prev Vet Med, 2018; 151, 5−12. doi:  10.1016/j.prevetmed.2017.12.018
    [4] The Global Health Security Agenda. Fact sheet: the Global Health Security Agenda. 2015. https://geneva.usmission.gov/2015/07/28/fact-sheet-the-global-health-security-agenda/. [2019-2-13]
    [5] Adamu AM, Alimi YA, Akefe IO, et al. Veterinary diagnostic services for the future: Nigeria’s pathway to progress. Biomed J Sci Tech Res, 2018; 6, 5−7.
    [6] Blood DC, Brightling P. National Animal Disease Databanks. In: veterinary information management. Bailliere Tindall, London, 1998; 153-60.
    [7] Kebede H, Melaku A, Kebede E. Constraints in animal health service delivery and sustainable improvement alternatives in North Gondar, Ethiopia. Onderstepoort J Vet Res, 2014; 81, 713−23.
    [8] Manickam TS, Ankanagari S. Evaluation of quality management systems implementation in medical diagnostic laboratories benchmarked for accreditation. J Med Lab Diagn, 2015; 6, 27−35. doi:  10.5897/JMLD2015.0104
    [9] Pacey AA. Quality assurance and quality control in the laboratory andrology. Asian J Androl, 2010; 12, 21−5. doi:  10.1038/aja.2009.16
    [10] Ahmed MM. Quality assurance & quality control in laboratories: a review. J Pharm Qual Assur, 2016; 2, 26−31.
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Capacities and Functionalities Assessment of Veterinary Laboratories in South-west Nigeria Using the FAO Laboratory Mapping Tool

doi: 10.3967/bes2020.062
    Corresponding author: Adebowale Oluwawemimo, Tel: 2349085608043, E-mail: oluwawemimo1@yahoo.com, adebowaleoluwawemimo1@gmail.com
Adebowale Oluwawemimo, Dipeolu Saheed, Oduguwa Adebankemo, Fasanmi Gabriel Olubunmi, Folorunso Oludayo Fasina. Capacities and Functionalities Assessment of Veterinary Laboratories in South-west Nigeria Using the FAO Laboratory Mapping Tool[J]. Biomedical and Environmental Sciences, 2020, 33(6): 458-463. doi: 10.3967/bes2020.062
Citation: Adebowale Oluwawemimo, Dipeolu Saheed, Oduguwa Adebankemo, Fasanmi Gabriel Olubunmi, Folorunso Oludayo Fasina. Capacities and Functionalities Assessment of Veterinary Laboratories in South-west Nigeria Using the FAO Laboratory Mapping Tool[J]. Biomedical and Environmental Sciences, 2020, 33(6): 458-463. doi: 10.3967/bes2020.062
  • Laboratories play significant roles in all the critical processes of detecting rapid infectious disease outbreaks, risk assessments, early warnings, early responses and notifications, and monitoring and surveillance[1,2]. Veterinary Laboratories (VLs) that rapidly identify, respond to and control rapidly spreading and emerging (or re-emerging) infectious and zoonotic diseases is critical to: (1) the financial performance of animal agriculture and international trade; (2) livelihoods of animal related industries; and (3) nutritional status, food security, and the socio-economic well-being of a country[3].

    Over the years, the Global Health Security Agenda (GHSA) has supported collective and sustainable capacity-building at the international, regional and local levels in order to promote rapid detection, prevention or mitigation, and to support responses needed to control emerging infectious diseases (EIDs) outbreaks before they become epidemic. Capacity-building is additionally designed to reduce the impact of naturally occurring outbreaks, as well as intentional or accidental releases of dangerous pathogens[4]. The agenda spurs progress toward implementation of the World Health Organization’s International Health Regulations (2005) (WHO/IHR) and other global health security frameworks, such as the World Organization for Animal Health. Since the Ebola outbreak in West Africa in 2014, the GHSA has been committed to strengthening capacity in infrastructure, equipment, and skilled personnel across sectors, sustainable national biosafety, biosecurity, and especially laboratory systems in Africa, all to ensure a safer world.

    The ability of VLs in developing countries, applicable to Nigeria, is frequently limited by many factors. These factors may be assessed along three dimensions: (1) skilled and competent personnel; (2) adequacy and upgrade of equipment/materials, and (3) the ability to mobilize technical support when needed[5]. To address these limitations in African countries, the Food and Agriculture Organization of the United Nations (FAO) developed a core laboratory mapping tool (LMT-core) to aid in pre-emptive laboratory assessment. Released for public use in May 2014, this instrument can determine and identify gaps in laboratory functions, define strategic pathways, and set targets for capacity building[2]. Currently, to the best of our knowledge, this is the first study in Nigeria to use the FAO LMT tool for veterinary laboratory assessments to determine the capacities and functional status in compliance with the GHSA requirements.

    This study was conducted in the south-western states of Oyo and Ogun in Nigeria, selected due to the higher numbers of livestock populations and VLs in these areas. A cross-sectional survey was conducted at eleven laboratories. These included: (i) seven veterinary laboratories that were based at academic institutions (three microbiology, two parasitology and two pathology laboratories); (ii) two government veterinary clinics and laboratories in each state; (iii) one private veterinary laboratory; and (iv) one national veterinary laboratory were purposively selected. The inclusion criteria for laboratories were performance of veterinary diagnostics, location within the study area, and establishment of minimum standards against which assessment might be carried out. Before the commencement of the study consent was obtained from each laboratory. Positive responses indicating a willingness to participate in the study triggered the initiation of the assessment and questionnaire process.

    The LMT-Core, is a standardized set of questions embedded in a Microsoft spreadsheet (Microsoft Excel 2007). Using such, we gathered information on five key aspects: (1) general laboratory profile; (2) infrastructure, equipment, and supplies; (3) laboratory performance; (4) quality assurance and bio-safety/bio-security; and (5) laboratory collaboration and networking. Within these areas were 17 categories and 108 subcategories, each of which addressed specific laboratory functions. For instance, the general laboratory profile aspect sought information on geographic location (in terms of strategic placement and accessibility, laboratory budget, basic electricity and potable water supplies, and sustainable personnel organization systems). The aspect of infrastructure, equipment, and supplies gathered information on containment facilities, laboratory biosafety, equipment for bacterial, viral, serological and parasitological diagnosis, and reagent supply. Every laboratory generated an individual profile or ‘map’ using automatic calculations embedded in the spreadsheet, thus allowing the laboratory to visualize their unique laboratory capability and capacity status for the five aspects assessed.

    We scored laboratories based on observations and interviews with heads of respective units of laboratories and by strictly following the guidelines provided by FAO for assessment of laboratories (Supplementary Table S1, available in www.besjournal.com). Briefly, for each question of the assessment set of four options were provided as responses. The single best option describing the existing situation in the laboratory was recorded by the assessor. Where a suitable answer was not available or no answer was provided, the respective scoring area was marked not applicable (N/A). For all questions where ‘N/A’ was entered, the associated subcategory was omitted from the summary score. Where a laboratory struggled to select between two scoring options, a preferred score best representing the laboratory’s situation was selected, and the reason for hesitation was documented as a comment in the assessors’ column for comment/observation (column K). Additional information guiding assessors to determine the appropriate score was provided in column L of the spreadsheet (e.g. specific observations or documents needed to select from the 4 possible options), and was used by all assessors to provide consistency in scoring between the different laboratories.

    The scoring within the LMT-core sums to 100% that is the ideal and achieved when a laboratory scores the maximum points (n = 4) in all the subcategories. Each laboratory was given a reliability score based on the number of questions answered, excluding N/A as a completed response. Questionnaires with 0%–69% completion rendered a low reliability score and completion of 70%–89% rendered a medium confidence score and, lastly, completion of 90%–100% rendered the questionnaire as confidently reliable.

