Review state-of-the-art of output-based methodological approaches for substantiating freedom from infection.

Meletis, Eleftherios; Conrady, Beate; Hopp, Petter; Lurier, Thibaut; Frössling, Jenny; Rosendal, Thomas; Faverjon, Céline; Carmo, Luís Pedro; Hodnik, Jaka Jakob; Ózsvári, László; Kostoulas, Polychronis; van Schaik, Gerdien; Comin, Arianna; Nielen, Mirjam; Knific, Tanja; Schulz, Jana; Šerić-Haračić, Sabina; Fourichon, Christine; Santman-Berends, Inge and Madouasse, Aurélien (2024). Review state-of-the-art of output-based methodological approaches for substantiating freedom from infection. Frontiers in veterinary science, 11(1337661) Frontiers Media 10.3389/fvets.2024.1337661

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A wide variety of control and surveillance programmes that are designed and implemented based on country-specific conditions exists for infectious cattle diseases that are not regulated. This heterogeneity renders difficult the comparison of probabilities of freedom from infection estimated from collected surveillance data. The objectives of this review were to outline the methodological and epidemiological considerations for the estimation of probabilities of freedom from infection from surveillance information and review state-of-the-art methods estimating the probabilities of freedom from infection from heterogeneous surveillance data. Substantiating freedom from infection consists in quantifying the evidence of absence from the absence of evidence. The quantification usually consists in estimating the probability of observing no positive test result, in a given sample, assuming that the infection is present at a chosen (low) prevalence, called the design prevalence. The usual surveillance outputs are the sensitivity of surveillance and the probability of freedom from infection. A variety of factors influencing the choice of a method are presented; disease prevalence context, performance of the tests used, risk factors of infection, structure of the surveillance programme and frequency of testing. The existing methods for estimating the probability of freedom from infection are scenario trees, Bayesian belief networks, simulation methods, Bayesian prevalence estimation methods and the STOC free model. Scenario trees analysis is the current reference method for proving freedom from infection and is widely used in countries that claim freedom. Bayesian belief networks and simulation methods are considered extensions of scenario trees. They can be applied to more complex surveillance schemes and represent complex infection dynamics. Bayesian prevalence estimation methods and the STOC free model allow freedom from infection estimation at the herd-level from longitudinal surveillance data, considering risk factor information and the structure of the population. Comparison of surveillance outputs from heterogeneous surveillance programmes for estimating the probability of freedom from infection is a difficult task. This paper is a 'guide towards substantiating freedom from infection' that describes both all assumptions-limitations and available methods that can be applied in different settings.

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