Table 3. Transmission models fitted to prospectively collected, genotyped swab data on the acquisition of third-generation cephalosporin-resistant (3GC-R) Klebsiella pneumoniae sensu lato.

The table shows the parameters, prior and posterior distributions along with the WAIC (model comparison measure where lower values indicate a better fit to data). See methods for equations. Normal prior distributions show the mean and standard deviation respectively within brackets, beta prior distributions show the two shape parameters within brackets.

Transmission Model (Equations in Methods)	Parameters	Priors	Posterior Median (95% CrI)*	WAIC †
(1) Constant risk of transmission	α (intercept)	beta(2, 8)	0.0038 (0.0032, 0.0044)	1919
(2) Pseudo mass action (PMA) principal	α (intercept) β (transmission)‡	beta(2, 8) beta(2, 8)	0.0019 (0.0015, 0.0024) 0.0096 (0.0075, 0.012)	1739
(3) PMA plus environmen- tal contamination, from colonised patients, which decays over time	α (intercept) β (transmission)‡ γ (environment) λ (decay term)	beta(2, 8) beta(2, 8) beta(2, 8) half-normal(1, 2)	0.0019 (0.0014, 0.0023) 0.0088 (0.0063, 0.011) 0.097 (0.0086, 0.37) 4.7 (2.2, 7.1)	1740
(4) Hierarchical PMA varying transmission coefficient by ST4	α (intercept) β (transmission)‡ αs (beta shape 1) βs (beta shape 2)	beta(2, 8) beta(αs , βs ) half-normal(2, 5) half-normal(8, 5)	0.0021 (0.0016, 0.0026) Varies by ST§ 0.23 (0.14, 0.38) 17 (9.7, 25)	1733
(5) Hierarchical PMA varying intercept by ST§	α (intercept) β (transmission)‡ αs (beta shape 1) βs (beta shape 2)	beta(αs , βs ) beta(2, 8) half-normal(2, 5) half-normal(8, 5)	Varies by ST§ 0.0094 (0.0073, 0.012) 0.23 (0.16, 0.31) 21 (13, 29)	1793

^* 95% Credible interval. ^† Widely applicable information criterion (WAIC). ^‡ Transmission parameter that is multiplied by the number of infants colonised with the sequence type on the same day to give the force of infection (colonisation pressure). ^§ 3GC-R K. pneumoniae s.l. sequence type (ST).