    Following verification for completeness, each LMT-core questionnaire was imported into the LMT automated analytic tool, available through an FAO interface. This process was supervised and eviewed by at least two researchers in every case. Outputs were generated in a ‘Summary sheet’ with scores as sub-values and graphs for the five core areas and seventeen different categories presented in a tabulated format. Graphic depictions of individual laboratory functionalities for each of the five key areas, including the specific strengths and weaknesses, were generated and analyzed. Scores were presented in percentages and compared with the theoretical ideal of 100%. The final laboratory capacity assessment was presented as either ‘advanced’ (67%–100%), ‘moderate’ (34%–66%) or ‘basic’ (0%–33%) (see Figure 1). Inter-laboratory comparisons, regarding performance, was conducted using ordinary one-way ANOVA and Tukey’s multiple comparisons test (P = 0.05). For confidentiality purposes, the study excluded any identifiers of individual laboratories, and facilities were further re-grouped into regions A (Oyo state) and B (Ogun state) to assure anonymity.

    Figure 1.  Final output of laboratory capacities and functionalities assessed against a sliding scale with advanced = (67%–100%), moderate = (34%–66%), or basic = (0%–33%).

    The preliminary evaluation of eleven veterinary diagnostic laboratories located in selected staes of south-west Nigeria resulted in an average reliability score of 81%, per LMT-core. Teaching and research services were provided by 9 out of the 11 laboratories (81.8%); diagnostic, clinical and hospital services by 81.8%; and a single laboratory additionally offered public health services. Pathogen types handled by laboratories included bacteria (8/11, 72.7%), viruses (4/11, 36.3%), fungi or mucor (3/11, 27.2%), and parasites (6/11, 54.5%). Overall, the capacity and functionality score obtained was 24.3% (ranging from 9.7%–39.7%), with an average score of 24.5% ± 10.0% (ranging from 9.7%–39.0%) for Oyo State and 24.1% ± 9.3% (ranging from 15.7%–39.7%) for Ogun State (Table 1).

    FacilityGLLBBSOIERSSS + ASAATTQABBSSHCMNLNLCGrand total
    Ogun StatePC66.766.766.766.744.450.057.161.152.437.027.815.229.222.255.622.218.539.7
    Uni-Para44.422.211.166.75.633.316.733.326.729.614.318.225.00.033.322.248.125.1
    Uni-Path33.322.211.10.014.350.027.826.78.373.39.521.220.00.041.70.03.721.0
    Uni-Mic33.322.222.266.720.820.028.616.716.714.822.216.725.00.041.70.03.719.1
    Pub Vet C&L44.411.10.066.74.20.00.033.3N/A13.3N/A5.641.711.133.3N/A23.815.7
    Oyo StateInst-Mic55.633.333.366.733.344.444.646.720.016.744.46.111.111.18.30.00.022.9
    Pub 2 Vet C&L44.40.00.066.78.34.816.70.011.116.711.19.111.10.00.011.10.09.7
    Inst L & V55.666.733.366.70.08.311.142.916.719.44.83.012.50.033.377.811.118.6
    Uni2- Mic44.416.722.266.745.866.757.183.338.925.933.312.128.60.041.711.159.339.0
    Uni2- Para44.444.444.466.733.350.053.344.426.723.819.023.325.00.041.70.03.728.0
    Uni2- Path44.433.344.466.728.666.738.961.133.336.428.618.233.30.08.30.03.728.6
    Mean value46.430.826.260.621.735.832.040.925.127.921.513.523.94.030.814.416.024.3
    Median44.422.222.266.733.344.427.833.323.319.425.018.225.00.041.70.023.822.9
    SEM2.96.46.26.14.97.35.96.94.35.23.92.02.92.35.37.66.12.8
    95% Confidence Interval37.1–55.816.5–45.112.4–40.147.1–74.110.7–32.719.6–52.118.8–45.225.5–56.215.4–34.816.4–39.412.8–30.29.0–18.117.4–30.30.0–9.119.0–42.6−2.8–31.62.3–29.618.1–30.5
      Note. Functionality categories assessed: GL = Geographic location; LB = Laboratory Budget; BS = Basic supply; O = Organization of the laboratory; I = Infrastructure; E = Equipment; RS = Reagent supply; SS + A = Staff skills + availability; SA = Sample accession; AT = Available technology; T = Training; QA = Quality Assurance; BB = Biosafety/Biosecurity; SSH = Staff Security/Health; CM = Communication means; NLN = National laboratory networking; LC = Laboratory collaboration. Categories of laboratories/facilities: PC = private clinic; Uni-Para = University parasitology; Uni-Path = University pathology; Uni-Mic = University microbiology; Pub Vet C&L = State Veterinary clinic and laboratory; Inst-Mic = Training institution microbiology; Pub 2 Vet C&L = 2nd State Veterinary clinic and laboratory; Inst L & V = Institution with laboratory and vaccine supply chain; Uni2-Para = 2nd University parasitology; Uni2-Path = 2nd University pathology; Uni2-Mic = 2nd University microbiology. SEM = Standard error of the mean. All values are expressed in percentages (%).

    Table 1.  Outputs from assessment of veterinary laboratories in south-west nigeria using the laboratory mapping tool-core, 2018

    The overall laboratory capacity scores were similar in both states (P = 0.73). The average scores were low (< 33%) across the different functionalities and capacities assessed (see Table 1). The LMT-core category ‘organization’ was generally strong across-the-board (average: 60.6%; 95% CI, 47.1–74.1) with the exception of a single pathology laboratory). Particularly low scores (≤ 25%) were obtained for the aspects of infrastructure, sample accessioning, on-the-job training, quality assurance, biosafety and biosecurity, staff security and health, and national laboratory networking and collaboration. The weakest scores were observed for staff security and health (e.g. regular health checks, protection against zoonoses through prophylactic immunizations, and medical health surveillance) (average 4.0%; 95% CI, 0.0–9.1). Other scores obtained were for the laboratory budgets in relation to finance, research autonomy and upgrading (30.8%; 95% CI, 16.5–45.1); basic electricity, water and deionized water supplies (26.2%; 95% CI, 12.4–40.1); reagent supplies (validity and affordability) (32.0%; 95% CI, 18.8–45.2); case sample throughputs (25.1%; 95% CI, 15.4–34.8); advanced technology for molecular and serological assays (27.9%; 95% CI, 16.4–39.4); communication including the availability of landlines, internet facilities, access to scientific publications and dissemination of data (30.8%; 95% CI, 19.0–42.6).

    Only two of the laboratories, a private laboratory with an overall average score of 39.7% and a university microbiology laboratory with 39.0%, were rated by the LMT-core as having moderate diagnostic capability. The remaining nine laboratories received scores placing them within the basic range for diagnostic laboratory services (< 30.0%). None of the laboratories had comprehensively advanced facilities for disease diagnosis, active surveillance or early warning systems. Inter-laboratory comparison of capacities and functionalities showed significant variations in laboratory capacities with the private laboratory performing best (ranging from 9.7%–39.7%; P = 0.04).

    In this study the performance, reported as functionality and capacity of veterinary laboratories, were systematically evaluated and documented using a standardized assessment tool, the FAO Core Laboratory Mapping Tool (LMT-core). The results provided for 11 veterinary laboratories in south-west Nigeria were quantitatively assessed and analyzed. The LMT-core has been tested and validated in at least fourteen African countries to date and resulting outputs have been used to recommend priority actions for laboratory improvements across Africa. Where such has been implemented, tremendous progress has been noticed in service delivery and laboratory outputs[2]. The use of the LMT-core to assess laboratories and assist them in identifying weaknesses and prioritize improvements is consistent with the Joint External Evaluation (JEE) protocol of the WHO/IHR[4].

    Although low-performance scores were reported across many functionalities accessed in this study, the outputs should be viewed not as negative findings, but as a valuable guide towards individual laboratory level improvements. The ongoing use of the LMT-core would ultimately provide a means for tracking positive changes and new enhancements in the overall functionality and capacity of VLs. Almost all of the VLs reported good organizational structure that is the basic requirement and template on which improvements can be made. Our findings will aid the various laboratory managements to begin the process of correcting the identified weak areas and moving towards the implementation of quality laboratory systems.

    Poor levels of laboratory infrastructure, sample accessioning, on-the-job training, quality assurance, biosafety and biosecurity, staff security and health, and national laboratory networking and collaboration hamper the functionalities and efficiencies of these laboratories. Poor infrastructure in particular, is a major drawback in animal disease detection, investigation, and control in many developing countries[6,7]. The lack of robust infrastructure, consistent with the findings documented for the small sub-set of laboratories reported here, is most often associated with insufficient funding for the purchase and maintenance of equipment, supplies, reagents and staff training; the designing and specification of proper sample collection, traceable accession methods, planned disease surveillance strategy, and regular appraisal of the performance of novel diagnostic techniques are all important.

    A consistent weakness identified in the current study was in training programs implemented to ensure that each staff member is suitably trained to meet the skills required for undertaking their job responsibilities. Such training (e.g. skills and competencies) is critical for efficiency in the day-to-day performance of routine duties, the handling of hazardous biological agents, the acquirement of knowledge and the interpretation of results, epidemiology, pathogenicity, and human susceptibility to various biological materials[8]. Without sound quality assurance and quality control, as observed in this study, performing procedures to standard is limited and may result in non-comparable data for other international laboratories with established capacity[9,10].

    In any laboratory, biosafety and biosecurity are key to ensure occupational health and safety of staff. However, the health and safety of staff in this study may be compromised routinely by the poor biosafety practices, the non-existence of medical health policies and surveillance, lack of adequate immunizations or emergency plans for control of laboratory-acquired diseases, and the absence of health and safety protocols. Only 1 of the 11 laboratories in the current study had networks and collaborations with other facilities at national, regional and international levels. We expect other VLs desire to enhanced their functions as per the WHO/IHR; the objective of the laboratory twinning and collaborations is to contribute to the sustainable improvement of public health services in developing countries through the establishment of partnerships between laboratories and institutions. Results of the LMT-core assessment indicated that more efforts to build collaborations and networking may be made a priority in order to facilitate future effective functioning of VLs in developing countries.

    Our study was limited by the inadequate record keeping in many of the laboratories visited. Where records were unavailable, the authors’ judgement was strictly based on the assessment guidelines provided by the FAO. Record keeping in many developing countries is an issue and continuous training, monitoring and evaluation, and the supply of recorded materials for laboratory staff is critical.

    The status of VLs in south-west, Nigeria is currently poor and falls below required standards. This is a major concern, especially when VLs are to ensure rapid responses to infectious diseases outbreaks and control. It is required that each VL should develop implementable actions plans aimed at progressively addressing the identified gaps. The weaknesses identified need timely interventions and political will to continuously invest in infrastructures that enhance research and disease surveillance in the country. VLs also need to contribute to the global health security agenda (GHSA) in combatting infections through the development of initiatives, projects, and partnerships with established international laboratories, that should promote capacitation for early detection and emergency response to infectious pathogens which threaten the public.

    The authors gratefully acknowledge all of the participating laboratories and staff who shared their time and experiences with us.

    #AreaCategorySub Category4321Assessments scores
    ABC Current
    1General Laboratory ProfileGeographic locationStrategic placingIsolated compound outside of any residential areaIsolated compound in low populated areaSingle building in low populated areaBuilding within residential area
    2AccessibilityProper containment + guard (24 hr) + Restricted access to building by use of Identity card (employees) onlyRestricted access, doors are locked + guard at the entrance for 24 hDoors are closed but not locked / low biosecurity level / guard is not always presentEasy access to laboratory compound even by visitor / stranger / doors are open / no guard present
    3Location, accessAccess to highway, airport, harbor and / or station within 30 minutesAccess to highway, airport, harbor or station within 60 minutesAccess to road; but sometimes limitations (traffic, road condition, flooding)Regular limitations in access to transport means (traffic, bad road, airport is far)
    4Laboratory BudgetFinancial autonomy (allocation of funds)Lab is financially autonomous, lab funds (>90%) from public source and/or self-generatedLab is almost financially autonomous; lab funds from public source or self-generated (>60%) AND development programmes (<40%)Lab has insufficient own budget (<60%), activities dependant on development partners (>40%)Lab has no autonomous budget; all activities exclusively rely on external funding source
    5Research autonomy (n of publication / year)Lab budget allows ample opportunity for research (>10 publications/year) besides routine diagnostic/productionLab budget allows limited research (1 to 10 publications/year according to the lab context), but mainly routine diagnostic/productionLab budget is insufficient for research, but results from ongoing work are published in national journals/bulletin or regularly presentedNo research activity due to insufficient lab budget
    6Autonomous infrastructural upgrading (n of constructions / year)Lab budget sufficient for regular (1/year) upgrading / renovation of larger lab infrastructureLab budget allows irregular (1 / 3 years) independent upgrading / renovation of infrastructureConstructions or renovation by use of lab budget irregular and only for minor infrastructural changesConstruction or renovation in general only possible under external funding
    7Basic supplyRegular (hours of) electricity supplyConstant (24 hours) stable electricity supply + stabilizer and automatic stand-by generator24 hours electricity supply + stabilizer and back-up generator (manually operated)Frequent electrical instability/voltage irregularity, manually/automatically operated generator + stabilizerElectricity supply (temporarily) less than 10 hours per day, generator does not run permanently (not existent, no fuel)
    8Regular water supply (access and quality)Daily and unlimited supply of good-quality (drinkable) water (pipe) through public source; no risk of water shortageSufficient daily supply of low quality (not drinkable) water through pipe or tank; back-up tank availableSupply of water through tank; sometimes insufficient or low quality (not drinkable)Irregular and insufficient water supply, also low quality (not drinkable)
    9General Laboratory ProfileBasic supplyAccess to purified, deionized, distilled waterUnlimited access to purified water; own production of deionised and distilled waterEasy access to deionised and distilled water (external/internal source)Limited access to deionised and/or distilled water (external/internal source)Difficult or no access to deionised and/or distilled water
    10OrganizationSustainable personnel organization systemOrganigram and organization system in place + written description of responsibilities according to personnel skill levelOrganigram and organization system in place; staff mostly know their roles, but not written downOrganization system in place, but frequent changes, staff not always clear on their rolesFrequent shifting of personnel, no stable organization system
    11Infrastructure, equipment, suppliesInfrastructureContainment (means of containment)All lab departments (of different Biosafety levels) are clearly separated and well contained by airlock, personnel shower/changing room, sterilizing and storage rooms; use of disinfections, identity badges or other means (then describe). It can be accessed only by lab staff from the departmentLab departments are separated (e.g. different buildings, different floors) with restricted access but can be accessed by lab staff from other department with change of lab clothes including shoes and use of disinfectantsLab departments are separated (e.g. different buildings or different floors for different departments), all lab staff can enter the different departments any time, change of lab clothes possible but not always required/followedNo clear separation, e.g. one-room-lab or one floor harbours different departments (rooms) that can be easily accessed without changing clothes, without using disinfectants
    12Functionality of all departments (safety)Lab facilities of all departments are air locked, have a fire extinguisher, gas supply; emergency exit and alarm system; monitoring for staff adherence to safety rules and practices; there is room for upgradeLab facilities of more than 70% of departments are well-maintained, have a fire extinguisher, gas supply; safety rules and practices are followed, but absence of monitoring system; there is room for upgradeOnly some facilities (<70%) are well-maintained, e.g. virology, pathology section, are regularly maintained; room for upgrade is limited; safety rules and practices are not always required/followed>60% of labs of the departments are in poor status, only few temperature control system/mainly window ventilation, no fire extinguisher, there are hardly any safety rules and practices; room for upgrade is limited
    13Biosafe virology labBSL-3/4 Virology lab (Biosafety Cabinets Class (BSC)-III)BSL-2/3 Virology Lab (BSC-II)BSL-1/2 Virology lab (one BSC-II)No biosafe Virology lab (BSC-II not functioning or not existent)
    14Biosafe post mortem roomBSL-3/4 Postmortem (PM) room + BSC-IIIBSL-2/3 PM-room + BSC-IIBSL-1/2 PM-room (BSC-II)No biosafe PM-room, no BSC
    15Infrastructure, equipment, suppliesInfrastructureBiosafe Bacteriology labBSL-3/4 Bacteriology lab + BSC-IIBSL-2/3 Bacteriology lab + BSC-IIBSL-1/2 Bacteriology lab + 1xBSC-IINo biosafe Bacteriology lab (BSC-II not functioning or not existent)
    16Animal facilitiesBSL-3 Animal facility in use for experiments and bioproducts (diagnosis)Animal facility in use (BSL 1-2) for production of diagnostic reagents (SPF-eggs, sera etc.)Animal facilities available but not in use; and no BSLAnimal facilities not available
    17Cleaning plan and checking processCleaning plan and checking process in place, regular microbiological controlsCleaning plan and checking process in place, no microbiological controlsOccasional cleaning, no cleaning plan draftedNo cleaning, no cleaning plan drafted
    18Separated rooms for PCR (number of rooms and BSC/PCR hood/laminar flow cabinet)PCR set-up (extraction, master mix, template, machine) separated (2-3 rooms/workstations, air flow controlled, 1-2 BSC-II + 1 PCR-hood) including change of lab clothes (coats and shoes) + dedicated small PCR equipment (centrifuges, vortex, micropipettes)PCR set-up (extraction, master mix, template, machine) separated (2-3 rooms/workstation, 1-2 BSC-II + 1 PCR hood), including change of lab clothes (coats and shoes), but no dedicated small PCR equipment (centrifuges, vortex, micropipettes)Different rooms available (3 rooms or 2 rooms and 1 BSC-II + 1 laminar flow far from each in one room), but not in consequent use for PCR set-up separation, no change of lab clothes and no dedicated micropipettesNo or insufficient separation of PCR set-up (1 room for all 4 activities or 0-1 BSC-II (not functional equals 0)
    19Biosafe and biosecure labs (no of labs without air-lock, AC)All labs are closed rooms and harbour Air Conditioner (AC) in all departmentsLabs of at least 3 departments (virology, bacteriology and molecular biological) are closed and lockable rooms and harbour ACOnly few labs in selected departments (e.g. AI-Lab in virology department) have closed rooms and harbour AC, other rooms have windows or not functional (old) ACIn the majority of labs doors or windows do not properly close, if AC in rooms they are not or rarely functional
    20EquipmentEquipment for diagnosis of viral diseasesVirology department sufficiently equipped to carry out biosafe and rapid diagnosis of various viral diseases (>10 viruses including TAD/zoonoses) by virus isolation and other tests (including cell culture, electronic microscopy, etc.); Samples received are processed within 24 hoursVirology department sufficiently equipped to carry out biosafe and rapid diagnosis of only selected diseases (5 to 10 viruses) by virus isolation and other tests (including cell culture, electronic microscopy, etc.); Samples received are processed within 24 to 48 hoursVirology department uses old equipment (more than 10 years). Some equipment may be broken or is not well-maintained. Only few diseases can be tested (less than 5)Virology department lacks functional equipment for appropriate diagnosis of viral diseases, for any technique
    21Equipment for serology departmentSerology department sufficiently equipped to carry out diagnosis of various diseases (>10 diseases including TAD/zoonoses) by various techniques.Serology department is equipped to carry out diagnosis of only selected diseases (5 to 10 diseases) by various techniques.Serology department uses old equipment (more than 10 years). Some equipment may be broken or is not well-maintained. Only few diseases can be tested (less than 5).Serology department lacks functional equipment. Only rough-and-ready techniques can be performed.
    22Equipment for molecular biological diagnosisMolecular section sufficiently equipped (functional BSC-II, PCR hood, PCR cycler…) to carry out diagnosis of various diseases (>15 pathogens); including real-time PCR and functional sequencer or access to efficient sequencing services (results within 48 hours)Molecular section sufficiently equipped to carry out diagnosis of 5 to 15 selected pathogens (including real-time PCR and access to sequencing machine/services)Molecular section lacks modern equipment but may harbour old PCR cyclers and gel-electrophoresis equipment for 3 to 15 selected pathogensMolecular section lacks even basic equipment, is not functional or is not existent
    23Pathology department equipment for necropsiesPathology department sufficiently equipped to carry out necropsies of variable size animals, including big animals. Biosafety and biosecurity conditions are good (protection against contamination of personnel and of the environment).Pathology department sufficiently equipped to carry out necropsies of variable size animals, including big animals. Biosafety and biosecurity conditions are not fully respected to protect against contamination of personnel and of the environment).Pathology department can carry out necropsies of some species. Some biosafety and biosecurity conditions are not respected (personal protective equipment, use of facilities, effluent management...) to protect against contamination of personnel and of the environment).Pathology department lacks basic equipment for appropriate necropsies. Biosafety and biosecurity conditions are not respected.
    24Pathology department equipment for histo-pathological techniquesPathology department sufficiently equipped to carry out up-to-date histo-pathological techniques (including immunohistochemistry)Pathology department is equipped to perform basic histopathological techniques. These techniques are routinely performed.Pathology department is equipped to perform basic histopathological techniques, but these techniques are performed rarely.Pathology department lacks basic equipment for appropriate histopathological analysis.
    25Equipment for diagnosis of bacterial diseasesBacteriology department sufficiently equipped to carry out biosafe and rapid diagnosis of a broad range of bacterial diseases (>10 bacterial diseases/ including TAD/zoonoses)Bacteriology department sufficiently equipped to carry out biosafe diagnosis of at least the most important bacterial diseases (5-10 TAD/zoonoses)Bacteriology department uses old (>8years) equipment for diagnosis of important bacterial diseases; only few (max 5) bacteria can be typed/cultivatedBacterial department lacks basic equipment for appropriate diagnosis of bacterial diseases (e.g. equipment not existent or not functional)
    26Equipment for diagnosis of parasitological diseasesParasitology department sufficiently equipped to carry out up-to-date diagnosis of a broad range of parasitological diseases (>10 including most important)Parasitology department sufficiently equipped to carry out up-to-date diagnosis of at least the most important parasitological diseases (5-10)Parasitology department uses old (>8years) equipment for diagnosis of important parasitological diseases; only few parasites (max 5) can be typedParasitology department lacks basic equipment for appropriate diagnosis of parasitological diseases (e.g. equipment not existent or not functional)
    27Maintenance procedures for autoclave(s)Periodic maintenance procedures in place for all autoclave(s); annual maintenance by specialist the last 3 years; systematic use of steam autoclave indicatorPeriodic maintenance procedures not fully in place for all autoclave(s); annual maintenance by specialist the last 3 years; systematic use of steam autoclave indicatorPeriodic maintenance procedures not fully in place for all autoclave(s); at least one full maintenance by specialist done the last 3 years; use of steam autoclave indicator not systematic.Autoclave(s) never maintained; no constant use of steam autoclave indicator
    28Reagent supplyFresh reagent supply, procurement, affordabilityReagents for all operating procedures can be autonomously procured; fresh supplies are always available for continuous service/workOnly selected reagents can be autonomously procured for diagnostic use; fresh supplies are not always availableOnly few reagents can be autonomously procured for diagnostic use; always come with delay upon request -> reagents are often missingAll reagents for diagnostic use must be procured by external funding/organization
    29Own production of diagnostic reagents (type, quality)Key diagnostic reagents/material (antigen, antisera, cell lines, buffer solution, red blood cells (RBC)…) is self-produced in good quality (according to standards and monitored, documented) in sufficient amount and validated; animals serving for diagnostic material are SPFSome reagents/material for diagnostic use (RBC, buffer solution, culture medium, chicken eggs) can be self-produced; efforts taken to produce in good quality according to standards (animals serving for reagent material are kept in quarantine and monitored for diseases (SAN)Limited reagents/material for diagnostic use are produced (e.g. RBC, buffer), quality questionable with regard to animal source for reagents (not quarantine, not monitored for diseases (not SPF, or not SAN)No self-production
    30Proper stocking/storage of reagentsSeparate storage and documentation (updated inventory log) of different material (reagents, sera, samples …) according to QA / QMS standardsSeparate storage of different material (reagents, sera, samples…), a list is available but no inventory log of all supplies and reagentsNo correct separation of storage of different material; expired reagents; a list may or may not be availableNo separation of storage of different material, storage conditions doubtful because of limitations in functionality or availability of appropriate rooms or freezer / fridges / electricity, insufficient documentation, expired supplies
    31Validity of reagents for virological investigationsReagents for daily virological diagnosis by several techniques (excluding serology) are available for a range of viral diseases, including cell culture (>10 viruses including TAD/zoonoses or all viral testing under their mission*)Reagents for daily virological diagnosis by several techniques (excluding serology) are available for a range of viral diseases, including cell culture (5-10 viruses including TAD/zoonoses or partial viral testing under their mission). Some reagents are expired.Limited reagents for diagnosis of few viral diseases (1-5) through rough-and-ready techniques; Reagents are usually not properly stored (no constant freezing), 40 to 70% of reagents are expiredVirology (excluding serology) department hardly harbours any reagents, or reagents are expired or have not been properly stored (>70%).
    32Validity of reagents for daily immuno-serological diagnosisReagents for daily immuno-serological diagnosis by several techniques are available for a range of diseases (>10 diseases including TAD/zoonoses or all diseases under their mission*)Reagents for daily immuno-serological diagnosis by several techniques by several techniques are available for a range of diseases (5-10 diseases including TAD/zoonoses or partial diseases under their mission*). Some reagents are expired.Limited reagents for immuno-serological diagnosis (1-5 diseases) through rough-and-ready techniques; Reagents are usualy not properly stored (no constant freezing), 40 to 70% of reagents are expiredImmuno-serological department hardly harbours any reagents, or reagents are expired or have not been properly stored (>70%).
    33Validity of reagents for PCR and sequencingReagents for daily molecular diagnosis are available in sufficient amount and stored in good condition (including for real-time PCR technology and for sequencing); enzymes are stored at constant -20°CReagents for daily molecular diagnosis are available -and stored in good conditions- but with some limitations (e.g. no real-time PCR, but conventional PCR, reagents for sequencing limited)Reagents for daily molecular diagnosis are frequently limited (frequent shortages, especially in real-time PCR reagents and extraction kits; not properly stored; some are expired)Molecular diagnosis cannot be carried out due to constant or almost constant lack of valid reagents
    34Validity of reagents for bacteriological investigationsAll necessary reagents for daily diagnosis of a broad range of bacterial diseases (excluding serology) are available (>10 bacterial diseases including TAD and zoonosis or all diseases under their mission*)All reagents for diagnosis of a limited range but of the most important bacterial diseases (excluding serology) (5-10; zoonosis, TADs or partial bacterial diseases under their mission*)Limited reagents for diagnosis of bacterial diseases (1-5); reagents are not properly stored (no constant freezing), 40-90% of reagents are expiredBacteriology department harbours hardly any reagents for diagnosis of bacterial diseases, or reagents are expired, or have not been properly stored
    35Validity of reagents for pathological methodsAll reagents for histo-pathological investigations are daily available (staining, IFT-antibodies, fluorescent dyes…)Pathology department harbours all necessary reagents for necropsies / gross-pathology but often lacks some reagents for histo-phatology (e.g. staining, IFT-antibodies…)Pathology department harbours limited reagents for pathology; in general, histo-pathology is not functional due to a lack of valid and appropriate reagentsPathology department hardly harbours any reagents for histo-pathological exam, or reagents are expired, or have not been properly stored; only gross pathology possible
    36Validity of reagents for parasitic methodsAll necessary reagents for diagnosis of a broad range of parasitic diseases are daily available (>10 parasitic diseases including TAD and zoonosis or all diseases under their mission*)All reagents for diagnosis of a limited range but of the key parasitic diseases (5-10; zoonosis, TADs)Limited reagents for diagnosis of parasitic diseases (1-5); reagents are not properly stored 40-90% of reagents are expiredParasitology department hardly harbours any reagents, or reagents are expired, or have not been properly stored
    37Laboratory performanceStaff skills + availabilityNumber of trained and experienced staff per departmentEach department counts at least one senior and two junior scientists and at least 2 technicians/co-workers. All staff is trained and experiencedEach department has at least one senior and one junior scientist and 2 or more technicians/ co-workers, but not all are well-trained or experienced or always availableIn each department, the number of staff is not sufficient (1 scientist, 1 technician) or are not available for more than 2 working days per weekSerious lack of skilled (trained and experienced) personnel in most of the departments (<1 scientist or <1 technician per department); or their availability is of less than 2 working days per week
    38Expertise of staff in virology/serology (continuing education and accuracy of testing)All staff in virology/serology department is experienced, well-trained and continuously educated (>2 training opportunities per year); all tests are reported within 48 hours, test results are validated and recorded before releaseWell-trained and motivated but not very experienced staff in virology/serology department; <2 opportunities per year for continuing education; tests reported sometimes with delay; test results are recordedTrained staff in virology/serology department, but lack experience/ motivation, <1 training opportunity per year; tests reported sometimes with delay, results not always recordedStaff in virology/serology department not trained or motivated; samples often left uninvestigated, no prompt reporting, results not always recorded
    39Expertise of staff in molecular biology (continuing education and accuracy of testing)All staff in molecular department is experienced, well-trained and continuously educated (>2 training opportunities per year); all tests are reported within 48 hours, test results are validated and recorded before releaseWell-trained and motivated but not very experienced staff in molecular department; <2 opportunities per year for continuing education; tests reported sometimes with delay; test results are recordedTrained staff in molecular department, but lack experience/ motivation, <1 training opportunity per year; tests reported sometimes with delay, results not always recordedMolecular section does not exist or staff in molecular section not trained or motivated; samples often left uninvestigated, no prompt reporting, results not always recorded
    40Expertise of staff in bacteriology and parasitology (continuing education and accuracy of testing)All staff in bacteriology and parasitology departments is experienced, well-trained and continuously educated (>2 training opportunities per year); all tests are reported within 48 hours, test results are validated and recorded before releaseWell-trained and motivated but not very experienced staff in bacteriology and parasitology departments; <2 opportunities per year for continuing education; tests reported sometimes with delay; test results are recordedTrained staff in bacteriology and/or parasitology department, but lack experience/ motivation, <1 training opportunity per year; tests reported sometimes with delay, results not always recordedStaff in bacteriology and/or parasitology department not trained or motivated; samples often left uninvestigated, no prompt reporting, results not always recorded
    41Expertise of staff in pathology (continuing education and accuracy of testing)All staff in pathology department is experienced, well-trained and continuously educated (>2 training opportunities per year); all tests are reported within 48 hours, test results are validated and recorded before releaseWell-trained and motivated but not very experienced staff in pathology department; <2 opportunities per year for continuing education; tests reported sometimes with delay; test results are recordedTrained staff in pathology department, but lack experience/ motivation, <1 training opportunity per year; tests reported sometimes with delay, results not always recordedStaff in pathology department not trained or motivated; samples often left uninvestigated, no prompt reporting, results not always recorded
    42Staff emergency serviceStaff for emergency available for 24 hours + weekend shiftsIrregular availability (only in special situation) of staff for emergency; weekend shifts are plannedIrregular availability of staff for emergency and weekend shifts only rarely (<20 weekends per year)Less than 10 weekend shift per year, no staff for emergency available;
    43Availability of maintenance staffMaintenance staff (plumbing, electricity, mechanics etc.) employed and daily available, with emergency serviceMaintenance staff available during working hoursMaintenance staff available with delay in arrival (sometimes hours, sometimes days of delay)Very difficult to get hold of maintenance staff
    44Sample accessionCarcass accession (number of carcasses per week, month or year)Pathology department receives carcasses >25 weekly or >100 monthly or >1200 per year for post-mortemPathology department receives 15-25 carcasses weekly or 60-100 monthly or 720-1200 yearly for post-mortemPathology department receives 5-15 carcasses weekly or 20-59 monthly or 240-719 yearly for post-mortemPathology department receives <5 carcasses weekly or <20 monthly or < 240 yearly for post-mortem
    45Case sample throughput in Immunoserology (nb of biological samples per year)Immunoserology laboratory receives more than 100,000 routine samples per year.Immunoserology laboratory receives between 50,000 to 100,000 routine samples per year.Immunoserology laboratory receives between 10,000 and 50,000 routine samples per year.Immunoserology laboratory receives less than 10 000 routine samples per year.
    46Case sample throughput in virology (nb of biological samples per year)Virology laboratory receives more than 5,000 routine samples per year.Virology laboratory receives between 2,500 and 5,000 routine samples per year.Virology laboratory receives between 1,000 and 2,500 routine samples per year.Virology laboratory receives less than 1,000 routine samples per year.
    47Case sample throughput in bacteriology (nb of biological samples per year)Bacteriology laboratory receives more than 5,000 routine samples per year.Bacteriology laboratory receives more between 2,500 and 5,000 routine samples per year.Bacteriology laboratory receives more between 1,000 and 2,500 routine samples per year.Bacteriology laboratory receives less than 1,000 routine samples per year.
    48Case sample throughput in paraistology (nb of biological samples per year)Parasitology laboratory receives more than 5,000 routine samples per year.Parasitology laboratory receives more between 2,500 and 5,000 routine samples per year.Parasitology laboratory receives more between 1,000 and 2,500 routine samples per year.Parasitology laboratory receives less than 1,000 routine samples per year.
    49Sample throughput by PCRInvestigation of samples by PCR: >20 samples weekly or >80 monthly or >960 per yearInvestigation of samples by PCR: 10-20 samples weekly or 40-80 monthly or 480-960 per yearInvestigation of samples by PCR: 5-9 sample weekly or 20-39 monthly or 240-479 per yearNo PCR performed, or only in rare circumstances (<5 sample weekly, <20 monthly, <240 per year)
    50Sample throughput from surveillance or monitoringLab is regularly involved in active surveillance or monitoring of >3 animal diseases that generates more than 20,000 samples per yearLab is involved in active surveillance of 2-3 animal diseases that generates 10,000-20,000 samples per yearLab is involved in surveillance of 1 animal disease and receives 1,000-9,999 samples per yearLab is currently not involved in active surveillance or monitoring
    51Prompt sample processingProcessing of overall diagnostic samples is carried out same day of reception by trained and experienced lab staffOverall sample processing is usually carried out within 1-2 days by trained and experienced lab staff (e.g. days before the week end or holidays or when samples arrive in the afternoon)Samples are usually put into fridge or freezer for some days until investigation; or samples are stored for maximum 3 days and then shipped to another laboratoryDiagnosis samples are usually put into fridge or freezer over 3 days before being processed because of lack of staff; OR: some samples are sent to another lab, but often not immediately
    52Available technologyPost mortem capability (skills and experience of pathologists) in necropsiesAll necropsies conducted by specifically trained and/or experienced (>5 years) pathologists. The volume of activity allows to maintain this skillAll necropsies conducted by specifically trained and/or experienced (>5 years) pathologists, but the volume of activity is not sufficient to maintain this skillNecropsies are not all conducted by specifically trained and/or experienced (>5 years) pathologistsNo available experience in necropsy in the laboratory
    53Skills and experience of histologistsSpecifically trained and/or experienced (>5 years) histologists. The volume of activity allows to maintain this skillSpecifically trained and/or experienced (>5 years) histologists, but the volume of activity is not sufficient to maintain this skillNo histology competence available in the laboratory, but has access to reliable and effective sub contracted servicesNo competence in histology available in the laboratory, and no access to reliable and effective sub contracted services
    54Prompt bacteria identificationAll required operating methods (SOPs) available at the laboratory describing the method of identification / isolation of all important bacteria* causing disease in animals and/or zoonotic. The laboratory regularly performs (at least once per quarter) these methodsMost SOPs describing the method of identification / isolation of all notifiable bacteria** causing disease in animals and/or zoonotic in the region are generally available in the laboratory. The laboratory regularly performs (at least once per quarter) these methodsOnly a few SOPs describing the method of identification / isolation of all notifiable bacteria** causing disease in animals and/or zoonotic in the region are available in the laboratory and/or the laboratory does not regularly performs (less than once per quarter) these methodsNo operating methods describing the method of identification / isolation of notifiable bacteria** causing disease in animals and/or zoonotic expected to be present in the region are available in the laboratory.
    55Prompt parasite identificationAll required operating methods (SOPs) available at the laboratory describing the method of identification of all important parasites* causing disease in animals and/or zoonotic. The laboratory regularly performs (at least once per quarter) these methodsMost SOPs describing the method of identification of all parasites** causing notifiable disease in animals and/or zoonotic in the region are generally available in the laboratory. The laboratory regularly performs (at least once per quarter) these methodsOnly a few SOPs describing the method of identification of parasites** causing notifiable disease in animals and/or zoonotic in the region are available in the laboratory and/or the laboratory does not regularly perform (less than once per quarter) these methodsNo SOPs describing the method of identification of parasites** causing notifiable disease in animals and/or zoonotic expected to be present in the region are available in the laboratory.
    56Microscopy capacityMicroscope functional and in regular (weekly) useMicroscope functional but no operator or infrequently used (< 1 per months)Microscope available but not satisfactoryNo microscope
    57Cell culture (virology) capabilityWell-established (>5 years) and biosafe/clean cell culturing with >5 different cell linesCell-culturing possible but with limited cell types (<5 cell lines) or established less than 5 years agoCell-culturing possible with limited cell types (<2 cell lines), but limited expertiseNo cell-culture
    58Egg culture (virology) capabilityBiosafe (BSC-II and III or BSL-3 conditions) virus isolation with Embryonated chicken eggs (ECE)Culturing with Embryonated chicken eggs (ECE) under limited BSL (BSC-II only)Limited and irregular use of ECE for various reasons (limited access to SPF or SAN eggs, no experienced operator, no functioning incubator, no BSC-II…)No or rare (<1 per 6 months) use of ECE, and limited BSL
    59Serological capabilityWeekly use of serological assays; all following assays are implemented: ELISA, HI, Immuno-histochemistry, Immuno-Fluorescence, AGID for diagnosis of broad range of diseases including all key animal diseases (>10)Weekly use of serological assays; all following assays are implemented: ELISA, HI, Immuno-histochemistry, Immuno-Fluorescence, AGID for diagnosis of key animal diseases (5-10)Only use of basic serological assays like HI, AGID for a few key diseases (<5); limitation in use of ELISA or immunofluorescenceNo use or rare use (<1 assay per 4 months) of serological assays like ELISA, HI, Immuno-histochemistry, AGID
    60Molecular capabilityPCR technology (including realtime) weekly used for >10 genome targetsPCR technology (including realtime) used for 5-10 genome targetsConventional PCR technology applied only for <5 genome targetsNo PCR technology applied
    61Annual maintenance of PCR cyclerAnnual maintenance of PCR cyclerIrregular maintenance of PCR cyclerNo/or rare maintenance of PCR cyclerNo PCR
    62Sequencing capabilitySequencing technology applied and frequently used (≥ 2 per month or more than 100 sequences per year) and maintained following manufacturer's instructionsSequencing technology is set up, but rarely used (<2 per month); infrequent maintenance; easy access to external sequencing servicesSequencing technology available but not in use (not functional, no kits, no experienced operator…) and/or some access to external sequencing servicesNo direct access to sequencing services
    63Animal experiment capabilityAnimal experiments as diagnostic method (esp. ICPI, IVPI, mouse inoculation, inoculation of larger animals) applied under biosafe conditionsAnimal experiments as diagnostic method applied under unsatisfactory conditions (e.g. insufficient biosafety)A few animal experiments (e.g. mouse inoculation for rabies) may be used but lacks of appropriate expertise/other conditions (no biosafe conditions, no easy access to animals, no experienced operator)No experiments performed on animals
    64QA, Biosafety/BiosecurityTrainingExternal training in lab performanceStaff (scientist, technicians) of each/every department receives at least 1 external training per year in lab diagnosisNot every staff, and/or not all department receives at least 1 external training per year in lab diagnosisOnly few selected staff* receives at least 1 external training per year in lab diagnosisOnly few selected staff* receive occasional (< 1 per year) external training in lab diagnosis
    65Internal training in lab performance/GLPEvery staff of each department receives documented weekly in house [training / updates / meetings] on GLPNot every staff, and/or not all department receives at least 1 internal [update/training/meeting] on GLP per monthOnly selected staff* receive rare (<1) internal [update training/meeting] on GLP per monthNo weekly or monthly in house [training/updates/meeting] on GLP
    66Training in QA/QCKey staff receives documented and regular (>1 per year) training in quality assurance (QA)/quality control (QC)Key staff receives regular (1 per year) training in QA/QC; consistent documentation on QA/QC not always availableKey staff rarely receives (< 1 per year) training in QA/QC; consistent documentation on QA/QC not availableNo (< 1 every 2 years) training opportunity in QA/QC
    67Training in maintenance and calibrationKey staff receives documented and regular (≥ 1 per year) training in equipment maintenance and calibrationKey staff receives irregular (<1 per year) training in equipment maintenance and calibration; consistent documentation on maintenance and calibration not always availableRare trainings (<1 every 2 years); consistent documentation on maintenance and calibration not availableNo training in equipment maintenance and calibration in the last 3 years
    68Training in lab managementDirectors/managers regularly (1/year) trained in lab managementDirectors/managers irregularly (1 every 2 years) trained in lab managementDirectors / managers irregularly train themselves through self-education or e-learning on lab managementNo training in lab management
    69Training in biosafetyAll staff receive regular documented training in biosafety practices (>1 per year)Selected* staff receive regular (1 per year) training in biosafety practices; and/or no consistent documentationStaff rarely trained but good level of awareness in biosafetyNo training opportunity for most of the staff in biosafety practices, low awareness level among the staff
    70Training in shipping of infectious substancesUp-to-date certification for shipping of infectious substances (IATA standards), -for more than one personUp-to-date certification for shipping of infectious substances (IATA standards), for one person in the labOut-of-date certification for shipping of infectious substances (IATA standards)No certification for shipping of infectious substances (IATA standards) (since 3 years)
    71Quality AssuranceStandard requirements for the competence to carry out tests and calibrationsQuality system applied in 80% of departments, accreditation of 80% of analytical parametersQuality system applied in 80% of departments, accreditation of 40% of analytical parametersNo accreditation yet but in the process of adapting ISO 17025 standards in most departments for future accreditationQuality system not in place
    72Corrective and preventive actions managementSystem established to manage corrective and preventive actions, registration in the quality management system, customer complaints managementSystem established to manage corrective and preventive actions, registration in the quality management system, no customer complaints managementSystem established to manage corrective and preventive actions, no registration in the quality management systemNo management of nonconforming testing
    73Best practice testing of particular diseasesSatisfactory results (>75% correct) in Proficiency Testing for at least 3 selected diseases* in the past 18 monthsParticipation to Proficiency Testing for at least 3 selected diseases* and satisfactory results (>75% correct) in at least one in the past 18 monthsParticipation in Proficiency Testing in the past 18 months for selected diseases*No participation in Proficiency testing within the past 18 months
    74Methodology standardizationSOPs for all performed tests prepared and in use; including available biosafety information relevant to the testsSOPs only for selected key diseases* in use including biosafety proceduresSOPs for selected test under development, or SOPs developed and in use but biosafety information missingNo or only a few SOPs available/under development
    75Correct performance of tests / methodology and kitsProper and documented validation of in house tests / commercial kits by using reference material before use on routine basisValidation of in house tests / commercial kits by using reference material before use on routine basis; but insufficient documentation availableNo regular validation of in house tests or kits by using reference material before use on routine basis; No documentation availableNo kits/test validation
    76Overall lab quality assuranceQuality officer/manager assigned + quality manual fully appliedNo quality officer/manager assigned, or Quality manual only partially appliedNo quality officer/manager assigned, and/or Quality manual still under processNo Quality officer/manager and no quality manual developed
    77Test quality assuranceUse of internal test quality control (QC) in all tests according to international standardsQC not always applied; not necessarily according to international standardsQC rarely applied for key tests, but not in all runs/testsNo experience in QC
    78Sample identification and follow-upIdentification and tracking of each sample entering the lab by use of LIMS or bar-coding or comparable technologyIdentification and tracking of each sample entering the lab by use of well documented Log-Book or Excel fileIdentification and tracking of each samples for only a few diseasesIrregular identification and tracking of samples
    79Application of international recommendationsOIE/WHO/FAO/CDC guidelines and OIE Terrestrial Manual are appliedOIE Manual and/or other guidelines are in place, but not sufficiently followedOIE Manual and/or other guidelines rarely usedNo notice of OIE Manual or other guidelines
    80Metrology proceduresAll departments have described and routinely implemented metrology procedures*Some departments have described and routinely implemented metrology procedures*All or some departments have metrology procedures described but not implemented routinelyNone of the departments have metrology procedures described
    81Maintenance proceduresAll departments have described and routinely implemented maintenance proceduresSome departments have described and routinely implemented maintenance proceduresAll or some departments have maintenance procedures described but not implemented routinelyNone of the departments have maintenance procedures described
    82Biosafety/BiosecurityBiosafety / biosecurity applicationBiorisk officer officially assigned and SOPs for personnel biosafety / biosecurity well documented, available at the right places and appliedKey-Staff is well-trained in biosafety/biosecurity; but SOPs for personnel biosafety / biosecurity not all finalized and appliedSome staff is aware of biosafety/biosecurity principles. No or rare SOPs developed and appliedOnly vague knowledge of biosafety/biosecurity principles, no SOPs
    83Preparation for emerging diseasesA risk assessment for biocontainment of all high consequence pathogens has been conductedA risk assessment for biocontainment of some high consequence pathogens has been conductedBiocontainment of high consequence pathogens has been discussed among the director and staffBiocontainment of high consequence pathogens has not been discussed
    84Biosafety cabinets testedBiosafety cabinets are tested (under recognized standard NSF49 or EN12469) and validated annually by NSF certified assessorsBiosafety cabinets are tested (under recognized standard NSF49 or EN12469) at least every 2 years by NSF certified assessors, and corrective measures are taken if neededBiosafety cabinets are tested (under recognized standard NSF49 or EN12469) at least every 2 years by NSF certified assessors but insufficient corrective measures are takenBiosafety cabinets have not been tested (NSF49 or EN12469) by NSF certified assessors for 5 years or more
    85Biosafety cabinets in conformity with international recognized standards100% biosafety cabinets (BSC) are in conformity with internationally recognized standards (NSF49 or EN12469) and are properly placed in the lab premises100% BSC are in conformity with internationally recognized standards (NSF49 or EN12469) but 5-10% are not properly placed in the lab premises100% BSC are in conformity with internationally recognized standards (NSF49 or EN12469) but more than 10% are not properly placed in the lab premisesSome BSC are not in conformity with internationally recognized standards (NSF49 or EN12469) and/or more than 10% are not properly placed in the lab premises
    86Staff protection from biohazardsPPE are available and used when required; consequent change of lab clothes including shoes according to requirements of respective biosafety levelPPE are available but used under rare occasions (in outbreak / critical situations); when necessary change of lab coat but not shoesPPE are available, but not used; inconsequent use of lab clothesPPE are not sufficiently available, inconsequent use of lab clothes
    87Unintentional release of pathogens from the lab (quarantine)Lab staff has to follow an obligatory quarantine period of 3-7 days (depending on pathogens manipulated) before entering any animal holding and is never involved in taking samples during active surveillanceLab staff generally follows a quarantine period of 1-3 days (depending on pathogens manipulated) before entering any animal holding, is not (or only in emergency situations) involved in taking samples during active surveillanceLaboratory staff is sometimes or often actively involved in taking samples from animals (esp. in outbreak times) but follows a quarantine period of 1-3 days prior entering any flock (depending on pathogens manipulated).Lab staff is actively involved in taking samples from farm / domestic animals without prior quarantine period
    88Unintentional release of pathogens from the lab (waste management)Proper waste management by compulsive use of incinerator, autoclave, chemical waste treatment, sharp disposalFrequent use of incinerator and autoclave, but sharp disposal rarely in the lab; chemical waste treatment partially addressedIncinerator, autoclave are available, but only used in situations where the lab deals with specific bio agents; no chemical waste treatmentImproper waste management, no incinerator (or not functional) and/or no autoclaving (or not functional) of infectious material
    89Intentional release of pathogens from the lab (controlled access)Completely controlled and restricted access only for key staff to BS-Labs and freezer rooms by use of security system (biometric system, ID-badges, camera)Controlled and restricted access only for key staff to BS-Labs and freezer rooms by physical security (eg. lock, guard)Controlled and restricted access only for staff to BS-Labs and freezer rooms but no use of locksEasy access to all labs and freezers / fridges during working hours
    90Staff Security/HealthHealth CheckHealth check of all lab staff on regular basis (at least annually)Irregular health check of lab staff (< 1 per year)Health check of lab staff only on request or in case of an accidentNo health check, even in case of an accident : staff has to seek doctor at own expenses
    91Staff protection from zoonoses (vaccination)Annual vaccination of staff working with zoonotic agents according to WHO recommendations (rabies, influenza…)Vaccination on request but possibly at own expensePost-exposure vaccination or immunization in case of accidentNo vaccination available
    92Eye wash and emergency showerEye wash and emergency shower available and functional in each department and after departing BSL-3 labsEye wash and/or shower available and functional in some labsEye wash and shower available in some labs but with limitations (not regular checked or not functional or only cold water etc.)Not available or not functional
    93Lab collaboration and networkingCommunication meansConnectivity to landline phone/fax (hours of availability, use of cell phones)24 hours of constant public cellphone/landline telephone and good fax connectivityGood public cellphone/landline telephone and/or fax connectivity, sometimes interrupted (not constant on 24 hours)Connectivity of public cellphone/landline phone and /or fax often interrupted, private cellphones are sometimes usedPublic cellphone/landline phone and/or fax not/badly working or not existent; private cell phones (if any) are exclusively used
    94Access to internet (hours per day or days/week)Good and speedy 24 h internet connection, all staff have access in all areas (labs, office…)Good internet connection (12-24 h) in offices; not all staff members have accessInternet connection limited (< 12 hours daily), but in general working; only selected staff member have accessInternet is slow and interrupted (availability <3 d/week); only selected staff member have access
    95Access to scientific publicationsAll Staff have free access to library during or even outside of working hours providing current scientific publications and to online-journals including at least 3-5 restricted-access journalsFree access to up-to-date library during working hours for all staff, but limited access to online-journals (free journals only)Library might be existent, but not up-to-date, limited access to freely accessible online-journalsNo access to library in the field of scientific interest, and only to few online journals (free access)
    96Distribution of scientific results (updates of website, frequency of publications)Institute have website with updates < 2 month old and produces periodic (>1/year) bulletin on generated scientific results and >10 publications in peer-reviewed international journalsInstitute has website (updates are older than 2 months) and irregularly (1-10 publications/year) publishes scientific information in peer-reviewed journalsAnnual reports are public documents and available on request; publications are rare (<1-5 publications per year in peer-reviewed international journals)No website, no regular information sharing
    97National lab networkingRegular contacts with national laboratory networkClose collaboration /communication (daily contact) with and constant support to/from members of the national lab networkRegular contact /communication (1 per week) with members of the national lab network, but support limited due to insufficient lab budgetContact with members of the national lab network, but collaboration/communication difficult (irregular contact, <1 per month)Very scarce collaboration/contact/communication with members of the national lab network (<1 per 3 months)
    98Support to/by members of the national lab network by training (n trainings/year)Support to/by members of the national lab network by provision of training on regular basis (>2/year)Support to/by members of the national lab network by training on irregular basis (<2/year)Support to/by members of the national lab network by rare training (<1/year)No training provided by/to members of the national lab network
    99Support to/by members of the national lab network by provision of materialSupport to/by members of the national lab network by provision of material/reagents/kits upon request and also regularly without requestSupport to/by members of the national lab network by irregular provision of material/reagents/kits upon request onlyRare provision of material/reagents/kits because of own limited resourcesNo possibility for provision of material/reagents/kits from a central lab to the national lab network
    100Laboratory collaborationIn-country lab networkingLab has regular (>1 per 3 months) contacts / collaborations with >3 labs/institutions within the countryLab has regular (1 per 3 months) contacts / collaborations with 1-3 labs/institutions within the countryLab has regular (1 per 3 months) contacts / collaborations with 1 lab/institution within the countryLab has no regular (<1 per 3 months) contacts / collaborations labs/institutions within the country
    101Regional lab networkingLab has key role in regional lab-networking (provision of material, expertise, training, meetings, PT) and takes this role very seriouslyLab is actively involved in regional lab-networking (presence at all meetings, participation in PT, training…) and shares dataLab attends meetings (not always present) for regional lab-networking, but is not active in regional networkingLab is not involved in regional lab-networking
    102International collaborationLab participates in >3 international projects for TAD/zoonotic diseases* of major importanceLab participates in 1-3 international projects for key TADs/zoonotic diseases of major importance*Lab participates in 1 international project for TAD/zoonotic diseases of major importance*Lab does not currently participate in any international project
    103Networking with international labsLab communicates and has regular direct or bilateral contacts (once a month) with >3 international laboratories (including reference or regional support/leading labs)Lab has some contacts (1 per 6 months) with international laboratories (reference or regional support/leading labs) AND/OR regular contacts (1 per month) with 2 or 3 international labsLab has irregular contacts (<1 per 6 months) with international laboratories (reference or regional support/leading labs) AND/OR regular contacts (1 per month) with 1 international labLab has hardly any contact (<1 per year) with international laboratories (including reference or regional support/leading labs)
    104International lab networking / twinningLab participates in >2 twinning projects (OIE, EU) or offers twinningLab participates in 1-2 twinning projectsLab considers/plans to participate in twinningNo twinning (considerations)
    105Information retrieval from public sourcesLab regularly (>1/month) consults (open-access) disease-related web pages (OIE, FAO, WHO, OFFLU, Promed…)Lab sometimes (1 per 6 months) uses (open-access) disease-related web pagesLab rarely (<1 per 6 months) uses (open-access) disease-related web pagesLab does not or cannot use (open-access) disease-related web pages
    106Information retrievalDatabases (GenBank, EMPRES, WAHIS..) are regularly (>1/month) used to access informationDatabases (GenBank, EMPRES, WAHIS..) are irregularly (1/month) used to access informationDatabases (GenBank, EMPRES, WAHIS..) are rarely (<1 per month) used to access informationDatabases are not used
    107Information sharingRegular (>1/month) information shared by lab staff through web-based platforms or databases; and/or submission of more than 20 sequences from 3 pathogens to public sequence database (eg. GenBank) within the last 12 monthsIrregular Information (1/month) shared by lab staff through web-based platforms; and/or submission of 6 to 19 sequences to public sequence database (eg. GenBank) within the last 12 monthsInformation only shared by lab staff very occasionally through web-based platforms; and/or submission of less than 6 sequences to public sequence database (eg. GenBank) within the last 12 monthsNo information shared by lab staff through web-based platforms within the last 12 months; no sequence submission to a public sequence database (eg. GenBank)
    108Expertise in using e-platforms for epidemiological data analysis / risk assessmentsLab / Epi department routinely works with e-platforms (TAD-Info, GIS, others)Lab / Epi department rarely uses e-platforms (TAD-Info, GIS, others)Lab / Epi department has e-platforms installed, but no expertise in usageNo use of such platforms
    Note. The tool can be obtained on request from the FAO EMPRES Laboratory Unit.

    Table S1.  FAO lab capacitation.

Reference (10)

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